Identification of membrane proteins by tandem mass spectrometry of protein ions

Science.gov (United States)

Carroll, Joe; Altman, Matthew C.; Fearnley, Ian M.; Walker, John E.

2007-01-01

The most common way of identifying proteins in proteomic analyses is to use short segments of sequence (“tags”) determined by mass spectrometric analysis of proteolytic fragments. The approach is effective with globular proteins and with membrane proteins with significant polar segments between membrane-spanning α-helices, but it is ineffective with other hydrophobic proteins where protease cleavage sites are either infrequent or absent. By developing methods to purify hydrophobic proteins in organic solvents and by fragmenting ions of these proteins by collision induced dissociation with argon, we have shown that partial sequences of many membrane proteins can be deduced easily by manual inspection. The spectra from small proteolipids (1–4 transmembrane α-helices) are dominated usually by fragment ions arising from internal amide cleavages, from which internal sequences can be obtained, whereas the spectra from larger membrane proteins (5–18 transmembrane α-helices) often contain fragment ions from N- and/or C-terminal parts yielding sequences in those regions. With these techniques, we have, for example, identified an abundant protein of unknown function from inner membranes of mitochondria that to our knowledge has escaped detection in proteomic studies, and we have produced sequences from 10 of 13 proteins encoded in mitochondrial DNA. They include the ND6 subunit of complex I, the last of its 45 subunits to be analyzed. The procedures have the potential to be developed further, for example by using newly introduced methods for protein ion dissociation to induce fragmentation of internal regions of large membrane proteins, which may remain partially folded in the gas phase. PMID:17720804

Interpretation of Tandem Mass Spectrometry (MSMS) Spectra for Peptide Analysis

DEFF Research Database (Denmark)

Hjernø, Karin; Højrup, Peter

2015-01-01

The aim of this chapter is to give a short introduction to peptide analysis by mass spectrometry (MS) and interpretation of fragment mass spectra. Through examples and guidelines we demonstrate how to understand and validate search results and how to perform de novo sequencing based on the often...... very complex fragmentation pattern obtained by tandem mass spectrometry (also referred to as MSMS). The focus is on simple rules for interpretation of MSMS spectra of tryptic as well as non-tryptic peptides....

INTRAMOLECULAR ISOTOPE EFFECTS IN HYDROCARBON MASS SPECTRA

Energy Technology Data Exchange (ETDEWEB)

Stevenson, D. P.; Schachtschneider, J. H.

1963-07-15

Approximate calculations based on the quasi-equilibrium rate theory of the origin of mass spectra are shown to lead to an approximately correct magnitude for the intramolecular ( pi /sup -/) isotope effect on C--H bond dissociation probabilities of various deuterohydrocarbons. (auth)

Production cross-sections for high mass particles and transverse momentum spectra

International Nuclear Information System (INIS)

Arnold, R.C.; Halzen, F.

1977-06-01

The concept of transverse-mass (msub(T)) scaling is examined. It is suggested that: (1) experimental data on pion transverse momentum (psub(T)) spectra provide a reliable guide to expectations for high mass particle production; (2) dimensional scaling, e.g. implied by quark-gluon dynamics, yields an estimate of msub(T) -4 spectra at ultra-high energies; however, stronger damping is expected at currently accessible energies; (3) values increase linearly with the produced particle mass. The results of msub(T) scaling are compared with estimates for high mass production in the context of the Drell-Yan model. (author)

Peptide de novo sequencing of mixture tandem mass spectra

DEFF Research Database (Denmark)

Gorshkov, Vladimir; Hotta, Stéphanie Yuki Kolbeck; Braga, Thiago Verano

2016-01-01

they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co-isolation and thus prone to false identifications. The deconvolution approach matched...... complementary b-, y-ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co-isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced...... peptides. The improvement was in the range of 20–35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight...

Characterisation of chemically-modified proteins by electrospray ionisation mass spectrometry

International Nuclear Information System (INIS)

Bennett, K.L.

1996-09-01

Electrospray mass spectrometry (ESI-MS) has been used to examine a range of intact monoclonal antibodies (MAbs), antibody fragments such as F(ab') 2 , F ab and F c , chemically-modified fragments and a range of other chemically-modified peptides and proteins as part of a broader study aimed at establishing ESI-MS as a method for the characterisation of radioimmunoconjugates (radiolabelled monoclonal antibodies). For example, the addition of up to 10 biotin molecules to the 'papain-sensitive' 50 kDa F ab fragment can be easily detected in ESI mass spectra. For intact MAbs, however, it is only possible to detect average shifts in the mass of intact antibodies following modification. Successful ESI-MS analysis of complexes formed between chelators and other small molecules conjugated to synthetic peptides, hen egg-white Iysozyme (HEL) (M r 14 306) and horse heart myoglobin (M r 16 951) has been demonstrated. ESI-MS offers considerable advantages compared with existing methods for the characterisation of chemically-conjugated proteins including speed and sensitivity of analysis and the capability for obtaining specific structural information. The conditions for ESI-MS of intact MAbs and MAb fragments have been examined in detail and it was found that 150 kDa MAbs generally required lower sample concentration and higher skimmer potentials compared with the 50 kDa F ab fragment and other lower molecular weight proteins. In addition, the m/z range over which ions from MAbs were observed was higher (m/z ∼2000-4500) than for smaller proteins. ESI-MS was also found to be useful for probing the action of the protease papain, that is used to generate MAb fragments (F(ab) '2, F ab and F c ). Further, different sensitivities to papain for different MAb preparations was demonstrated. Finally, the tandem mass spectra of a range of peptides modified by iodine and biotin were examined. In the case of biotinylated peptides, a characteristic fragment ion was identified that could

Automated data processing of high-resolution mass spectra

DEFF Research Database (Denmark)

Hansen, Michael Adsetts Edberg; Smedsgaard, Jørn

of the massive amounts of data. We present an automated data processing method to quantitatively compare large numbers of spectra from the analysis of complex mixtures, exploiting the full quality of high-resolution mass spectra. By projecting all detected ions - within defined intervals on both the time...... infusion of crude extracts into the source taking advantage of the high sensitivity, high mass resolution and accuracy and the limited fragmentation. Unfortunately, there has not been a comparable development in the data processing techniques to fully exploit gain in high resolution and accuracy...... infusion analyses of crude extract to find the relationship between species from several species terverticillate Penicillium, and also that the ions responsible for the segregation can be identified. Furthermore the process can automate the process of detecting unique species and unique metabolites....

Jet mass spectra in Higgs+one jet at NNLL

International Nuclear Information System (INIS)

Jouttenus, Teppo T.; Stewart, Iain W.; Waalewijn, Wouter J.

2013-02-01

The invariant mass of a jet is a benchmark variable describing the structure of jets at the LHC. We calculate the jet mass spectrum for Higgs plus one jet at the LHC at next-to-next-to-leading logarithmic (NNLL) order using a factorization formula. At this order, the cross section becomes sensitive to perturbation theory at the soft m 2 jet /p jet T scale. Our calculation is exclusive and uses the 1-jettiness global event shape to implement a veto on additional jets. The dominant dependence on the jet veto is removed by normalizing the spectrum, leaving residual dependence from non-global logarithms depending on the ratio of the jet mass and jet veto variables. For our exclusive jet cross section these non-global logarithms are parametrically smaller than in the inclusive case, allowing us to obtain a complete NNLL result. Results for the dependence of the jet mass spectrum on the kinematics, jet algorithm, and jet size R are given. Using individual partonic channels we illustrate the difference between the jet mass spectra for quark and gluon jets. We also study the effect of hadronization and underlying event on the jet mass in Pythia. To highlight the similarity of inclusive and exclusive jet mass spectra, a comparison to LHC data is presented.

ESIprot: a universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data.

Science.gov (United States)

Winkler, Robert

2010-02-01

Electrospray ionization (ESI) ion trap mass spectrometers with relatively low resolution are frequently used for the analysis of natural products and peptides. Although ESI spectra of multiply charged protein molecules also can be measured on this type of devices, only average spectra are produced for the majority of naturally occurring proteins. Evaluating such ESI protein spectra would provide valuable information about the native state of investigated proteins. However, no suitable and freely available software could be found which allows the charge state determination and molecular weight calculation of single proteins from average ESI-MS data. Therefore, an algorithm based on standard deviation optimization (scatter minimization) was implemented for the analysis of protein ESI-MS data. The resulting software ESIprot was tested with ESI-MS data of six intact reference proteins between 12.4 and 66.7 kDa. In all cases, the correct charge states could be determined. The obtained absolute mass errors were in a range between -0.2 and 1.2 Da, the relative errors below 30 ppm. The possible mass accuracy allows for valid conclusions about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates an extraordinary robustness and allows spectral interpretation from as little as two peaks, given sufficient quality of the provided m/z data, without the necessity for peak intensity data. ESIprot is independent from the raw data format and the computer platform, making it a versatile tool for mass spectrometrists. The program code was released under the open-source GPLv3 license to support future developments of mass spectrometry software. Copyright 2010 John Wiley & Sons, Ltd.

Jet mass spectra in Higgs+one jet at NNLL

Energy Technology Data Exchange (ETDEWEB)

Jouttenus, Teppo T.; Stewart, Iain W. [Massachusetts Institute of Technology, Cambridge, MA (United States). Center for Theoretical Physics; Tackmann, Frank J. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Waalewijn, Wouter J. [California Univ., San Diego, La Jolla, CA (United States). Dept. of Physics

2013-02-15

The invariant mass of a jet is a benchmark variable describing the structure of jets at the LHC. We calculate the jet mass spectrum for Higgs plus one jet at the LHC at next-to-next-to-leading logarithmic (NNLL) order using a factorization formula. At this order, the cross section becomes sensitive to perturbation theory at the soft m{sup 2}{sub jet}/p{sup jet}{sub T} scale. Our calculation is exclusive and uses the 1-jettiness global event shape to implement a veto on additional jets. The dominant dependence on the jet veto is removed by normalizing the spectrum, leaving residual dependence from non-global logarithms depending on the ratio of the jet mass and jet veto variables. For our exclusive jet cross section these non-global logarithms are parametrically smaller than in the inclusive case, allowing us to obtain a complete NNLL result. Results for the dependence of the jet mass spectrum on the kinematics, jet algorithm, and jet size R are given. Using individual partonic channels we illustrate the difference between the jet mass spectra for quark and gluon jets. We also study the effect of hadronization and underlying event on the jet mass in Pythia. To highlight the similarity of inclusive and exclusive jet mass spectra, a comparison to LHC data is presented.

Maximum entropy decomposition of quadrupole mass spectra

International Nuclear Information System (INIS)

Toussaint, U. von; Dose, V.; Golan, A.

2004-01-01

We present an information-theoretic method called generalized maximum entropy (GME) for decomposing mass spectra of gas mixtures from noisy measurements. In this GME approach to the noisy, underdetermined inverse problem, the joint entropies of concentration, cracking, and noise probabilities are maximized subject to the measured data. This provides a robust estimation for the unknown cracking patterns and the concentrations of the contributing molecules. The method is applied to mass spectroscopic data of hydrocarbons, and the estimates are compared with those received from a Bayesian approach. We show that the GME method is efficient and is computationally fast

Optimization of search algorithms for a mass spectra library

International Nuclear Information System (INIS)

Domokos, L.; Henneberg, D.; Weimann, B.

1983-01-01

The SISCOM mass spectra library search is mainly an interpretative system producing a ''hit list'' of similar spectra based on six comparison factors. This paper deals with extension of the system; the aim is exact identification (retrieval) of those reference spectra in the SISCOM hit list that correspond to the unknown compounds or components of the mixture. Thus, instead of a similarity measure, a decision (retrieval) function is needed to establish the identity of reference and unknown compounds by comparison of their spectra. To facilitate estimation of the weightings of the different variables in the retrieval function, pattern recognition algorithms were applied. Numerous statistical evaluations of three different library collections were made to check the quality of data bases and to derive appropriate variables for the retrieval function. (Auth.)

Mass Spectra Analyses of Amides and Amide Dimers of Steviol, Isosteviol, and Steviolbioside

Directory of Open Access Journals (Sweden)

Lin-Wen Lee

2012-01-01

Full Text Available The mass spectra of a series of stevioside analogues including the amide and dimer compounds of steviol, isosteviol, and steviolbioside were examined. Positive ion mass spectral fragmentation of new steviol, isosteviol, and steviolbioside amides and the amide dimers are reported and discussed. The techniques included their synthesis procedures, fast-atom bombardment (FAB, and LC/MS/MS mass spectra. Intense [M+H]+ and [M+Na]+ ion peaks were observed on the FAB and ESI spectra. LC/MS/MS also yielded ES+ and ES− ion peaks that fairly agreed with the results of the FAB and ESI studies. Mass spectral analysis of compounds 4p-q, 5a-g, 6, and 7 revealed the different cleavage pathway patterns that can help in identifying the structures of steviolbioside and its amide derivatives.

Heavy meson mass spectra by general relativistic methods

International Nuclear Information System (INIS)

Italiano, A.; Lattuada, M.; Maccarrone, G.D.; Recami, E.; Riggi, F.; Vinciguerra, D.

1984-01-01

By applying the classical methods of general relativity to elementary particles one can get, in a natural way, the observed confinement of their constituents, avoiding any recourse to phenome-nological models such as bag model and allowing the deduction of the heavy meson (i.e. charmonium (J/psi) and bottomium (UPSILON)) mass spectra

Improved mass resolution and mass accuracy in TOF-SIMS spectra and images using argon gas cluster ion beams.

Science.gov (United States)

Shon, Hyun Kyong; Yoon, Sohee; Moon, Jeong Hee; Lee, Tae Geol

2016-06-09

The popularity of argon gas cluster ion beams (Ar-GCIB) as primary ion beams in time-of-flight secondary ion mass spectrometry (TOF-SIMS) has increased because the molecular ions of large organic- and biomolecules can be detected with less damage to the sample surfaces. However, Ar-GCIB is limited by poor mass resolution as well as poor mass accuracy. The inferior quality of the mass resolution in a TOF-SIMS spectrum obtained by using Ar-GCIB compared to the one obtained by a bismuth liquid metal cluster ion beam and others makes it difficult to identify unknown peaks because of the mass interference from the neighboring peaks. However, in this study, the authors demonstrate improved mass resolution in TOF-SIMS using Ar-GCIB through the delayed extraction of secondary ions, a method typically used in TOF mass spectrometry to increase mass resolution. As for poor mass accuracy, although mass calibration using internal peaks with low mass such as hydrogen and carbon is a common approach in TOF-SIMS, it is unsuited to the present study because of the disappearance of the low-mass peaks in the delayed extraction mode. To resolve this issue, external mass calibration, another regularly used method in TOF-MS, was adapted to enhance mass accuracy in the spectrum and image generated by TOF-SIMS using Ar-GCIB in the delayed extraction mode. By producing spectra analyses of a peptide mixture and bovine serum albumin protein digested with trypsin, along with image analyses of rat brain samples, the authors demonstrate for the first time the enhancement of mass resolution and mass accuracy for the purpose of analyzing large biomolecules in TOF-SIMS using Ar-GCIB through the use of delayed extraction and external mass calibration.

MS2Analyzer: A Software for Small Molecule Substructure Annotations from Accurate Tandem Mass Spectra

Science.gov (United States)

2015-01-01

Systematic analysis and interpretation of the large number of tandem mass spectra (MS/MS) obtained in metabolomics experiments is a bottleneck in discovery-driven research. MS/MS mass spectral libraries are small compared to all known small molecule structures and are often not freely available. MS2Analyzer was therefore developed to enable user-defined searches of thousands of spectra for mass spectral features such as neutral losses, m/z differences, and product and precursor ions from MS/MS spectra in MSP/MGF files. The software is freely available at http://fiehnlab.ucdavis.edu/projects/MS2Analyzer/. As the reference query set, 147 literature-reported neutral losses and their corresponding substructures were collected. This set was tested for accuracy of linking neutral loss analysis to substructure annotations using 19 329 accurate mass tandem mass spectra of structurally known compounds from the NIST11 MS/MS library. Validation studies showed that 92.1 ± 6.4% of 13 typical neutral losses such as acetylations, cysteine conjugates, or glycosylations are correct annotating the associated substructures, while the absence of mass spectra features does not necessarily imply the absence of such substructures. Use of this tool has been successfully demonstrated for complex lipids in microalgae. PMID:25263576

Quantifying Protein-Carbohydrate Interactions Using Liquid Sample Desorption Electrospray Ionization Mass Spectrometry

Science.gov (United States)

Yao, Yuyu; Shams-Ud-Doha, Km; Daneshfar, Rambod; Kitova, Elena N.; Klassen, John S.

2015-01-01

The application of liquid sample desorption electrospray ionization mass spectrometry (liquid sample DESI-MS) for quantifying protein-carbohydrate interactions in vitro is described. Association constants for the interactions between lysozyme and β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc and β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc, and between a single chain antibody and α-D-Galp-(1 → 2)-[α-D-Abep-(1 → 3)]-α-D-Manp-OCH3 and β-D-Glcp-(1 → 2)-[α-D-Abep-(1 → 3)]-α-D-Manp-OCH3 measured using liquid sample DESI-MS were found to be in good agreement with values measured by isothermal titration calorimetry and the direct ESI-MS assay. The reference protein method, which was originally developed to correct ESI mass spectra for the occurrence of nonspecific ligand-protein binding, was shown to reliably correct liquid sample DESI mass spectra for nonspecific binding. The suitability of liquid sample DESI-MS for quantitative binding measurements carried out using solutions containing high concentrations of the nonvolatile biological buffer phosphate buffered saline (PBS) was also explored. Binding of lysozyme to β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc in aqueous solutions containing up to 1× PBS was successfully monitored using liquid sample DESI-MS; with ESI-MS the binding measurements were limited to concentrations less than 0.02 X PBS.

De novo analysis of electron impact mass spectra using fragmentation trees

International Nuclear Information System (INIS)

Hufsky, Franziska; Rempt, Martin; Rasche, Florian; Pohnert, Georg; Böcker, Sebastian

2012-01-01

Highlights: ► We present a method for de novo analysis of accurate mass EI mass spectra of small molecules. ► This method identifies the molecular ion and thus the molecular formula where the molecular ion is present in the spectrum. ► Fragmentation trees are constructed by automated signal extraction and evaluation. ► These trees explain relevant fragmentation reactions. ► This method will be very helpful in the automated analysis of unknown metabolites. - Abstract: The automated fragmentation analysis of high resolution EI mass spectra based on a fragmentation tree algorithm is introduced. Fragmentation trees are constructed from EI spectra by automated signal extraction and evaluation. These trees explain relevant fragmentation reactions and assign molecular formulas to fragments. The method enables the identification of the molecular ion and the molecular formula of a metabolite if the molecular ion is present in the spectrum. These identifications are independent of existing library knowledge and, thus, support assignment and structural elucidation of unknown compounds. The method works even if the molecular ion is of very low abundance or hidden under contaminants with higher masses. We apply the algorithm to a selection of 50 derivatized and underivatized metabolites and demonstrate that in 78% of cases the molecular ion can be correctly assigned. The automatically constructed fragmentation trees correspond very well to published mechanisms and allow the assignment of specific relevant fragments and fragmentation pathways even in the most complex EI-spectra in our dataset. This method will be very helpful in the automated analysis of metabolites that are not included in common libraries and it thus has the potential to support the explorative character of metabolomics studies.

Interpretation of tandem mass spectra of posttranslationally modified peptides

DEFF Research Database (Denmark)

Bunkenborg, J.; Matthiesen, R.

2013-01-01

spectra and protein database search engines have been developed to match the experimental data to peptide candidates. In most studies there is a schism between discarding perfectly valid data and including nonsensical peptide identifications-this is currently a major bottleneck in data...

Synthesis and Electrospray Ionization Mass Spectra of N-(1,3,2-Dioxaphosphorinan-2-ylmethyl)thiophosphoramidates

Institute of Scientific and Technical Information of China (English)

MIAO,Zhi-Wei; FU,Cui-Rong; WANG,Bin; CUI,Zhan-Wei; ZHANG,Jian-Feng; CHEN,Ru-Yu

2007-01-01

N-(1,3,2-Dioxaphosphorinan-2-ylmethyl) thiophosphoramidates were synthesized and determined by NMR spectra and positive ion electrospray ionization mass spectrometry (ESI-MS) in conjunction with tandem mass spectrometry (MS/MS). The fragmentation pathways were investigated. The results show that these characteristic ions in ESI mass spectra are useful in the structural determination of N-(1,3,2-dioxaphosphorinan-2-ylmethyl)thiophosphoramidates.

Mass spectra of alicylic compounds Pt. 8

International Nuclear Information System (INIS)

Remane, H.; Haufe, G.

1980-01-01

Mass spectrometric fragmentation of C 5 -C 8 as well as C 12 ring systems of tBHC and tBMC is discussed and compared to the fragmentation of Br-, hydroxy- and methoxy cycloalkanes of similar ring sizes. The dominant processes are the splitting of the functional groups yielding M-H 2 O 1+ , M-HOCH 3 1+ and M-Br 1+ fragments, and the disintegration of the rings producing C 3 H 4 X 1+ fragments (X=Br, OH, OCH 3 ). Intensities of the more important fragments correspond to the size of the ring. The isomers can be distinguished by their mass spectra due to the inequality of the intensities of the trans- and cis-forms of BHC and BMC. Functional groups influence mass spectrometric fragmentation as it is indicated by the correlation of the fragments of the bis-functional tBHC and tBMC and the fragments of monofractional compounds. (Sz.J.)

Localization and mass spectra of various matter fields on Weyl thin brane

Energy Technology Data Exchange (ETDEWEB)

Sui, Tao-Tao; Zhao, Li; Zhang, Yu-Peng [Lanzhou University, Institute of Theoretical Physics, Lanzhou (China); Xie, Qun-Ying [Lanzhou University, School of Information Science and Engineering, Lanzhou (China)

2017-06-15

It has been shown that the thin brane model in a five-dimensional Weyl gravity can deal with the wrong-signed Friedmann-like equation in the Randall-Sundrum-1 (RS1) model. In the Weyl brane model, there are also two branes with opposite brane tensions, but the four-dimensional graviton (the gravity zero mode) is localized near the negative tension brane, while our four-dimensional universe is localized on the positive tension brane. In this paper, we consider the mass spectra of various bulk matter fields (i.e., scalar, vector, and fermion fields) on the Weyl brane. It is shown that the zero modes of those matter fields can be localized on the positive tension brane under some conditions. The mass spectra of the bulk matter fields are equidistant for the higher excited states, and relatively sparse for the lower excited states. The size of the extra dimension determines the gap of the mass spectra. We also consider the correction to the Newtonian potential in this model and it is proportional to 1/r{sup 3}. (orig.)

Optical and Near-infrared Spectra of σ Orionis Isolated Planetary-mass Objects

Energy Technology Data Exchange (ETDEWEB)

Zapatero Osorio, M. R. [Centro de Astrobiología (CSIC-INTA), Crta. Ajalvir km 4, E-28850 Torrejón de Ardoz, Madrid (Spain); Béjar, V. J. S. [Instituto de Astrofísica de Canarias, C/. Vía Láctea s/n, E-38205 La Laguna, Tenerife (Spain); Ramírez, K. Peña, E-mail: mosorio@cab.inta-csic.es, E-mail: vbejar@iac.es, E-mail: karla.pena@uantof.cl [Unidad de Astronomía de la Universidad de Antofagasta, Av. U. de Antofagasta. 02800 Antofagasta (Chile)

2017-06-10

We have obtained low-resolution optical (0.7–0.98 μ m) and near-infrared (1.11–1.34 μ m and 0.8–2.5 μ m) spectra of 12 isolated planetary-mass candidates ( J = 18.2–19.9 mag) of the 3 Myr σ Orionis star cluster with the aim of determining the spectroscopic properties of very young, substellar dwarfs and assembling a complete cluster mass function. We have classified our targets by visual comparison with high- and low-gravity standards and by measuring newly defined spectroscopic indices. We derived L0–L4.5 and M9–L2.5 using high- and low-gravity standards, respectively. Our targets reveal clear signposts of youth, thus corroborating their cluster membership and planetary masses (6–13 M {sub Jup}). These observations complete the σ Orionis mass function by spectroscopically confirming the planetary-mass domain to a confidence level of ∼75%. The comparison of our spectra with BT-Settl solar metallicity model atmospheres yields a temperature scale of 2350–1800 K and a low surface gravity of log g ≈ 4.0 [cm s{sup −2}], as would be expected for young planetary-mass objects. We discuss the properties of the cluster’s least-massive population as a function of spectral type. We have also obtained the first optical spectrum of S Ori 70, a T dwarf in the direction of σ Orionis. Our data provide reference optical and near-infrared spectra of very young L dwarfs and a mass function that may be used as templates for future studies of low-mass substellar objects and exoplanets. The extrapolation of the σ Orionis mass function to the solar neighborhood may indicate that isolated planetary-mass objects with temperatures of ∼200–300 K and masses in the interval 6–13 M {sub Jup} may be as numerous as very low-mass stars.

Mass spectrometric analysis of protein interactions

DEFF Research Database (Denmark)

Borch, Jonas; Jørgensen, Thomas J. D.; Roepstorff, Peter

2005-01-01

Mass spectrometry is a powerful tool for identification of interaction partners and structural characterization of protein interactions because of its high sensitivity, mass accuracy and tolerance towards sample heterogeneity. Several tools that allow studies of protein interaction are now...... available and recent developments that increase the confidence of studies of protein interaction by mass spectrometry include quantification of affinity-purified proteins by stable isotope labeling and reagents for surface topology studies that can be identified by mass-contributing reporters (e.g. isotope...... labels, cleavable cross-linkers or fragment ions. The use of mass spectrometers to study protein interactions using deuterium exchange and for analysis of intact protein complexes recently has progressed considerably....

In silico fragmentation for computer assisted identification of metabolite mass spectra

Directory of Open Access Journals (Sweden)

Müller-Hannemann Matthias

2010-03-01

Full Text Available Abstract Background Mass spectrometry has become the analytical method of choice in metabolomics research. The identification of unknown compounds is the main bottleneck. In addition to the precursor mass, tandem MS spectra carry informative fragment peaks, but the coverage of spectral libraries of measured reference compounds are far from covering the complete chemical space. Compound libraries such as PubChem or KEGG describe a larger number of compounds, which can be used to compare their in silico fragmentation with spectra of unknown metabolites. Results We created the MetFrag suite to obtain a candidate list from compound libraries based on the precursor mass, subsequently ranked by the agreement between measured and in silico fragments. In the evaluation MetFrag was able to rank most of the correct compounds within the top 3 candidates returned by an exact mass query in KEGG. Compared to a previously published study, MetFrag obtained better results than the commercial MassFrontier software. Especially for large compound libraries, the candidates with a good score show a high structural similarity or just different stereochemistry, a subsequent clustering based on chemical distances reduces this redundancy. The in silico fragmentation requires less than a second to process a molecule, and MetFrag performs a search in KEGG or PubChem on average within 30 to 300 seconds, respectively, on an average desktop PC. Conclusions We presented a method that is able to identify small molecules from tandem MS measurements, even without spectral reference data or a large set of fragmentation rules. With today's massive general purpose compound libraries we obtain dozens of very similar candidates, which still allows a confident estimate of the correct compound class. Our tool MetFrag improves the identification of unknown substances from tandem MS spectra and delivers better results than comparable commercial software. MetFrag is available through a web

Re-hardening of hadron transverse mass spectra in relativistic heavy-ion collisions

International Nuclear Information System (INIS)

Ohnishi, A.; Otuka, N.; Sahu, P.K.; Isse, M.; Nara, Y.

2001-01-01

We analyze the spectra of pions and protons in heavy-ion collisions at relativistic energies from 2 A GeV to 65 + 65 A GeV by using a jet-implemented hadron-string cascade model. In this energy region, hadron transverse mass spectra first show softening until SPS energies, and re-hardening may emerge at RHIC energies. Since hadronic matter is expected to show only softening at higher energy densities, this re-hardening of spectra can be interpreted as a good signature of the quark-gluon plasma formation. (author)

Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry.

Science.gov (United States)

Yao, Jingwen; Utsunomiya, Shin-Ichi; Kajihara, Shigeki; Tabata, Tsuyoshi; Aoshima, Ken; Oda, Yoshiya; Tanaka, Koichi

2014-01-01

A new peak detection method has been developed for rapid selection of peptide and its fragment ion peaks for protein identification using tandem mass spectrometry. The algorithm applies classification of peak intensities present in the defined mass range to determine the noise level. A threshold is then given to select ion peaks according to the determined noise level in each mass range. This algorithm was initially designed for the peak detection of low resolution peptide mass spectra, such as matrix-assisted laser desorption/ionization Time-of-Flight (MALDI-TOF) mass spectra. But it can also be applied to other type of mass spectra. This method has demonstrated obtaining a good rate of number of real ions to noises for even poorly fragmented peptide spectra. The effect of using peak lists generated from this method produces improved protein scores in database search results. The reliability of the protein identifications is increased by finding more peptide identifications. This software tool is freely available at the Mass++ home page (http://www.first-ms3d.jp/english/achievement/software/).

Mass spectra features of biomass burning boiler and coal burning boiler emitted particles by single particle aerosol mass spectrometer.

Science.gov (United States)

Xu, Jiao; Li, Mei; Shi, Guoliang; Wang, Haiting; Ma, Xian; Wu, Jianhui; Shi, Xurong; Feng, Yinchang

2017-11-15

In this study, single particle mass spectra signatures of both coal burning boiler and biomass burning boiler emitted particles were studied. Particle samples were suspended in clean Resuspension Chamber, and analyzed by ELPI and SPAMS simultaneously. The size distribution of BBB (biomass burning boiler sample) and CBB (coal burning boiler sample) are different, as BBB peaks at smaller size, and CBB peaks at larger size. Mass spectra signatures of two samples were studied by analyzing the average mass spectrum of each particle cluster extracted by ART-2a in different size ranges. In conclusion, BBB sample mostly consists of OC and EC containing particles, and a small fraction of K-rich particles in the size range of 0.2-0.5μm. In 0.5-1.0μm, BBB sample consists of EC, OC, K-rich and Al_Silicate containing particles; CBB sample consists of EC, ECOC containing particles, while Al_Silicate (including Al_Ca_Ti_Silicate, Al_Ti_Silicate, Al_Silicate) containing particles got higher fractions as size increase. The similarity of single particle mass spectrum signatures between two samples were studied by analyzing the dot product, results indicated that part of the single particle mass spectra of two samples in the same size range are similar, which bring challenge to the future source apportionment activity by using single particle aerosol mass spectrometer. Results of this study will provide physicochemical information of important sources which contribute to particle pollution, and will support source apportionment activities. Copyright © 2017. Published by Elsevier B.V.

STRAPS v1.0: evaluating a methodology for predicting electron impact ionisation mass spectra for the aerosol mass spectrometer

Directory of Open Access Journals (Sweden)

D. O. Topping

2017-06-01

Full Text Available Our ability to model the chemical and thermodynamic processes that lead to secondary organic aerosol (SOA formation is thought to be hampered by the complexity of the system. While there are fundamental models now available that can simulate the tens of thousands of reactions thought to take place, validation against experiments is highly challenging. Techniques capable of identifying individual molecules such as chromatography are generally only capable of quantifying a subset of the material present, making it unsuitable for a carbon budget analysis. Integrative analytical methods such as the Aerosol Mass Spectrometer (AMS are capable of quantifying all mass, but because of their inability to isolate individual molecules, comparisons have been limited to simple data products such as total organic mass and the O : C ratio. More detailed comparisons could be made if more of the mass spectral information could be used, but because a discrete inversion of AMS data is not possible, this activity requires a system of predicting mass spectra based on molecular composition. In this proof-of-concept study, the ability to train supervised methods to predict electron impact ionisation (EI mass spectra for the AMS is evaluated. Supervised Training Regression for the Arbitrary Prediction of Spectra (STRAPS is not built from first principles. A methodology is constructed whereby the presence of specific mass-to-charge ratio (m∕z channels is fitted as a function of molecular structure before the relative peak height for each channel is similarly fitted using a range of regression methods. The widely used AMS mass spectral database is used as a basis for this, using unit mass resolution spectra of laboratory standards. Key to the fitting process is choice of structural information, or molecular fingerprint. Our approach relies on using supervised methods to automatically optimise the relationship between spectral characteristics and these molecular

STRAPS v1.0: evaluating a methodology for predicting electron impact ionisation mass spectra for the aerosol mass spectrometer

Science.gov (United States)

Topping, David O.; Allan, James; Rami Alfarra, M.; Aumont, Bernard

2017-06-01

Our ability to model the chemical and thermodynamic processes that lead to secondary organic aerosol (SOA) formation is thought to be hampered by the complexity of the system. While there are fundamental models now available that can simulate the tens of thousands of reactions thought to take place, validation against experiments is highly challenging. Techniques capable of identifying individual molecules such as chromatography are generally only capable of quantifying a subset of the material present, making it unsuitable for a carbon budget analysis. Integrative analytical methods such as the Aerosol Mass Spectrometer (AMS) are capable of quantifying all mass, but because of their inability to isolate individual molecules, comparisons have been limited to simple data products such as total organic mass and the O : C ratio. More detailed comparisons could be made if more of the mass spectral information could be used, but because a discrete inversion of AMS data is not possible, this activity requires a system of predicting mass spectra based on molecular composition. In this proof-of-concept study, the ability to train supervised methods to predict electron impact ionisation (EI) mass spectra for the AMS is evaluated. Supervised Training Regression for the Arbitrary Prediction of Spectra (STRAPS) is not built from first principles. A methodology is constructed whereby the presence of specific mass-to-charge ratio (m/z) channels is fitted as a function of molecular structure before the relative peak height for each channel is similarly fitted using a range of regression methods. The widely used AMS mass spectral database is used as a basis for this, using unit mass resolution spectra of laboratory standards. Key to the fitting process is choice of structural information, or molecular fingerprint. Our approach relies on using supervised methods to automatically optimise the relationship between spectral characteristics and these molecular fingerprints. Therefore

Surface Induced Dissociation Coupled with High Resolution Mass Spectrometry Unveils Heterogeneity of a 211 kDa Multicopper Oxidase Protein Complex

Science.gov (United States)

Zhou, Mowei; Yan, Jing; Romano, Christine A.; Tebo, Bradley M.; Wysocki, Vicki H.; Paša-Tolić, Ljiljana

2018-01-01

Manganese oxidation is an important biogeochemical process that is largely regulated by bacteria through enzymatic reactions. However, the detailed mechanism is poorly understood due to challenges in isolating and characterizing these unknown enzymes. A manganese oxidase, Mnx, from Bacillus sp. PL-12 has been successfully overexpressed in active form as a protein complex with a molecular mass of 211 kDa. We have recently used surface induced dissociation (SID) and ion mobility-mass spectrometry (IM-MS) to release and detect folded subcomplexes for determining subunit connectivity and quaternary structure. The data from the native mass spectrometry experiments led to a plausible structural model of this multicopper oxidase, which has been difficult to study by conventional structural biology methods. It was also revealed that each Mnx subunit binds a variable number of copper ions. Becasue of the heterogeneity of the protein and limited mass resolution, ambiguities in assigning some of the observed peaks remained as a barrier to fully understanding the role of metals and potential unknown ligands in Mnx. In this study, we performed SID in a modified Fourier transform-ion cyclotron resonance (FTICR) mass spectrometer. The high mass accuracy and resolution offered by FTICR unveiled unexpected artificial modifications on the protein that had been previously thought to be iron bound species based on lower resolution spectra. Additionally, isotopically resolved spectra of the released subcomplexes revealed the metal binding stoichiometry at different structural levels. This method holds great potential for in-depth characterization of metalloproteins and protein-ligand complexes. [Figure not available: see fulltext.

Dielectric spectra of proteins in conducting media

International Nuclear Information System (INIS)

Ruderman, G.; Xammar Oro, J.R. de

1990-10-01

Dielectric measurements of serum albumin and myoglobin in solutions of varying conductivities were performed. The results presented confirm that also for protein solutions, the Maxwell predictions of a threshold frequency in conducting materials holds. The threshold frequency of a serum albumin solution was experimentally determined. Attention should be recalled that, if the dielectric spectra of proteins solutions want to be measured, three distinct frequency regions are to be observed: a low frequency region, where the sample behaves like a conductor; an intermediate region centered around the threshold frequency, where the free charges partially screen the fixed ones; and a high frequency region where the sample behaves like a good dielectric. (author). 8 refs, 5 figs

Plant cell wall proteomics: mass spectrometry data, a trove for research on protein structure/function relationships.

Science.gov (United States)

Albenne, Cécile; Canut, Hervé; Boudart, Georges; Zhang, Yu; San Clemente, Hélène; Pont-Lezica, Rafael; Jamet, Elisabeth

2009-09-01

Proteomics allows the large-scale study of protein expression either in whole organisms or in purified organelles. In particular, mass spectrometry (MS) analysis of gel-separated proteins produces data not only for protein identification, but for protein structure, location, and processing as well. An in-depth analysis was performed on MS data from etiolated hypocotyl cell wall proteomics of Arabidopsis thaliana. These analyses show that highly homologous members of multigene families can be differentiated. Two lectins presenting 93% amino acid identity were identified using peptide mass fingerprinting. Although the identification of structural proteins such as extensins or hydroxyproline/proline-rich proteins (H/PRPs) is arduous, different types of MS spectra were exploited to identify and characterize an H/PRP. Maturation events in a couple of cell wall proteins (CWPs) were analyzed using site mapping. N-glycosylation of CWPs as well as the hydroxylation or oxidation of amino acids were also explored, adding information to improve our understanding of CWP structure/function relationships. A bioinformatic tool was developed to locate by means of MS the N-terminus of mature secreted proteins and N-glycosylation.

Mass spectrometry protein expression profiles in colorectal cancer tissue associated with clinico-pathological features of disease

Directory of Open Access Journals (Sweden)

Liao Christopher CL

2010-08-01

Full Text Available Abstract Background Studies of several tumour types have shown that expression profiling of cellular protein extracted from surgical tissue specimens by direct mass spectrometry analysis can accurately discriminate tumour from normal tissue and in some cases can sub-classify disease. We have evaluated the potential value of this approach to classify various clinico-pathological features in colorectal cancer by employing matrix-assisted laser desorption ionisation time of-flight-mass spectrometry (MALDI-TOF MS. Methods Protein extracts from 31 tumour and 33 normal mucosa specimens were purified, subjected to MALDI-Tof MS and then analysed using the 'GenePattern' suite of computational tools (Broad Institute, MIT, USA. Comparative Gene Marker Selection with either a t-test or a signal-to-noise ratio (SNR test statistic was used to identify and rank differentially expressed marker peaks. The k-nearest neighbours algorithm was used to build classification models either using separate training and test datasets or else by using an iterative, 'leave-one-out' cross-validation method. Results 73 protein peaks in the mass range 1800-16000Da were differentially expressed in tumour verses adjacent normal mucosa tissue (P ≤ 0.01, false discovery rate ≤ 0.05. Unsupervised hierarchical cluster analysis classified most tumour and normal mucosa into distinct cluster groups. Supervised prediction correctly classified the tumour/normal mucosa status of specimens in an independent test spectra dataset with 100% sensitivity and specificity (95% confidence interval: 67.9-99.2%. Supervised prediction using 'leave-one-out' cross validation algorithms for tumour spectra correctly classified 10/13 poorly differentiated and 16/18 well/moderately differentiated tumours (P = P = P = 0.001; ROC error, 0.212. Conclusions Protein expression profiling of surgically resected CRC tissue extracts by MALDI-TOF MS has potential value in studies aimed at improved molecular

U(3)-flavor nonet scalar as an origin of the flavor mass spectra

International Nuclear Information System (INIS)

Koide, Yoshio

2008-01-01

According to an idea that the quark and lepton mass spectra originate in a VEV structure of a U(3)-flavor nonet scalar Φ, the mass spectra of the down-quarks and charged leptons are investigated. The U(3) flavor symmetry is spontaneously and completely broken by non-zero and non-degenerated VEVs of Φ, without passing any subgroup of U(3). The ratios (m e +m μ +m τ )/(√(m e )+√(m μ )+√(m τ )) 2 and √(m e m μ m τ )/(√(m e )+√(m μ )+√(m τ )) 3 are investigated based on a toy model

Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra

KAUST Repository

Cannistraci, Carlo Vittorio

2015-01-26

Denoising multidimensional NMR-spectra is a fundamental step in NMR protein structure determination. The state-of-the-art method uses wavelet-denoising, which may suffer when applied to non-stationary signals affected by Gaussian-white-noise mixed with strong impulsive artifacts, like those in multi-dimensional NMR-spectra. Regrettably, Wavelet\\'s performance depends on a combinatorial search of wavelet shapes and parameters; and multi-dimensional extension of wavelet-denoising is highly non-trivial, which hampers its application to multidimensional NMR-spectra. Here, we endorse a diverse philosophy of denoising NMR-spectra: less is more! We consider spatial filters that have only one parameter to tune: the window-size. We propose, for the first time, the 3D extension of the median-modified-Wiener-filter (MMWF), an adaptive variant of the median-filter, and also its novel variation named MMWF*. We test the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR-spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Noticeably, MMWF* produces stable high performance almost invariant for diverse window-size settings: this signifies a consistent advantage in the implementation of automatic pipelines for protein NMR-spectra analysis.

Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra

KAUST Repository

Cannistraci, Carlo Vittorio; Abbas, Ahmed; Gao, Xin

2015-01-01

Denoising multidimensional NMR-spectra is a fundamental step in NMR protein structure determination. The state-of-the-art method uses wavelet-denoising, which may suffer when applied to non-stationary signals affected by Gaussian-white-noise mixed with strong impulsive artifacts, like those in multi-dimensional NMR-spectra. Regrettably, Wavelet's performance depends on a combinatorial search of wavelet shapes and parameters; and multi-dimensional extension of wavelet-denoising is highly non-trivial, which hampers its application to multidimensional NMR-spectra. Here, we endorse a diverse philosophy of denoising NMR-spectra: less is more! We consider spatial filters that have only one parameter to tune: the window-size. We propose, for the first time, the 3D extension of the median-modified-Wiener-filter (MMWF), an adaptive variant of the median-filter, and also its novel variation named MMWF*. We test the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR-spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Noticeably, MMWF* produces stable high performance almost invariant for diverse window-size settings: this signifies a consistent advantage in the implementation of automatic pipelines for protein NMR-spectra analysis.

Calibration of matrix-assisted laser desorption/ionization time-of-flight peptide mass fingerprinting spectra

DEFF Research Database (Denmark)

Hjernø, Karin; Højrup, Peter

2007-01-01

This chapter describes a number of aspects important for calibration of matrix-assisted laser desorption/ionization time-of-flight spectra prior to peptide mass fingerprinting searches. Both multipoint internal calibration and mass defect-based calibration is illustrated. The chapter describes ho...

UV-POSIT: Web-Based Tools for Rapid and Facile Structural Interpretation of Ultraviolet Photodissociation (UVPD) Mass Spectra

Science.gov (United States)

Rosenberg, Jake; Parker, W. Ryan; Cammarata, Michael B.; Brodbelt, Jennifer S.

2018-04-01

UV-POSIT (Ultraviolet Photodissociation Online Structure Interrogation Tools) is a suite of web-based tools designed to facilitate the rapid interpretation of data from native mass spectrometry experiments making use of 193 nm ultraviolet photodissociation (UVPD). The suite includes four separate utilities which assist in the calculation of fragment ion abundances as a function of backbone cleavage sites and sequence position; the localization of charge sites in intact proteins; the calculation of hydrogen elimination propensity for a-type fragment ions; and mass-offset searching of UVPD spectra to identify unknown modifications and assess false positive fragment identifications. UV-POSIT is implemented as a Python/Flask web application hosted at http://uv-posit.cm.utexas.edu. UV-POSIT is available under the MIT license, and the source code is available at https://github.com/jarosenb/UV_POSIT. [Figure not available: see fulltext.

UV-POSIT: Web-Based Tools for Rapid and Facile Structural Interpretation of Ultraviolet Photodissociation (UVPD) Mass Spectra.

Science.gov (United States)

Rosenberg, Jake; Parker, W Ryan; Cammarata, Michael B; Brodbelt, Jennifer S

2018-04-06

UV-POSIT (Ultraviolet Photodissociation Online Structure Interrogation Tools) is a suite of web-based tools designed to facilitate the rapid interpretation of data from native mass spectrometry experiments making use of 193 nm ultraviolet photodissociation (UVPD). The suite includes four separate utilities which assist in the calculation of fragment ion abundances as a function of backbone cleavage sites and sequence position; the localization of charge sites in intact proteins; the calculation of hydrogen elimination propensity for a-type fragment ions; and mass-offset searching of UVPD spectra to identify unknown modifications and assess false positive fragment identifications. UV-POSIT is implemented as a Python/Flask web application hosted at http://uv-posit.cm.utexas.edu . UV-POSIT is available under the MIT license, and the source code is available at https://github.com/jarosenb/UV_POSIT . Graphical Abstract.

A SELDI mass spectrometry study of experimental autoimmune encephalomyelitis: sample preparation, reproducibility, and differential protein expression patterns.

Science.gov (United States)

Azzam, Sausan; Broadwater, Laurie; Li, Shuo; Freeman, Ernest J; McDonough, Jennifer; Gregory, Roger B

2013-05-01

Experimental autoimmune encephalomyelitis (EAE) is an autoimmune, inflammatory disease of the central nervous system that is widely used as a model of multiple sclerosis (MS). Mitochondrial dysfunction appears to play a role in the development of neuropathology in MS and may also play a role in disease pathology in EAE. Here, surface enhanced laser desorption ionization mass spectrometry (SELDI-MS) has been employed to obtain protein expression profiles from mitochondrially enriched fractions derived from EAE and control mouse brain. To gain insight into experimental variation, the reproducibility of sub-cellular fractionation, anion exchange fractionation as well as spot-to-spot and chip-to-chip variation using pooled samples from brain tissue was examined. Variability of SELDI mass spectral peak intensities indicates a coefficient of variation (CV) of 15.6% and 17.6% between spots on a given chip and between different chips, respectively. Thinly slicing tissue prior to homogenization with a rotor homogenizer showed better reproducibility (CV = 17.0%) than homogenization of blocks of brain tissue with a Teflon® pestle (CV = 27.0%). Fractionation of proteins with anion exchange beads prior to SELDI-MS analysis gave overall CV values from 16.1% to 18.6%. SELDI mass spectra of mitochondrial fractions obtained from brain tissue from EAE mice and controls displayed 39 differentially expressed proteins (p≤ 0.05) out of a total of 241 protein peaks observed in anion exchange fractions. Hierarchical clustering analysis showed that protein fractions from EAE animals with severe disability clearly segregated from controls. Several components of electron transport chain complexes (cytochrome c oxidase subunit 6b1, subunit 6C, and subunit 4; NADH dehydrogenase flavoprotein 3, alpha subcomplex subunit 2, Fe-S protein 4, and Fe-S protein 6; and ATP synthase subunit e) were identified as possible differentially expressed proteins. Myelin Basic Protein isoform 8 (MBP8) (14.2 k

Mass spectrometry protein expression profiles in colorectal cancer tissue associated with clinico-pathological features of disease

International Nuclear Information System (INIS)

Liao, Christopher CL; Ward, Nicholas; Marsh, Simon; Arulampalam, Tan; Norton, John D

2010-01-01

Studies of several tumour types have shown that expression profiling of cellular protein extracted from surgical tissue specimens by direct mass spectrometry analysis can accurately discriminate tumour from normal tissue and in some cases can sub-classify disease. We have evaluated the potential value of this approach to classify various clinico-pathological features in colorectal cancer by employing matrix-assisted laser desorption ionisation time of-flight-mass spectrometry (MALDI-TOF MS). Protein extracts from 31 tumour and 33 normal mucosa specimens were purified, subjected to MALDI-Tof MS and then analysed using the 'GenePattern' suite of computational tools (Broad Institute, MIT, USA). Comparative Gene Marker Selection with either a t-test or a signal-to-noise ratio (SNR) test statistic was used to identify and rank differentially expressed marker peaks. The k-nearest neighbours algorithm was used to build classification models either using separate training and test datasets or else by using an iterative, 'leave-one-out' cross-validation method. 73 protein peaks in the mass range 1800-16000Da were differentially expressed in tumour verses adjacent normal mucosa tissue (P ≤ 0.01, false discovery rate ≤ 0.05). Unsupervised hierarchical cluster analysis classified most tumour and normal mucosa into distinct cluster groups. Supervised prediction correctly classified the tumour/normal mucosa status of specimens in an independent test spectra dataset with 100% sensitivity and specificity (95% confidence interval: 67.9-99.2%). Supervised prediction using 'leave-one-out' cross validation algorithms for tumour spectra correctly classified 10/13 poorly differentiated and 16/18 well/moderately differentiated tumours (P = < 0.001; receiver-operator characteristics - ROC - error, 0.171); disease recurrence was correctly predicted in 5/6 cases and disease-free survival (median follow-up time, 25 months) was correctly predicted in 22

NMRKIN: Simulating line shapes from two-dimensional spectra of proteins upon ligand binding

International Nuclear Information System (INIS)

Guenther, Ulrich L.; Schaffhausen, Brian

2002-01-01

The analysis of the shape of signals in NMR spectra is a powerful tool to study exchange and reaction kinetics. Line shapes in two-dimensional spectra of proteins recorded for titrations with ligands provide information about binding rates observed at individual residues. Here we describe a fast method to simulate a series of line shapes derived from two-dimensional spectra of a protein during a ligand titration. This procedure, which takes the mutual effects of two dimensions into account, has been implemented in MATLAB as an add-on to NMRLab (Guenther et al., 2000). In addition, more complex kinetic models, including sequential and parallel reactions, were simulated to demonstrate common features of more complex line shapes which could be encountered in protein-ligand interactions. As an example of this method, we describe its application to line shapes obtained for a titration of the p85 N-SH2 domain of PI3-kinase with a peptide derived from polyomavirus middle T antigen (MT)

Protein-Level Integration Strategy of Multiengine MS Spectra Search Results for Higher Confidence and Sequence Coverage.

Science.gov (United States)

Zhao, Panpan; Zhong, Jiayong; Liu, Wanting; Zhao, Jing; Zhang, Gong

2017-12-01

Multiple search engines based on various models have been developed to search MS/MS spectra against a reference database, providing different results for the same data set. How to integrate these results efficiently with minimal compromise on false discoveries is an open question due to the lack of an independent, reliable, and highly sensitive standard. We took the advantage of the translating mRNA sequencing (RNC-seq) result as a standard to evaluate the integration strategies of the protein identifications from various search engines. We used seven mainstream search engines (Andromeda, Mascot, OMSSA, X!Tandem, pFind, InsPecT, and ProVerB) to search the same label-free MS data sets of human cell lines Hep3B, MHCCLM3, and MHCC97H from the Chinese C-HPP Consortium for Chromosomes 1, 8, and 20. As expected, the union of seven engines resulted in a boosted false identification, whereas the intersection of seven engines remarkably decreased the identification power. We found that identifications of at least two out of seven engines resulted in maximizing the protein identification power while minimizing the ratio of suspicious/translation-supported identifications (STR), as monitored by our STR index, based on RNC-Seq. Furthermore, this strategy also significantly improves the peptides coverage of the protein amino acid sequence. In summary, we demonstrated a simple strategy to significantly improve the performance for shotgun mass spectrometry by protein-level integrating multiple search engines, maximizing the utilization of the current MS spectra without additional experimental work.

Systematic Uncertainties in Black Hole Masses Determined from Single Epoch Spectra

DEFF Research Database (Denmark)

Denney, Kelly D.; Peterson, Bradley M.; Dietrich, Matthias

2008-01-01

We explore the nature of systematic errors that can arise in measurement of black hole masses from single-epoch spectra of active galactic nuclei (AGNs) by utilizing the many epochs available for NGC 5548 and PG1229+204 from reverberation mapping databases. In particular, we examine systematics due...

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

Science.gov (United States)

Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G; Martens, Lennart; Vaudel, Marc; Barsnes, Harald

2014-02-07

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .

Binomial probability distribution model-based protein identification algorithm for tandem mass spectrometry utilizing peak intensity information.

Science.gov (United States)

Xiao, Chuan-Le; Chen, Xiao-Zhou; Du, Yang-Li; Sun, Xuesong; Zhang, Gong; He, Qing-Yu

2013-01-04

Mass spectrometry has become one of the most important technologies in proteomic analysis. Tandem mass spectrometry (LC-MS/MS) is a major tool for the analysis of peptide mixtures from protein samples. The key step of MS data processing is the identification of peptides from experimental spectra by searching public sequence databases. Although a number of algorithms to identify peptides from MS/MS data have been already proposed, e.g. Sequest, OMSSA, X!Tandem, Mascot, etc., they are mainly based on statistical models considering only peak-matches between experimental and theoretical spectra, but not peak intensity information. Moreover, different algorithms gave different results from the same MS data, implying their probable incompleteness and questionable reproducibility. We developed a novel peptide identification algorithm, ProVerB, based on a binomial probability distribution model of protein tandem mass spectrometry combined with a new scoring function, making full use of peak intensity information and, thus, enhancing the ability of identification. Compared with Mascot, Sequest, and SQID, ProVerB identified significantly more peptides from LC-MS/MS data sets than the current algorithms at 1% False Discovery Rate (FDR) and provided more confident peptide identifications. ProVerB is also compatible with various platforms and experimental data sets, showing its robustness and versatility. The open-source program ProVerB is available at http://bioinformatics.jnu.edu.cn/software/proverb/ .

Phylogenetic Analysis Using Protein Mass Spectrometry.

Science.gov (United States)

Ma, Shiyong; Downard, Kevin M; Wong, Jason W H

2017-01-01

Through advances in molecular biology, comparative analysis of DNA sequences is currently the cornerstone in the study of molecular evolution and phylogenetics. Nevertheless, protein mass spectrometry offers some unique opportunities to enable phylogenetic analyses in organisms where DNA may be difficult or costly to obtain. To date, the methods of phylogenetic analysis using protein mass spectrometry can be classified into three categories: (1) de novo protein sequencing followed by classical phylogenetic reconstruction, (2) direct phylogenetic reconstruction using proteolytic peptide mass maps, and (3) mapping of mass spectral data onto classical phylogenetic trees. In this chapter, we provide a brief description of the three methods and the protocol for each method along with relevant tools and algorithms.

Structural determination of intact proteins using mass spectrometry

Science.gov (United States)

Kruppa, Gary [San Francisco, CA; Schoeniger, Joseph S [Oakland, CA; Young, Malin M [Livermore, CA

2008-05-06

The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

Robust automated mass spectra interpretation and chemical formula calculation using mixed integer linear programming.

Science.gov (United States)

Baran, Richard; Northen, Trent R

2013-10-15

Untargeted metabolite profiling using liquid chromatography and mass spectrometry coupled via electrospray ionization is a powerful tool for the discovery of novel natural products, metabolic capabilities, and biomarkers. However, the elucidation of the identities of uncharacterized metabolites from spectral features remains challenging. A critical step in the metabolite identification workflow is the assignment of redundant spectral features (adducts, fragments, multimers) and calculation of the underlying chemical formula. Inspection of the data by experts using computational tools solving partial problems (e.g., chemical formula calculation for individual ions) can be performed to disambiguate alternative solutions and provide reliable results. However, manual curation is tedious and not readily scalable or standardized. Here we describe an automated procedure for the robust automated mass spectra interpretation and chemical formula calculation using mixed integer linear programming optimization (RAMSI). Chemical rules among related ions are expressed as linear constraints and both the spectra interpretation and chemical formula calculation are performed in a single optimization step. This approach is unbiased in that it does not require predefined sets of neutral losses and positive and negative polarity spectra can be combined in a single optimization. The procedure was evaluated with 30 experimental mass spectra and was found to effectively identify the protonated or deprotonated molecule ([M + H](+) or [M - H](-)) while being robust to the presence of background ions. RAMSI provides a much-needed standardized tool for interpreting ions for subsequent identification in untargeted metabolomics workflows.

A scale space approach for unsupervised feature selection in mass spectra classification for ovarian cancer detection.

Science.gov (United States)

Ceccarelli, Michele; d'Acierno, Antonio; Facchiano, Angelo

2009-10-15

Mass spectrometry spectra, widely used in proteomics studies as a screening tool for protein profiling and to detect discriminatory signals, are high dimensional data. A large number of local maxima (a.k.a. peaks) have to be analyzed as part of computational pipelines aimed at the realization of efficient predictive and screening protocols. With this kind of data dimensions and samples size the risk of over-fitting and selection bias is pervasive. Therefore the development of bio-informatics methods based on unsupervised feature extraction can lead to general tools which can be applied to several fields of predictive proteomics. We propose a method for feature selection and extraction grounded on the theory of multi-scale spaces for high resolution spectra derived from analysis of serum. Then we use support vector machines for classification. In particular we use a database containing 216 samples spectra divided in 115 cancer and 91 control samples. The overall accuracy averaged over a large cross validation study is 98.18. The area under the ROC curve of the best selected model is 0.9962. We improved previous known results on the problem on the same data, with the advantage that the proposed method has an unsupervised feature selection phase. All the developed code, as MATLAB scripts, can be downloaded from http://medeaserver.isa.cnr.it/dacierno/spectracode.htm.

Protein identification by peptide mass fingerprinting

DEFF Research Database (Denmark)

Hjernø, Karin

2007-01-01

  Peptide mass fingerprinting is an effective way of identifying, e.g., gel-separated proteins, by matching experimentally obtained peptide mass data against large databases. However, several factors are known to influence the quality of the resulting matches, such as proteins contaminating the s...

QCD's Partner Needed for Mass Spectra and Parton Structure Functions

International Nuclear Information System (INIS)

Kim, Y.S.

2009-01-01

as in the case of the hydrogen atom, bound-state wave functions are needed to generate hadronic spectra. For this purpose, in 1971, Feynman and his students wrote down a Lorentz-invariant harmonic oscillator equation. This differential equation has one set of solutions satisfying the Lorentz-covariant boundary condition. This covariant set generates Lorentz-invariant mass spectra with their degeneracies. Furthermore, the Lorentz-covariant wave functions allow us to calculate the valence parton distribution by Lorentz-boosting the quark-model wave function from the hadronic rest frame. However, this boosted wave function does not give an accurate parton distribution. The wave function needs QCD corrections to make a contact with the real world. Likewise, QCD needs the wave function as a starting point for calculating the parton structure function. (author)

Towards automated discrimination of lipids versus peptides from full scan mass spectra

Directory of Open Access Journals (Sweden)

Piotr Dittwald

2014-09-01

Full Text Available Although physicochemical fractionation techniques play a crucial role in the analysis of complex mixtures, they are not necessarily the best solution to separate specific molecular classes, such as lipids and peptides. Any physical fractionation step such as, for example, those based on liquid chromatography, will introduce its own variation and noise. In this paper we investigate to what extent the high sensitivity and resolution of contemporary mass spectrometers offers viable opportunities for computational separation of signals in full scan spectra. We introduce an automatic method that can discriminate peptide from lipid peaks in full scan mass spectra, based on their isotopic properties. We systematically evaluate which features maximally contribute to a peptide versus lipid classification. The selected features are subsequently used to build a random forest classifier that enables almost perfect separation between lipid and peptide signals without requiring ion fragmentation and classical tandem MS-based identification approaches. The classifier is trained on in silico data, but is also capable of discriminating signals in real world experiments. We evaluate the influence of typical data inaccuracies of common classes of mass spectrometry instruments on the optimal set of discriminant features. Finally, the method is successfully extended towards the classification of individual lipid classes from full scan mass spectral features, based on input data defined by the Lipid Maps Consortium.

Quantitative Interpretation of Multifrequency Multimode EPR Spectra of Metal Containing Proteins, Enzymes, and Biomimetic Complexes.

Science.gov (United States)

Petasis, Doros T; Hendrich, Michael P

2015-01-01

Electron paramagnetic resonance (EPR) spectroscopy has long been a primary method for characterization of paramagnetic centers in materials and biological complexes. Transition metals in biological complexes have valence d-orbitals that largely define the chemistry of the metal centers. EPR spectra are distinctive for metal type, oxidation state, protein environment, substrates, and inhibitors. The study of many metal centers in proteins, enzymes, and biomimetic complexes has led to the development of a systematic methodology for quantitative interpretation of EPR spectra from a wide array of metal containing complexes. The methodology is now contained in the computer program SpinCount. SpinCount allows simulation of EPR spectra from any sample containing multiple species composed of one or two metals in any spin state. The simulations are quantitative, thus allowing determination of all species concentrations in a sample directly from spectra. This chapter will focus on applications to transition metals in biological systems using EPR spectra from multiple microwave frequencies and modes. © 2015 Elsevier Inc. All rights reserved.

A new application of hierarchical cluster analysis to investigate organic peaks in bulk mass spectra obtained with an Aerodyne Aerosol Mass Spectrometer

Science.gov (United States)

Middlebrook, A. M.; Marcolli, C.; Canagaratna, M. R.; Worsnop, D. R.; Bahreini, R.; de Gouw, J. A.; Warneke, C.; Goldan, P. D.; Kuster, W. C.; Williams, E. J.; Lerner, B. M.; Roberts, J. M.; Meagher, J. F.; Fehsenfeld, F. C.; Marchewka, M. L.; Bertman, S. B.

2006-12-01

We applied hierarchical cluster analysis to an Aerodyne aerosol mass spectrometer (AMS) bulk mass spectral dataset collected aboard the NOAA research vessel Ronald H. Brown during the 2002 New England Air Quality Study off the east coast of the United States. Emphasizing the organic peaks, the cluster analysis yielded a series of categories that are distinguishable with respect to their mass spectra and their occurrence as a function of time. The differences between the categories mainly arise from relative intensity changes rather than from the presence or absence of specific peaks. The most frequent category exhibits a strong signal at m/z 44 and represents oxidized organic matter probably originating from both anthropogenic as well as biogenic sources. On the basis of spectral and trace gas correlations, the second most common category with strong signals at m/z 29, 43, and 44 contains contributions from isoprene oxidation products. The third through the fifth most common categories have peak patterns characteristic of monoterpene oxidation products and were most frequently observed when air masses from monoterpene rich regions were sampled. Taken together, the second through the fifth most common categories represent on average 17% of the total organic mass that stems likely from biogenic sources during the ship's cruise. These numbers have to be viewed as lower limits since the most common category was attributed to anthropogenic sources for this calculation. The cluster analysis was also very effective in identifying a few contaminated mass spectra that were not removed during pre-processing. This study demonstrates that hierarchical clustering is a useful tool to analyze the complex patterns of the organic peaks in bulk aerosol mass spectra from a field study.

The laser desorption/laser ionization mass spectra of some methylated xanthines and the laser desorption of caffeine and theophylline from thin layer chromatography plates

Science.gov (United States)

Rogers, Kevin; Milnes, John; Gormally, John

1993-02-01

Laser desorption/laser ionization time-of-flight mass spectra of caffeine, theophylline, theobromine and xanthine are reported. These mass spectra are compared with published spectra obtained using electron impact ionization. Mass spectra of caffeine and theophylline obtained by IR laser desorption from thin layer chromatography plates are also described. The laser desorption of materials from thin layer chromatography plates is discussed.

Are neutral loss and internal product ions useful for top-down protein identification?

Science.gov (United States)

Xiao, Kaijie; Yu, Fan; Fang, Houqin; Xue, Bingbing; Liu, Yan; Li, Yunhui; Tian, Zhixin

2017-05-08

Neutral loss and internal product ions have been found to be significant in both peptide and protein tandem mass spectra and they have been proposed to be included in database search and for protein identification. In addition to common canonical b/y ions in collision-based dissociation or c/z ions in electron-based dissociation, inclusion of neutral loss and internal product ions would certainly make better use of tandem mass spectra data; however, their ultimate utility for protein identification with false discovery rate control remains unclear. Here we report our proteome-level utility benchmarking of neutral loss and internal product ions with tandem mass spectra of intact E. coli proteome. Utility of internal product ions was further evaluated at the protein level using selected tandem mass spectra of individual E. coli proteins. We found that both neutral loss and internal products ions do not have direct utility for protein identification when they were used for scoring of P Score; but they do have indirect utility for provision of more canonical b/y ions when they are included in the database search and overlapping ions between different ion types are resolved. Tandem mass spectrometry has evolved to be a state-of-the-art method for characterization of protein primary structures (including amino acid sequence, post-translational modifications (PTMs) as well as their site location), where full study and utilization tandem mass spectra and product ions are indispensable. This primary structure information is essential for higher order structure and eventual function study of proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

NMRNet: A deep learning approach to automated peak picking of protein NMR spectra.

Science.gov (United States)

Klukowski, Piotr; Augoff, Michal; Zieba, Maciej; Drwal, Maciej; Gonczarek, Adam; Walczak, Michal J

2018-03-14

Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy. In particular, deep learning has proven to systematically achieve human-level performance in various recognition tasks, and thus emerges as an ideal tool to address automated identification of NMR signals. We have applied a convolutional neural network for visual analysis of multidimensional NMR spectra. A comprehensive test on 31 manually-annotated spectra has demonstrated top-tier average precision (AP) of 0.9596, 0.9058 and 0.8271 for backbone, side-chain and NOESY spectra, respectively. Furthermore, a combination of extracted peak lists with automated assignment routine, FLYA, outperformed other methods, including the manual one, and led to correct resonance assignment at the levels of 90.40%, 89.90% and 90.20% for three benchmark proteins. The proposed model is a part of a Dumpling software (platform for protein NMR data analysis), and is available at https://dumpling.bio/. michaljerzywalczak@gmail.compiotr.klukowski@pwr.edu.pl. Supplementary data are available at Bioinformatics online.

Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications.

Science.gov (United States)

Sajic, Tatjana; Liu, Yansheng; Aebersold, Ruedi

2015-04-01

In medicine, there is an urgent need for protein biomarkers in a range of applications that includes diagnostics, disease stratification, and therapeutic decisions. One of the main technologies to address this need is MS, used for protein biomarker discovery and, increasingly, also for protein biomarker validation. Currently, data-dependent analysis (also referred to as shotgun proteomics) and targeted MS, exemplified by SRM, are the most frequently used mass spectrometric methods. Recently developed data-independent acquisition techniques combine the strength of shotgun and targeted proteomics, while avoiding some of the limitations of the respective methods. They provide high-throughput, accurate quantification, and reproducible measurements within a single experimental setup. Here, we describe and review data-independent acquisition strategies and their recent use in clinically oriented studies. In addition, we also provide a detailed guide for the implementation of SWATH-MS (where SWATH is sequential window acquisition of all theoretical mass spectra)-one of the data-independent strategies that have gained wide application of late. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls

Directory of Open Access Journals (Sweden)

Sillevis Smitt Peter A

2006-09-01

Full Text Available Abstract Background Statistical comparison of peptide profiles in biomarker discovery requires fast, user-friendly software for high throughput data analysis. Important features are flexibility in changing input variables and statistical analysis of peptides that are differentially expressed between patient and control groups. In addition, integration the mass spectrometry data with the results of other experiments, such as microarray analysis, and information from other databases requires a central storage of the profile matrix, where protein id's can be added to peptide masses of interest. Results A new database application is presented, to detect and identify significantly differentially expressed peptides in peptide profiles obtained from body fluids of patient and control groups. The presented modular software is capable of central storage of mass spectra and results in fast analysis. The software architecture consists of 4 pillars, 1 a Graphical User Interface written in Java, 2 a MySQL database, which contains all metadata, such as experiment numbers and sample codes, 3 a FTP (File Transport Protocol server to store all raw mass spectrometry files and processed data, and 4 the software package R, which is used for modular statistical calculations, such as the Wilcoxon-Mann-Whitney rank sum test. Statistic analysis by the Wilcoxon-Mann-Whitney test in R demonstrates that peptide-profiles of two patient groups 1 breast cancer patients with leptomeningeal metastases and 2 prostate cancer patients in end stage disease can be distinguished from those of control groups. Conclusion The database application is capable to distinguish patient Matrix Assisted Laser Desorption Ionization (MALDI-TOF peptide profiles from control groups using large size datasets. The modular architecture of the application makes it possible to adapt the application to handle also large sized data from MS/MS- and Fourier Transform Ion Cyclotron Resonance (FT-ICR mass

A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls.

Science.gov (United States)

Titulaer, Mark K; Siccama, Ivar; Dekker, Lennard J; van Rijswijk, Angelique L C T; Heeren, Ron M A; Sillevis Smitt, Peter A; Luider, Theo M

2006-09-05

Statistical comparison of peptide profiles in biomarker discovery requires fast, user-friendly software for high throughput data analysis. Important features are flexibility in changing input variables and statistical analysis of peptides that are differentially expressed between patient and control groups. In addition, integration the mass spectrometry data with the results of other experiments, such as microarray analysis, and information from other databases requires a central storage of the profile matrix, where protein id's can be added to peptide masses of interest. A new database application is presented, to detect and identify significantly differentially expressed peptides in peptide profiles obtained from body fluids of patient and control groups. The presented modular software is capable of central storage of mass spectra and results in fast analysis. The software architecture consists of 4 pillars, 1) a Graphical User Interface written in Java, 2) a MySQL database, which contains all metadata, such as experiment numbers and sample codes, 3) a FTP (File Transport Protocol) server to store all raw mass spectrometry files and processed data, and 4) the software package R, which is used for modular statistical calculations, such as the Wilcoxon-Mann-Whitney rank sum test. Statistic analysis by the Wilcoxon-Mann-Whitney test in R demonstrates that peptide-profiles of two patient groups 1) breast cancer patients with leptomeningeal metastases and 2) prostate cancer patients in end stage disease can be distinguished from those of control groups. The database application is capable to distinguish patient Matrix Assisted Laser Desorption Ionization (MALDI-TOF) peptide profiles from control groups using large size datasets. The modular architecture of the application makes it possible to adapt the application to handle also large sized data from MS/MS- and Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry experiments. It is expected that the

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.

Science.gov (United States)

Kou, Qiang; Wu, Si; Tolic, Nikola; Paša-Tolic, Ljiljana; Liu, Yunlong; Liu, Xiaowen

2017-05-01

Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a 'bird's eye view' of intact proteoforms. The combinatorial explosion of various alterations on a protein may result in billions of possible proteoforms, making proteoform identification a challenging computational problem. We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry datasets showed that TopMG outperformed existing methods in identifying complex proteoforms. http://proteomics.informatics.iupui.edu/software/topmg/. xwliu@iupui.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Blind deconvolution of time-of-flight mass spectra from atom probe tomography

International Nuclear Information System (INIS)

Johnson, L.J.S.; Thuvander, M.; Stiller, K.; Odén, M.; Hultman, L.

2013-01-01

A major source of uncertainty in compositional measurements in atom probe tomography stems from the uncertainties of assigning peaks or parts of peaks in the mass spectrum to their correct identities. In particular, peak overlap is a limiting factor, whereas an ideal mass spectrum would have peaks at their correct positions with zero broadening. Here, we report a method to deconvolute the experimental mass spectrum into such an ideal spectrum and a system function describing the peak broadening introduced by the field evaporation and detection of each ion. By making the assumption of a linear and time-invariant behavior, a system of equations is derived that describes the peak shape and peak intensities. The model is fitted to the observed spectrum by minimizing the squared residuals, regularized by the maximum entropy method. For synthetic data perfectly obeying the assumptions, the method recovered peak intensities to within ±0.33at%. The application of this model to experimental APT data is exemplified with Fe–Cr data. Knowledge of the peak shape opens up several new possibilities, not just for better overall compositional determination, but, e.g., for the estimation of errors of ranging due to peak overlap or peak separation constrained by isotope abundances. - Highlights: • A method for the deconvolution of atom probe mass spectra is proposed. • Applied to synthetic randomly generated spectra the accuracy was ±0.33 at. • Application of the method to an experimental Fe–Cr spectrum is demonstrated

Excited state mass spectra of doubly heavy Ξ baryons

Energy Technology Data Exchange (ETDEWEB)

Shah, Zalak; Rai, Ajay Kumar [Sardar Vallabhbhai National Institute of Technology, Department of Applied Physics, Surat, Gujarat (India)

2017-02-15

In this paper, the mass spectra are obtained for doubly heavy Ξ baryons, namely, Ξ{sub cc}{sup +}, Ξ{sub cc}{sup ++}, Ξ{sub bb}{sup -}, Ξ{sub bb}{sup 0}, Ξ{sub bc}{sup 0} and Ξ{sub bc}{sup +}. These baryons consist of two heavy quarks (cc, bb, and bc) with a light (d or u) quark. The ground, radial, and orbital states are calculated in the framework of the hypercentral constituent quark model with Coulomb plus linear potential. Our results are also compared with other predictions, thus, the average possible range of excited states masses of these Ξ baryons can be determined. The study of the Regge trajectories is performed in (n, M{sup 2}) and (J, M{sup 2}) planes and their slopes and intercepts are also determined. Lastly, the ground state magnetic moments of these doubly heavy baryons are also calculated. (orig.)

Similarity of High-Resolution Tandem Mass Spectrometry Spectra of Structurally Related Micropollutants and Transformation Products

Science.gov (United States)

Schollée, Jennifer E.; Schymanski, Emma L.; Stravs, Michael A.; Gulde, Rebekka; Thomaidis, Nikolaos S.; Hollender, Juliane

2017-12-01

High-resolution tandem mass spectrometry (HRMS2) with electrospray ionization is frequently applied to study polar organic molecules such as micropollutants. Fragmentation provides structural information to confirm structures of known compounds or propose structures of unknown compounds. Similarity of HRMS2 spectra between structurally related compounds has been suggested to facilitate identification of unknown compounds. To test this hypothesis, the similarity of reference standard HRMS2 spectra was calculated for 243 pairs of micropollutants and their structurally related transformation products (TPs); for comparison, spectral similarity was also calculated for 219 pairs of unrelated compounds. Spectra were measured on Orbitrap and QTOF mass spectrometers and similarity was calculated with the dot product. The influence of different factors on spectral similarity [e.g., normalized collision energy (NCE), merging fragments from all NCEs, and shifting fragments by the mass difference of the pair] was considered. Spectral similarity increased at higher NCEs and highest similarity scores for related pairs were obtained with merged spectra including measured fragments and shifted fragments. Removal of the monoisotopic peak was critical to reduce false positives. Using a spectral similarity score threshold of 0.52, 40% of related pairs and 0% of unrelated pairs were above this value. Structural similarity was estimated with the Tanimoto coefficient and pairs with higher structural similarity generally had higher spectral similarity. Pairs where one or both compounds contained heteroatoms such as sulfur often resulted in dissimilar spectra. This work demonstrates that HRMS2 spectral similarity may indicate structural similarity and that spectral similarity can be used in the future to screen complex samples for related compounds such as micropollutants and TPs, assisting in the prioritization of non-target compounds. [Figure not available: see fulltext.

Identification of ultramodified proteins using top-down spectra

Energy Technology Data Exchange (ETDEWEB)

Liu, Xiaowen; Hengel, Shawna M.; Wu, Si; Tolic, Nikola; Pasa-Tolic, Ljiljana; Pevzner, Pavel A.

2013-04-10

Post-translational modifications (PTMs) play an important role in various biological processes through changing protein structure and function. Some ultramodified proteins (like histones) have multiple PTMs forming PTM patterns that define the functionality of a protein. While bottom-up mass spectrometry (MS) has been successful in identifying individual PTMs within short peptides, it is unable to identify PTM patterns spread along entire proteins in a coordinated fashion. In contrast, top-down MS analyzes intact proteins and reveals PTM patterns along the entire proteins. However, while recent advances in instrumentation have made top-down MS accessible to many laboratories, most computational tools for top-down MS focus on proteins with few PTMs and are unable to identify complex PTM patterns. We propose a new algorithm, MS-Align-E, that identifies both expected and unexpected PTMs in ultramodified proteins. We demonstrate that MS-Align-E identifies many protein forms of histone H4 and benchmark it against the currently accepted software tools.

Assignment strategies in homonuclear three-dimensional 1H NMR spectra of proteins

International Nuclear Information System (INIS)

Vuister, G.W.; Boelens, R.; Padilla, A.; Kleywegt, G.J.; Kaptein, R.

1990-01-01

The increase in dimensionality of three-dimensional (3D) NMR greatly enhances the spectral resolution in comparison to 2D NMR. It alleviates the problem of resonance overlap and may extend the range of molecules amenable to structure determination by high-resolution NMR spectroscopy. Here, the authors present strategies for the assignment of protein resonances from homonuclear nonselective 3D NOE-HOHAHA spectra. A notation for connectivities between protons, corresponding to cross peaks in 3D spectra, is introduced. They show how spin systems can be identified by tracing cross-peak patterns in cross sections perpendicular to the three frequency axes. The observable 3D sequential connectivities in proteins are tabulated, and estimates for the relative intensities of the corresponding cross peaks are given for α-helical and β-sheet conformations. Intensities of the cross peaks in the 3D spectrum of pike III paravalbumin follow the predictions. The sequential-assignment procedure is illustrated for loop regions, extended and α-helical conformations for the residues Ala 54-Leu 63 of paravalbumin. NOEs that were not previously identified in 2D spectra of paravalbumin due to overlap are found

Electroweak symmetry breaking and mass spectra in six-dimensional gauge-Higgs grand unification

Science.gov (United States)

Hosotani, Yutaka; Yamatsu, Naoki

2018-02-01

The mass spectra of the standard model particles are reproduced in the SO(11) gauge-Higgs grand unification in six-dimensional warped space without introducing exotic light fermions. Light neutrino masses are explained by the gauge-Higgs seesaw mechanism. We evaluate the effective potential of the four-dimensional Higgs boson appearing as a fluctuation mode of the Aharonov-Bohm phase θ_H in the extra-dimensional space, and show that the dynamical electroweak symmetry breaking takes place with the Higgs boson mass m_H ˜ 125 GeV and θ_H ˜ 0.1. The Kaluza-Klein mass scale in the fifth dimension is approximately given by m_KK ˜ 1.230 TeV/sin θ_H.

Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR)

Science.gov (United States)

Laszlo, Kenneth J.; Bush, Matthew F.

2015-12-01

Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/ z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/ z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures.

Atmospheric proton and deuterium energy spectra determination with the MASS2 experiment

Energy Technology Data Exchange (ETDEWEB)

Grimani, C.; Brunetti, M.T.; Codino, A.; Finetti, N. [Perugia Univ. (Italy)]|[INFN, Perugia (Italy); Papini, P.; Massimo Brancaccio, F. [Florence Univ. (Italy)]|[INFN, Florence (Italy); Basini, G.; Bongiorno, F. [INFN, Laboratori Nazionali di Frascati, Rome (Italy); Golden, R.L. [New Mexico State Univ., Las Cruces, NM (United States). Particle Astrophysics Lab.; Hof, M. [Siegen Univ. (Germany). Fachbereich Physik

1995-09-01

The energy spectra of atmospheric-secondary protons and deuterium nuclei have been measured during the September 23, 1991, balloon flight of the NMSU/Wizard - MASS2 instrument. The apparatus was launched from Fort Sumner, New Mexico. The geomagnetic cutoff at the launch site is about 4.5 GV/c. The instrument was flown for 9.8 hours at an altitude of over 100,000 feet. Particles detected below the geomagnetic cutoff have been produced mainly by the interactions of the primary cosmic rays with the atmosphere. The measurement of cosmic ray energy spectra below the geomagnetic cutoff provide direct insights into the particle production mechanism and allows comparison to atmospheric cascade calculations.

SYSTEMATIC UNCERTAINTIES IN BLACK HOLE MASSES DETERMINED FROM SINGLE-EPOCH SPECTRA

International Nuclear Information System (INIS)

Denney, Kelly D.; Peterson, Bradley M.; Dietrich, Matthias; Bentz, Misty C.; Vestergaard, Marianne

2009-01-01

We explore the nature of systematic errors that can arise in measurement of black hole masses from single-epoch (SE) spectra of active galactic nuclei (AGNs) by utilizing the many epochs available for NGC 5548 and PG1229+204 from reverberation mapping (RM) databases. In particular, we examine systematics due to AGN variability, contamination due to constant spectral components (i.e., narrow lines and host galaxy flux), data quality (i.e., signal-to-noise ratio (S/N)), and blending of spectral features. We investigate the effect that each of these systematics has on the precision and accuracy of SE masses calculated from two commonly used line width measures by comparing these results to recent RM studies. We calculate masses by characterizing the broad Hβ emission line by both the full width at half maximum and the line dispersion, and demonstrate the importance of removing narrow emission-line components and host starlight. We find that the reliability of line width measurements rapidly decreases for S/N lower than ∼ 10-20 (per pixel), and that fitting the line profiles instead of direct measurement of the data does not mitigate this problem but can, in fact, introduce systematic errors. We also conclude that a full spectral decomposition to deblend the AGN and galaxy spectral features is unnecessary, except to judge the contribution of the host galaxy to the luminosity and to deblend any emission lines that may inhibit accurate line width measurements. Finally, we present an error budget which summarizes the minimum observable uncertainties as well as the amount of additional scatter and/or systematic offset that can be expected from the individual sources of error investigated. In particular, we find that the minimum observable uncertainty in SE mass estimates due to variability is ∼ 20 pixel -1 ) spectra.

Negative ion mass spectra and particulate formation in rf silane plasma deposition experiments

International Nuclear Information System (INIS)

Howling, A.A.; Dorier, J.L.; Hollenstein, C.

1992-09-01

Negative ions have been clearly identified in silane rf plasmas used for the deposition of amorphous silicon. Mass spectra were measured for monosilicon up to pentasilicon negative ion radical groups in power-modulated plasmas by means of a mass spectrometer mounted just outside the glow region. Negative ions were only observed over a limited range of power modulation frequency which corresponds to particle-free conditions. The importance of negative ions regarding particulate formation is demonstrated and commented upon. (author) 3 figs., 19 refs

The Spectra Count Label-free Quantitation in Cancer Proteomics

OpenAIRE

Zhou, Weidong; Liotta, Lance A.; Petricoin, Emanuel F.

2012-01-01

Mass spectrometry is used routinely for large-scale protein identification from complex biological mixtures. Recently, relative quantitation approach on the basis of spectra count has been applied in several cancer proteomic studies. In this review, we examine the mechanism of this technique and highlight several important parameters associated with its application.

Mass spectra in N = 1 SQCD with additional colorless but flavored fields

Energy Technology Data Exchange (ETDEWEB)

Chernyak, Victor L. [Budker Institute of Nuclear Physics, Novosibirsk (Russian Federation); Novosibirsk State University, Novosibirsk (Russian Federation)

2017-01-15

Considered is the N = 1 supersymmetric QCD-like Φ-theory with SU(N{sub c}) colors and 0 < N{sub F} < 2N{sub c} flavors of light quarks Q{sup i}{sub a}, Q{sup a}{sub j} with equal small masses. In addition to quarks and gluons of the standard N = 1 SQCD, it includes N{sup 2}{sub F} colorless but flavored fields Φ{sub i}{sup j}, with the large mass parameter μ{sub Φ} >> Λ{sub Q} (Λ{sub Q} is the scale factor of the gauge coupling), interacting with quarks through the Yukawa coupling in the superpotential. The mass spectra of this (direct) Φ-theory are first directly calculated in all vacua with the unbroken or spontaneously broken flavor symmetry U(N{sub F}) → U(n{sub 1}) x U(n{sub 2}) at 0 < N{sub F} < N{sub c}, in which case this theory is logarithmically weakly coupled. Further, the mass spectra of both, this direct Φ-theory and its Seiberg's dual variant with SU(N{sub F}-N{sub c}) dual colors, the dΦ-theory, are calculated at 3N{sub c}/2 < N{sub F} < 2N{sub c} and at various values of μ{sub Φ} (in strong coupling regimes with coupling constants O(1)), now using the dynamical scenario introduced by the author in his previous article (Chernyak in JETP 114:61, arXiv:0811.4283 [hep-th], 2012). This scenario assumes that quarks in this case can be in two different standard phases only: either this is the HQ (heavy quark) phase with left angle Q{sup i}{sub a} right angle = 0 where they are confined, or they are higgsed with some components left angle Q{sup i}{sub a} right angle ≠ 0, at appropriate values of lagrangian parameters. It is shown that mass spectra of the direct Φ- and dual dΦ-theories are parametrically different, so that they are not equivalent. Besides it is shown in the direct Φ-theory that a qualitatively new phenomenon takes place: under appropriate conditions, the seemingly heavy and dynamically irrelevant fields Φ 'turn back' and there appear two additional generations of light Φ-particles with small masses �

Evolution of organic aerosol mass spectra upon heating: implications for OA phase and partitioning behavior

Energy Technology Data Exchange (ETDEWEB)

UC Davis; Cappa, Christopher D.; Wilson, Kevin R.

2010-10-28

Vacuum Ultraviolet (VUV) photoionization mass spectrometry has been used to measure the evolution of chemical composition for two distinct organic aerosol types as they are passed through a thermodenuder at different temperatures. The two organic aerosol types considered are primary lubricating oil (LO) aerosol and secondary aerosol from the alpha-pinene + O3 reaction (alphaP). The evolution of the VUV mass spectra for the two aerosol types with temperature are observed to differ dramatically. For LO particles, the spectra exhibit distinct changes with temperature in which the lower m/z peaks, corresponding to compounds with higher vapor pressures, disappear more rapidly than the high m/z peaks. In contrast, the alphaP aerosol spectrum is essentially unchanged by temperature even though the particles experience significant mass loss due to evaporation. The variations in the LO spectra are found to be quantitatively in agreement with expectations from absorptive partitioning theory whereas the alphaP spectra suggest that the evaporation of alphaP derived aerosol appears to not be governed by partitioning theory. We postulate that this difference arises from the alphaP particles existing as in a glassy state instead of having the expected liquid-like behavior. To reconcile these observations with decades of aerosol growth measurements, which indicate that OA formation is described by equilibrium partitioning, we present a conceptual model wherein the secondary OA is formed and then rapidly converted from an absorbing form to a non-absorbing form. The results suggest that although OA growth may be describable by equilibrium partitioning theory, the properties of organic aerosol once formed may differ significantly from the properties determined in the equilibrium framework.

A feedback framework for protein inference with peptides identified from tandem mass spectra

Directory of Open Access Journals (Sweden)

Shi Jinhong

2012-11-01

Full Text Available Abstract Background Protein inference is an important computational step in proteomics. There exists a natural nest relationship between protein inference and peptide identification, but these two steps are usually performed separately in existing methods. We believe that both peptide identification and protein inference can be improved by exploring such nest relationship. Results In this study, a feedback framework is proposed to process peptide identification reports from search engines, and an iterative method is implemented to exemplify the processing of Sequest peptide identification reports according to the framework. The iterative method is verified on two datasets with known validity of proteins and peptides, and compared with ProteinProphet and PeptideProphet. The results have shown that not only can the iterative method infer more true positive and less false positive proteins than ProteinProphet, but also identify more true positive and less false positive peptides than PeptideProphet. Conclusions The proposed iterative method implemented according to the feedback framework can unify and improve the results of peptide identification and protein inference.

Interpretation of laser desorption mass spectra of unexpected inorganic species found in a cosmetic sample of forensic interest: fingernail polish.

Science.gov (United States)

O'Neill, Emily; Harrington, Danielle; Allison, John

2009-08-01

When analytes containing color are irradiated with a pulsed UV laser in the ion source of a mass spectrometer, molecules such as dyes or pigments absorb energy, resulting in their desorption and ionization. This method, laser desorption mass spectrometry (LDMS), has been used successfully to analyze colorants of forensic interest in a wide variety of materials. Here, we present and interpret the most complex of such spectra obtained to date from a sample of fingernail polish. Interpretation of the spectrum provides a unique opportunity to characterize the laser desorption mass spectra of some unexpected inorganic materials found in cosmetics, such as "broken glass", cyanide compounds, and heavy metals. Also, the possibility of a useful forensic database of LDMS spectra of fingernail polishes is considered.

Identification of protein biomarkers in Dupuytren's contracture using surface enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS).

Science.gov (United States)

O'Gorman, David; Howard, Jeffrey C; Varallo, Vincenzo M; Cadieux, Peter; Bowley, Erin; McLean, Kris; Pak, Brian J; Gan, Bing Siang

2006-06-01

To study the protein expression profiles associated with Dupuytren's contracture (DC) to identify potential disease protein biomarkers (PBM) using a proteomic technology--Surface Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (SELDI-TOF-MS). Normal and disease palmar fascia from DC patients were analyzed using Ciphergen's SELDI-TOF-MS Protein Biological System II (PBSII) ProteinChip reader. Analysis of the resulting SELDI-TOF spectra was carried out using the peak cluster analysis program (BioMarker Wizard, Ciphergen). Common peak clusters were then filtered using a bootstrap algorithm called SAM (Significant Analysis of Microarrays) for increased fidelity in our analysis. Several differentially expressed low molecular weight (mass standard deviation for both methods of biomarker-rich low molecular weight region of the human proteome. Application of such novel technology may help clinicians to focus on specific molecular abnormalities in diseases with no known molecular pathogenesis, and uncover therapeutic and/or diagnostic targets.

Simultaneous quantification of protein phosphorylation sites using liquid chromatography-tandem mass spectrometry-based targeted proteomics: a linear algebra approach for isobaric phosphopeptides.

Science.gov (United States)

Xu, Feifei; Yang, Ting; Sheng, Yuan; Zhong, Ting; Yang, Mi; Chen, Yun

2014-12-05

As one of the most studied post-translational modifications (PTM), protein phosphorylation plays an essential role in almost all cellular processes. Current methods are able to predict and determine thousands of phosphorylation sites, whereas stoichiometric quantification of these sites is still challenging. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS)-based targeted proteomics is emerging as a promising technique for site-specific quantification of protein phosphorylation using proteolytic peptides as surrogates of proteins. However, several issues may limit its application, one of which relates to the phosphopeptides with different phosphorylation sites and the same mass (i.e., isobaric phosphopeptides). While employment of site-specific product ions allows for these isobaric phosphopeptides to be distinguished and quantified, site-specific product ions are often absent or weak in tandem mass spectra. In this study, linear algebra algorithms were employed as an add-on to targeted proteomics to retrieve information on individual phosphopeptides from their common spectra. To achieve this simultaneous quantification, a LC-MS/MS-based targeted proteomics assay was first developed and validated for each phosphopeptide. Given the slope and intercept of calibration curves of phosphopeptides in each transition, linear algebraic equations were developed. Using a series of mock mixtures prepared with varying concentrations of each phosphopeptide, the reliability of the approach to quantify isobaric phosphopeptides containing multiple phosphorylation sites (≥ 2) was discussed. Finally, we applied this approach to determine the phosphorylation stoichiometry of heat shock protein 27 (HSP27) at Ser78 and Ser82 in breast cancer cells and tissue samples.

Matrix-assisted laser-desorption-ionization mass spectrometry of proteins using a free-electron laser

International Nuclear Information System (INIS)

Cramer, R.; Hillenkamp, F.; Haglund, R.

1995-01-01

Matrix-assisted laser desorption-ionization (MALDI) mass spectrometry (MS) is one of the most promising techniques for spectral fingerprinting large molecules, such as proteins, oligonucleotides and carbohydrates. In the usual implementation of this technique, the analyte molecule is dissolved in an aromatic liquid matrix material which resonantly absorbs ultraviolet laser light. Resonant absorption by π-π* transitions volatilizes the matrix and initiates subsequent charge transfer to the analyte molecules, which are detected by time-of-flight mass spectrometry. Recent MALDI-MS studies with Er:YAG (2.94 μm) and CO 2 4 (9.4-10.6 μm) lasers suggest that them is significant unexplored potential for mass spectrometry of macromolecules, including oligonucleotide, in the mid-infrared. Preliminary experiments show that it is possible to capitalize on the rich rovibronic absorption spectrum of virtually all organics to initiate resonant desorption in matrix material over the entire range of pH values. However, the mechanism of charge transfer is particularly problematic for infrared MALDI because of the low photon energy. In this paper, we report the results of MALI-MS studies on small proteins using the Vanderbilt FEL and several matrix materials. Proteins with masses up to roughly 6,000 amu were detected with high resolution in a linear time-of-flight mass spectrometer. By varying the pulse duration using a broadband Pockels cell, we have been able to compare the results of relatively long (5 μs) and short (0.1 μs) irradiation on the desorption and ionization processes. Compared to uv-MALDI spectra of identical analytes obtained with a nitrogen laser (337 nm) in the same time-of-flight spectrometer, the infrared results appear to show that the desorption and ionization process goes on over a somewhat longer time scale

Cluster Analysis of the Organic Peaks in Bulk Mass Spectra Obtained During the 2002 New England Air Quality Study with an Aerodyne Aerosol Mass Spectrometer

Science.gov (United States)

Marcolli, C.; Canagaratna, M. R.; Worsnop, D. R.; Bahreini, R.; de Gouw, J. A.; Warneke, C.; Goldan, P. D.; Kuster, W. C.; Williams, E. J.; Lerner, B. M.; Roberts, J. M.; Meagher, J. F.; Fehsenfeld, F. C.; Marchewka, M.; Bertman, S. B.; Middlebrook, A. M.

2006-12-01

We applied hierarchical cluster analysis to an Aerodyne aerosol mass spectrometer (AMS) bulk mass spectral dataset collected aboard the NOAA research vessel R. H. Brown during the 2002 New England Air Quality Study off the east coast of the United States. Emphasizing the organic peaks, the cluster analysis yielded a series of categories that are distinguishable with respect to their mass spectra and their occurrence as a function of time. The differences between the categories mainly arise from relative intensity changes rather than from the presence or absence of specific peaks. The most frequent category exhibits a strong signal at m/z 44 and represents oxidized organic matter probably originating from both anthropogenic as well as biogenic sources. On the basis of spectral and trace gas correlations, the second most common category with strong signals at m/z 29, 43, and 44 contains contributions from isoprene oxidation products. The third through the fifth most common categories have peak patterns characteristic of monoterpene oxidation products and were most frequently observed when air masses from monoterpene rich regions were sampled. Taken together, the second through the fifth most common categories represent on average 17% of the total organic mass that stems likely from biogenic sources during the ship's cruise. These numbers have to be viewed as lower limits since the most common category was attributed to anthropogenic sources for this calculation. The cluster analysis was also very effective in identifying a few contaminated mass spectra that were not removed during pre-processing. This study demonstrates that hierarchical clustering is a useful tool to analyze the complex patterns of the organic peaks in bulk aerosol mass spectra from a field study.

PepArML: A Meta-Search Peptide Identification Platform for Tandem Mass Spectra.

Science.gov (United States)

Edwards, Nathan J

2013-12-01

The PepArML meta-search peptide identification platform for tandem mass spectra provides a unified search interface to seven search engines; a robust cluster, grid, and cloud computing scheduler for large-scale searches; and an unsupervised, model-free, machine-learning-based result combiner, which selects the best peptide identification for each spectrum, estimates false-discovery rates, and outputs pepXML format identifications. The meta-search platform supports Mascot; Tandem with native, k-score and s-score scoring; OMSSA; MyriMatch; and InsPecT with MS-GF spectral probability scores—reformatting spectral data and constructing search configurations for each search engine on the fly. The combiner selects the best peptide identification for each spectrum based on search engine results and features that model enzymatic digestion, retention time, precursor isotope clusters, mass accuracy, and proteotypic peptide properties, requiring no prior knowledge of feature utility or weighting. The PepArML meta-search peptide identification platform often identifies two to three times more spectra than individual search engines at 10% FDR.

Genetic multivariate calibration for near infrared spectroscopic determination of protein, moisture, dry mass, hardness and other residues of wheat

OpenAIRE

Özdemir, Durmuş

2006-01-01

Determination of wheat flour quality parameters, such as protein, moisture, dry mass by wet chemistry analyses takes long time. Near infrared spectroscopy (NIR) coupled with multivariate calibration offers a fast and nondestructive alternative to obtain reliable results. However, due to the complexity of the spectra obtained from NIR, some wavelength selection is generally required to improve the predictive ability of multivariate calibration methods. In this study, two different wheat data s...

Parsimonious Charge Deconvolution for Native Mass Spectrometry

Science.gov (United States)

2018-01-01

Charge deconvolution infers the mass from mass over charge (m/z) measurements in electrospray ionization mass spectra. When applied over a wide input m/z or broad target mass range, charge-deconvolution algorithms can produce artifacts, such as false masses at one-half or one-third of the correct mass. Indeed, a maximum entropy term in the objective function of MaxEnt, the most commonly used charge deconvolution algorithm, favors a deconvolved spectrum with many peaks over one with fewer peaks. Here we describe a new “parsimonious” charge deconvolution algorithm that produces fewer artifacts. The algorithm is especially well-suited to high-resolution native mass spectrometry of intact glycoproteins and protein complexes. Deconvolution of native mass spectra poses special challenges due to salt and small molecule adducts, multimers, wide mass ranges, and fewer and lower charge states. We demonstrate the performance of the new deconvolution algorithm on a range of samples. On the heavily glycosylated plasma properdin glycoprotein, the new algorithm could deconvolve monomer and dimer simultaneously and, when focused on the m/z range of the monomer, gave accurate and interpretable masses for glycoforms that had previously been analyzed manually using m/z peaks rather than deconvolved masses. On therapeutic antibodies, the new algorithm facilitated the analysis of extensions, truncations, and Fab glycosylation. The algorithm facilitates the use of native mass spectrometry for the qualitative and quantitative analysis of protein and protein assemblies. PMID:29376659

Pigments and proteins in green bacterial chlorosomes studied by matrix-assisted laser desorption ionization mass spectrometry

DEFF Research Database (Denmark)

Persson, S; Sönksen, C P; Frigaard, N U

2000-01-01

We have used matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for mass determination of pigments and proteins in chlorosomes, the light-harvesting organelles from the photosynthetic green sulfur bacterium Chlorobium tepidum. By applying a small volume (1...... microL) of a concentrated suspension of isolated chlorosomes directly to the target of the mass spectrometer we have been able to detect bacteriochlorophyll a and all the major homologs of bacteriochlorophyll c. The peak heights of the different bacteriochlorophyll c homologs in the MALDI spectra were...... proportional to peak areas obtained from HPLC analysis of the same sample. The same result was also obtained when whole cells of Chl. tepidum were applied to the target, indicating that MALDI-MS can provide a rapid method for obtaining a semiquantitative determination or finger-print of the bacteriochlorophyll...

Excited state mass spectra of singly charmed baryons

Energy Technology Data Exchange (ETDEWEB)

Shah, Zalak; Kumar Rai, Ajay [Sardar Vallabhbhai National Institute of Technology, Department of Applied Physics, Surat, Gujarat (India); Thakkar, Kaushal [GIDC Degree Engineering College, Department of Applied Sciences and Humanities, Abrama (India); Vinodkumar, P.C. [Sardar Patel University, Department of Physics, V.V. Nagar (India)

2016-10-15

Mass spectra of excited states of the singly charmed baryons are calculated using the hypercentral description of the three-body system. The baryons consist of a charm quark and light quarks (u, d and s) are studied in the framework of QCD motivated constituent quark model. The form of the confinement potential is hyper-Coloumb plus power potential with potential index ν, varying from 0.5 to 2.0. The first-order correction to the confinement potential is also incorporated in this approach. The radial as well as orbital excited state masses of Σ{sub c}{sup ++}, Σ{sub c}{sup +}, Σ{sub c}{sup 0}, Ξ{sub c}{sup +}, Ξ{sub c}{sup 0}, Λ{sub c}{sup +}, Ω{sub c}{sup 0} baryons, are reported in this paper. We have incorporated spin-spin, spin-orbit and tensor interactions perturbatively in the present study. The semi-electronic decay of Ω{sub c} and Ξ{sub c} are also calculated using the spectroscopic parameters of these baryons. The computed results are compared with other theoretical predictions as well as with the available experimental observations. We also construct the Regge trajectory in (n{sub r},M{sup 2}) and (J,M{sup 2}) planes for these baryons. (orig.)

Variety identification of wheat using mass spectrometry with neural networks and the influence of mass spectra processing prior to neural network analysis

DEFF Research Database (Denmark)

Sørensen, Helle Aagaard; Sperotto, Maria Maddalena; Petersen, M.

2002-01-01

The performance of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks in wheat variety classification is further evaluated.(1) Two principal issues were studied: (a) the number of varieties that could be classified correctly; and (b) various means of....... With the final method, it was possible to classify 30 wheat varieties with 87% correctly classified mass spectra and a correlation coefficient of 0.90....

The Effect of Stellar Contamination on Transmission Spectra of Low-mass Exoplanets

Science.gov (United States)

Rackham, Benjamin V.; Apai, Daniel; Giampapa, Mark S.

2017-10-01

of small exoplanets, including those of the TRAPPIST-1 system. Constraining stellar contamination will likely be a limiting factor for detecting atmospheric features in transmission spectra of low-mass exoplanets around late-type stars from TESS.

[Progress in the spectral library based protein identification strategy].

Science.gov (United States)

Yu, Derui; Ma, Jie; Xie, Zengyan; Bai, Mingze; Zhu, Yunping; Shu, Kunxian

2018-04-25

Exponential growth of the mass spectrometry (MS) data is exhibited when the mass spectrometry-based proteomics has been developing rapidly. It is a great challenge to develop some quick, accurate and repeatable methods to identify peptides and proteins. Nowadays, the spectral library searching has become a mature strategy for tandem mass spectra based proteins identification in proteomics, which searches the experiment spectra against a collection of confidently identified MS/MS spectra that have been observed previously, and fully utilizes the abundance in the spectrum, peaks from non-canonical fragment ions, and other features. This review provides an overview of the implement of spectral library search strategy, and two key steps, spectral library construction and spectral library searching comprehensively, and discusses the progress and challenge of the library search strategy.

Geena 2, improved automated analysis of MALDI/TOF mass spectra.

Science.gov (United States)

Romano, Paolo; Profumo, Aldo; Rocco, Mattia; Mangerini, Rosa; Ferri, Fabio; Facchiano, Angelo

2016-03-02

Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps. For the analysis of MALDI/TOF spectra, a number of pre-processing steps are required, including joining of isotopic abundances for a given molecular species, normalization of signals against an internal standard, background noise removal, averaging multiple spectra from the same sample, and aligning spectra from different samples. In this paper, we present Geena 2, a public software tool for the automated execution of these pre-processing steps for MALDI/TOF spectra. Geena 2 has been developed in a Linux-Apache-MySQL-PHP web development environment, with scripts in PHP and Perl. Input and output are managed as simple formats that can be consumed by any database system and spreadsheet software. Input data may also be stored in a MySQL database. Processing methods are based on original heuristic algorithms which are introduced in the paper. Three simple and intuitive web interfaces are available: the Standard Search Interface, which allows a complete control over all parameters, the Bright Search Interface, which leaves to the user the possibility to tune parameters for alignment of spectra, and the Quick Search Interface, which limits the number of parameters to a minimum by using default values for the majority of parameters. Geena 2 has been utilized, in conjunction with a statistical analysis tool, in three published experimental works: a proteomic study on the effects of long-term cryopreservation on the low molecular weight fraction of serum proteome, and two retrospective serum proteomic studies, one on the risk of developing breat cancer in patients affected by gross cystic disease of the breast (GCDB) and the other for the identification of a predictor of

A Simple Spreadsheet Program to Simulate and Analyze the Far-UV Circular Dichroism Spectra of Proteins

Science.gov (United States)

Abriata, Luciano A.

2011-01-01

A simple algorithm was implemented in a spreadsheet program to simulate the circular dichroism spectra of proteins from their secondary structure content and to fit [alpha]-helix, [beta]-sheet, and random coil contents from experimental far-UV circular dichroism spectra. The physical basis of the method is briefly reviewed within the context of…

Mass spectra and wave functions of meson systems and the covariant oscillator quark model as an expansion basis

International Nuclear Information System (INIS)

Oda, Ryuichi; Ishida, Shin; Wada, Hiroaki; Yamada, Kenji; Sekiguchi, Motoo

1999-01-01

We examine mass spectra and wave functions of the nn-bar, cc-bar and bb-bar meson systems within the framework of the covariant oscillator quark model with the boosted LS-coupling scheme. We solve nonperturbatively an eigenvalue problem for the squared-mass operator, which incorporates the four-dimensional color-Coulomb-type interaction, by taking a set of covariant oscillator wave functions as an expansion basis. We obtain mass spectra of these meson systems, which reproduce quite well their experimental behavior. The resultant manifestly covariant wave functions, which are applicable to analyses of various reaction phenomena, are given. Our results seem to suggest that the present model may be considered effectively as a covariant version of the nonrelativistic linear-plus-Coulomb potential quark model. (author)

Cluster Analysis of the Organic Peaks in Bulk Mass Spectra Obtained During the 2002 New England Air Quality Study with an Aerodyne Aerosol Mass Spectrometer

Directory of Open Access Journals (Sweden)

C. Marcolli

2006-01-01

Full Text Available We applied hierarchical cluster analysis to an Aerodyne aerosol mass spectrometer (AMS bulk mass spectral dataset collected aboard the NOAA research vessel R. H. Brown during the 2002 New England Air Quality Study off the east coast of the United States. Emphasizing the organic peaks, the cluster analysis yielded a series of categories that are distinguishable with respect to their mass spectra and their occurrence as a function of time. The differences between the categories mainly arise from relative intensity changes rather than from the presence or absence of specific peaks. The most frequent category exhibits a strong signal at m/z 44 and represents oxidized organic matter probably originating from both anthropogenic as well as biogenic sources. On the basis of spectral and trace gas correlations, the second most common category with strong signals at m/z 29, 43, and 44 contains contributions from isoprene oxidation products. The third through the fifth most common categories have peak patterns characteristic of monoterpene oxidation products and were most frequently observed when air masses from monoterpene rich regions were sampled. Taken together, the second through the fifth most common categories represent on average 17% of the total organic mass that stems likely from biogenic sources during the ship's cruise. These numbers have to be viewed as lower limits since the most common category was attributed to anthropogenic sources for this calculation. The cluster analysis was also very effective in identifying a few contaminated mass spectra that were not removed during pre-processing. This study demonstrates that hierarchical clustering is a useful tool to analyze the complex patterns of the organic peaks in bulk aerosol mass spectra from a field study.

Peptide Mass Fingerprinting of Egg White Proteins

Science.gov (United States)

Alty, Lisa T.; LaRiviere, Frederick J.

2016-01-01

Use of advanced mass spectrometry techniques in the undergraduate setting has burgeoned in the past decade. However, relatively few undergraduate experiments examine the proteomics tools of protein digestion, peptide accurate mass determination, and database searching, also known as peptide mass fingerprinting. In this experiment, biochemistry…

Affinity purification combined with mass spectrometry to identify herpes simplex virus protein-protein interactions.

Science.gov (United States)

Meckes, David G

2014-01-01

The identification and characterization of herpes simplex virus protein interaction complexes are fundamental to understanding the molecular mechanisms governing the replication and pathogenesis of the virus. Recent advances in affinity-based methods, mass spectrometry configurations, and bioinformatics tools have greatly increased the quantity and quality of protein-protein interaction datasets. In this chapter, detailed and reliable methods that can easily be implemented are presented for the identification of protein-protein interactions using cryogenic cell lysis, affinity purification, trypsin digestion, and mass spectrometry.

An investigation of the mass spectra of secondary ions ejected from the single crystal surface of semiconductors

International Nuclear Information System (INIS)

Koval', A.G.; Mel'nikov, V.N.; Enukov, Yu.V.

1976-01-01

The mass spectra of secondary positive and negative ions, ejected by an Ar + ion beam from the (100) face of an epitaxial film of the semiconductor Alsub(x)Gasub(1-x)As were investigated. There are many various secondary ions in the mass spectrum under investigation. They may be divided into four groups according to their origins. Mass spectra of secondary positive and negative secondary ions differ much, either in their composition or the intensities of homogeneous ions. The I(T) dependences (I=the current of corresponding secondary ions, T=target temperature) were obtained for secondary and negative ions taken from groups differing by their origin. The I(T) dependences were obtained at several oxygen pressures in a chamber. For the ions with 'superficial' origin a strong dependence of their current on target temperature is observed. Oxygen pressure increase leads to substantial change of the I(T)curves. (Auth.)

Analysis of posttranslational modifications of proteins by tandem mass spectrometry

DEFF Research Database (Denmark)

Larsen, Martin Røssel; Trelle, Morten B; Thingholm, Tine E

2006-01-01

-temporal distribution in cells and tissues. Most PTMs can be detected by protein and peptide analysis by mass spectrometry (MS), either as a mass increment or a mass deficit relative to the nascent unmodified protein. Tandem mass spectrometry (MS/MS) provides a series of analytical features that are highly useful...

Tandem mass spectrometry data quality assessment by self-convolution

Directory of Open Access Journals (Sweden)

Tham Wai

2007-09-01

Full Text Available Abstract Background Many algorithms have been developed for deciphering the tandem mass spectrometry (MS data sets. They can be essentially clustered into two classes. The first performs searches on theoretical mass spectrum database, while the second based itself on de novo sequencing from raw mass spectrometry data. It was noted that the quality of mass spectra affects significantly the protein identification processes in both instances. This prompted the authors to explore ways to measure the quality of MS data sets before subjecting them to the protein identification algorithms, thus allowing for more meaningful searches and increased confidence level of proteins identified. Results The proposed method measures the qualities of MS data sets based on the symmetric property of b- and y-ion peaks present in a MS spectrum. Self-convolution on MS data and its time-reversal copy was employed. Due to the symmetric nature of b-ions and y-ions peaks, the self-convolution result of a good spectrum would produce a highest mid point intensity peak. To reduce processing time, self-convolution was achieved using Fast Fourier Transform and its inverse transform, followed by the removal of the "DC" (Direct Current component and the normalisation of the data set. The quality score was defined as the ratio of the intensity at the mid point to the remaining peaks of the convolution result. The method was validated using both theoretical mass spectra, with various permutations, and several real MS data sets. The results were encouraging, revealing a high percentage of positive prediction rates for spectra with good quality scores. Conclusion We have demonstrated in this work a method for determining the quality of tandem MS data set. By pre-determining the quality of tandem MS data before subjecting them to protein identification algorithms, spurious protein predictions due to poor tandem MS data are avoided, giving scientists greater confidence in the

Tandem mass spectrometry data quality assessment by self-convolution.

Science.gov (United States)

Choo, Keng Wah; Tham, Wai Mun

2007-09-20

Many algorithms have been developed for deciphering the tandem mass spectrometry (MS) data sets. They can be essentially clustered into two classes. The first performs searches on theoretical mass spectrum database, while the second based itself on de novo sequencing from raw mass spectrometry data. It was noted that the quality of mass spectra affects significantly the protein identification processes in both instances. This prompted the authors to explore ways to measure the quality of MS data sets before subjecting them to the protein identification algorithms, thus allowing for more meaningful searches and increased confidence level of proteins identified. The proposed method measures the qualities of MS data sets based on the symmetric property of b- and y-ion peaks present in a MS spectrum. Self-convolution on MS data and its time-reversal copy was employed. Due to the symmetric nature of b-ions and y-ions peaks, the self-convolution result of a good spectrum would produce a highest mid point intensity peak. To reduce processing time, self-convolution was achieved using Fast Fourier Transform and its inverse transform, followed by the removal of the "DC" (Direct Current) component and the normalisation of the data set. The quality score was defined as the ratio of the intensity at the mid point to the remaining peaks of the convolution result. The method was validated using both theoretical mass spectra, with various permutations, and several real MS data sets. The results were encouraging, revealing a high percentage of positive prediction rates for spectra with good quality scores. We have demonstrated in this work a method for determining the quality of tandem MS data set. By pre-determining the quality of tandem MS data before subjecting them to protein identification algorithms, spurious protein predictions due to poor tandem MS data are avoided, giving scientists greater confidence in the predicted results. We conclude that the algorithm performs well

Seed Storage Proteins as a System for Teaching Protein Identification by Mass Spectrometry in Biochemistry Laboratory

Science.gov (United States)

Wilson, Karl A.; Tan-Wilson, Anna

2013-01-01

Mass spectrometry (MS) has become an important tool in studying biological systems. One application is the identification of proteins and peptides by the matching of peptide and peptide fragment masses to the sequences of proteins in protein sequence databases. Often prior protein separation of complex protein mixtures by 2D-PAGE is needed,…

Supplemental protein in support of muscle mass and health: advantage whey.

Science.gov (United States)

Devries, Michaela C; Phillips, Stuart M

2015-03-01

Skeletal muscle is an integral body tissue playing key roles in strength, performance, physical function, and metabolic regulation. It is essential for athletes to ensure that they have optimal amounts of muscle mass to ensure peak performance in their given sport. However, the role of maintaining muscle mass during weight loss and as we age is an emerging concept, having implications in chronic disease prevention, functional capacity, and quality of life. Higher-protein diets have been shown to: (1) promote gains in muscle mass, especially when paired with resistance training; (2) spare muscle mass loss during caloric restriction; and (3) attenuate the natural loss of muscle mass that accompanies aging. Protein quality is important to the gain and maintenance of muscle mass. Protein quality is a function of protein digestibility, amino acid content, and the resulting amino acid availability to support metabolic function. Whey protein is one of the highest-quality proteins given its amino acid content (high essential, branched-chain, and leucine amino acid content) and rapid digestibility. Consumption of whey protein has a robust ability to stimulate muscle protein synthesis. In fact, whey protein has been found to stimulate muscle protein synthesis to a greater degree than other proteins such as casein and soy. This review examines the existing data supporting the role for protein consumption, with an emphasis on whey protein, in the regulation of muscle mass and body composition in response to resistance training, caloric restriction, and aging. © 2015 Institute of Food Technologists®

Reduction of chemical formulas from the isotopic peak distributions of high-resolution mass spectra.

Science.gov (United States)

Roussis, Stilianos G; Proulx, Richard

2003-03-15

A method has been developed for the reduction of the chemical formulas of compounds in complex mixtures from the isotopic peak distributions of high-resolution mass spectra. The method is based on the principle that the observed isotopic peak distribution of a mixture of compounds is a linear combination of the isotopic peak distributions of the individual compounds in the mixture. All possible chemical formulas that meet specific criteria (e.g., type and number of atoms in structure, limits of unsaturation, etc.) are enumerated, and theoretical isotopic peak distributions are generated for each formula. The relative amount of each formula is obtained from the accurately measured isotopic peak distribution and the calculated isotopic peak distributions of all candidate formulas. The formulas of compounds in simple spectra, where peak components are fully resolved, are rapidly determined by direct comparison of the calculated and experimental isotopic peak distributions. The singular value decomposition linear algebra method is used to determine the contributions of compounds in complex spectra containing unresolved peak components. The principles of the approach and typical application examples are presented. The method is most useful for the characterization of complex spectra containing partially resolved peaks and structures with multiisotopic elements.

Mass spectrum analysis of serum biomarker proteins from patients with schizophrenia.

Science.gov (United States)

Zhou, Na; Wang, Jie; Yu, Yaqin; Shi, Jieping; Li, Xiaokun; Xu, Bin; Yu, Qiong

2014-05-01

Diagnosis of schizophrenia does not have a clear objective test at present, so we aimed to identify the potential biomarkers for the diagnosis of schizophrenia by comparison of serum protein profiling between first-episode schizophrenia patients and healthy controls. The combination of a magnetic bead separation system with matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS) was used to analyze the serum protein spectra of 286 first-episode patients with schizophrenia, 41 chronic disease patients and 304 healthy controls. FlexAnlysis 3.0 and ClinProTools(TM) 2.1 software was used to establish a diagnostic model for schizophrenia. The results demonstrated that 10 fragmented peptides demonstrated an optimal discriminatory performance. Among these fragmented peptides, the peptide with m/z 1206.58 was identified as a fragment of fibrinopeptide A. Receiver operating characteristic analysis for m/z 1206.58 showed that the area under the curve was 0.981 for schizophrenia vs healthy controls, and 0.999 for schizophrenia vs other chronic disease controls. From our result, we consider that the analysis of serum protein spectrum using the magnetic bead separation system and MALDI-TOF/TOF-MS is an objective diagnostic tool. We conclude that fibrinopeptide A has the potential to be a biomarker for diagnosis of schizophrenia. This protein may also help to elucidate schizophrenia disease pathogenesis. Copyright © 2013 John Wiley & Sons, Ltd.

Detection of lung cancer using plasma protein profiling by matrix-assisted laser desorption/ionization mass spectrometry.

Science.gov (United States)

Shevchenko, Valeriy E; Arnotskaya, Natalia E; Zaridze, David G

2010-01-01

There are no satisfactory plasma biomarkers which are available for the early detection and monitoring of lung cancer, one of the most frequent cancers worldwide. The aim of this study is to explore the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) to plasma proteomic patterns to distinguish lung cancer patients from healthy individuals. The EDTA plasma samples have been pre-fractionated using magnetic bead kits functionalized with weak cation exchange coatings. We compiled MS protein profiles for 90 patients with squamous cell carcinomas (SCC) and compared them with profiles from 187 healthy controls. The MALDI-ToF spectra were analyzed statistically using ClinProTools bioinformatics software. Depending on the sample used, up to 441 peaks/spectrum could be detected in a mass range of 1000-20,000 Da; 33 of these proteins had statistically differential expression levels between SCC and control plasma (P 90%) in external validation test. These results suggest that plasma MALDI-ToF MS protein profiling can distinguish patients with SCC and also from healthy individuals with relatively high sensitivity and specificity and that MALDI- ToF MS is a potential tool for the screening of lung cancer.

Bayesian model comparison using Gauss approximation on multicomponent mass spectra from CH4 plasma

International Nuclear Information System (INIS)

Kang, H.D.; Dose, V.

2004-01-01

We performed Bayesian model comparison on mass spectra from CH4 rf process plasmas to detect radicals produced in the plasma. The key ingredient for its implementation is the high-dimensional evidence integral. We apply Gauss approximation to evaluate the evidence. The results were compared with those calculated by the thermodynamic integration method using Markov Chain Monte Carlo technique. In spite of very large difference in the computation time between two methods a very good agreement was obtained. Alternatively, a Monte Carlo integration method based on the approximated Gaussian posterior density is presented. Its applicability to the problem of mass spectrometry is discussed

Approaches towards the automated interpretation and prediction of electrospray tandem mass spectra of non-peptidic combinatorial compounds.

Science.gov (United States)

Klagkou, Katerina; Pullen, Frank; Harrison, Mark; Organ, Andy; Firth, Alistair; Langley, G John

2003-01-01

Combinatorial chemistry is widely used within the pharmaceutical industry as a means of rapid identification of potential drugs. With the growth of combinatorial libraries, mass spectrometry (MS) became the key analytical technique because of its speed of analysis, sensitivity, accuracy and ability to be coupled with other analytical techniques. In the majority of cases, electrospray mass spectrometry (ES-MS) has become the default ionisation technique. However, due to the absence of fragment ions in the resulting spectra, tandem mass spectrometry (MS/MS) is required to provide structural information for the identification of an unknown analyte. This work discusses the first steps of an investigation into the fragmentation pathways taking place in electrospray tandem mass spectrometry. The ultimate goal for this project is to set general fragmentation rules for non-peptidic, pharmaceutical, combinatorial compounds. As an aid, an artificial intelligence (AI) software package is used to facilitate interpretation of the spectra. This initial study has focused on determining the fragmentation rules for some classes of compound types that fit the remit as outlined above. Based on studies carried out on several combinatorial libraries of these compounds, it was established that different classes of drug molecules follow unique fragmentation pathways. In addition to these general observations, the specific ionisation processes and the fragmentation pathways involved in the electrospray mass spectra of these systems were explored. The ultimate goal will be to incorporate our findings into the computer program and allow identification of an unknown, non-peptidic compound following insertion of its ES-MS/MS spectrum into the AI package. The work herein demonstrates the potential benefit of such an approach in addressing the issue of high-throughput, automated MS/MS data interpretation. Copyright 2003 John Wiley & Sons, Ltd.

Study on the Interaction between Cadmium Sulphide Nanoparticles and Proteins by Resonance Rayleigh Scattering Spectra

Directory of Open Access Journals (Sweden)

Weiwei Zhu

2013-01-01

Full Text Available The interaction of cadmium sulphide nanoparticles [(CdSn] with proteins has been studied by resonance Rayleigh scattering spectra (RRS. Below the isoelectric point, proteins such as bovine serum albumin (BSA, human serum albumin (HSA, lysozyme (Lys, hemoglobin (HGB, and ovalbumin (OVA can bind with CdSn to form macromolecules by virtue of electrostatic attraction and hydrophobic force. It can result in the enhancement of resonance Rayleigh scattering spectra (RRS intensity. Their maximum scattering peaks were 280 nm, and there was a smaller peak at 370 nm. The scattering enhancement (ΔIRRS is directly proportional to the concentration of proteins. A new RRS method for the determination of trace proteins using uncapped CdSn nanoparticles probe has been developed. The detection limits are 19.6 ng/mL for HSA, 16.7 ng/mL for BSA, 18.5 ng/mL for OVA, 80.2 ng/mL for HGB, and 67.4 ng/mL for Lys, separately. In this work, the optimum condition of reaction, the effect of foreign, and the analytical application had been investigated.

Factor analysis of combined organic and inorganic aerosol mass spectra from high resolution aerosol mass spectrometer measurements

Directory of Open Access Journals (Sweden)

Y. L. Sun

2012-09-01

Full Text Available Positive matrix factorization (PMF was applied to the merged high resolution mass spectra of organic and inorganic aerosols from aerosol mass spectrometer (AMS measurements to investigate the sources and evolution processes of submicron aerosols in New York City in summer 2009. This new approach is able to study the distribution of organic and inorganic species in different types of aerosols, the acidity of organic aerosol (OA factors, and the fragment ion patterns related to photochemical processing. In this study, PMF analysis of the unified AMS spectral matrix resolved 8 factors. The hydrocarbon-like OA (HOA and cooking OA (COA factors contain negligible amounts of inorganic species. The two factors that are primarily ammonium sulfate (SO₄-OA and ammonium nitrate (NO₃-OA, respectively, are overall neutralized. Among all OA factors the organic fraction of SO₄-OA shows the highest degree of oxidation (O/C = 0.69. Two semi-volatile oxygenated OA (OOA factors, i.e., a less oxidized (LO-OOA and a more oxidized (MO-OOA, were also identified. MO-OOA represents local photochemical products with a diurnal profile exhibiting a pronounced noon peak, consistent with those of formaldehyde (HCHO and O_x(= O₃ + NO₂. The NO⁺/NO₂⁺ ion ratio in MO-OOA is much higher than that in NO₃-OA and in pure ammonium nitrate, indicating the formation of organic nitrates. The nitrogen-enriched OA (NOA factor contains ~25% of acidic inorganic salts, suggesting the formation of secondary OA via acid-base reactions of amines. The size distributions of OA factors derived from the size-resolved mass spectra show distinct diurnal evolving behaviors but overall a progressing evolution from smaller to larger particle mode as the oxidation degree of OA increases. Our results demonstrate that PMF analysis of the unified aerosol mass spectral matrix which contains both

Identification of multiply charged proteins and amino acid clusters by liquid nitrogen assisted spray ionization mass spectrometry.

Science.gov (United States)

Kumar Kailasa, Suresh; Hasan, Nazim; Wu, Hui-Fen

2012-08-15

The development of liquid nitrogen assisted spray ionization mass spectrometry (LNASI MS) for the analysis of multiply charged proteins (insulin, ubiquitin, cytochrome c, α-lactalbumin, myoglobin and BSA), peptides (glutathione, HW6, angiotensin-II and valinomycin) and amino acid (arginine) clusters is described. The charged droplets are formed by liquid nitrogen assisted sample spray through a stainless steel nebulizer and transported into mass analyzer for the identification of multiply charged protein ions. The effects of acids and modifier volumes for the efficient ionization of the above analytes in LNASI MS were carefully investigated. Multiply charged proteins and amino acid clusters were effectively identified by LNASI MS. The present approach can effectively detect the multiply charged states of cytochrome c at 400 nM. A comparison between LNASI and ESI, CSI, SSI and V-EASI methods on instrumental conditions, applied temperature and observed charge states for the multiply charged proteins, shows that the LNASI method produces the good quality spectra of amino acid clusters at ambient conditions without applied any electric field and heat. To date, we believe that the LNASI method is the most simple, low cost and provided an alternative paradigm for production of multiply charged ions by LNASI MS, just as ESI-like ions yet no need for applying any electrical field and it could be operated at low temperature for generation of highly charged protein/peptide ions. Copyright © 2012 Elsevier B.V. All rights reserved.

Studying Protein-Protein Interactions by Biotin AP-Tagged Pulldown and LTQ-Orbitrap Mass Spectrometry.

Science.gov (United States)

Xie, Zhongqiu; Jia, Yuemeng; Li, Hui

2017-01-01

The study of protein-protein interactions represents a key aspect of biological research. Identifying unknown protein binding partners using mass spectrometry (MS)-based proteomics has evolved into an indispensable strategy in drug discovery. The classic approach of immunoprecipitation with specific antibodies against the proteins of interest has limitations, such as the need for immunoprecipitation-qualified antibody. The biotin AP-tag pull-down system has the advantage of high specificity, ease of use, and no requirement for antibody. It is based on the high specificity, high affinity interaction between biotin and streptavidin. After pulldown, in-gel tryptic digestion and tandem mass spectrometry (MS/MS) analysis of sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) protein bands can be performed. In this work, we provide protocols that can be used for the identification of proteins that interact with FOXM1, a protein that has recently emerged as a potential biomarker and drug target in oncotherapy, as an example. We focus on the pull-down procedure and assess the efficacy of the pulldown with known FOXM1 interactors such as β-catenin. We use a high performance LTQ Orbitrap MSn system that combines rapid LTQ ion trap data acquisition with high mass accuracy Orbitrap analysis to identify the interacting proteins.

Chemometric analysis of mass spectra of cis and trans fatty acid picolinyl esters

DEFF Research Database (Denmark)

Leth, Torben

1997-01-01

and trans fatty acids of C16:1, C18:1,n-9, C18:1,n-12, C18:2 and C22:1 in two- and three-dimensional score plots. With Soft Independent Modelling of Class Analogy (SIMCA), it is possible to calculate models that can predict from the mass spectra of unknown fatty acids whether they are of the cis or trans...... configuration, which is demonstrated for C18:1 trans from hardened margarine and butter....

Mass spectra and fusion cross sections for 20Ne+24Mg interaction at 55 and 85 MeV

International Nuclear Information System (INIS)

Grotowski, K.; Belery, P.; Delbar, T.; El Masri, Y.; Gregoire, G.; Janssens, R.; Vervier, J.; Paic, G.; Albinska, M.; Albinski, J.; Kopta, S.; Kozik, T.; Planeta, R.

1981-01-01

Inclusive γ spectra from the 20 Ne+ 24 Mg interaction have been measured using 55- and 85-MeV 20 Ne ions. The identification of γ lines allows the determination of mass spectra in the region 12< or =A< or =43. Experimental results are compared with statistical model calculations. The total reaction and fusion cross sections are extracted. Cross sections for inelastic scattering, few nucleon transfers, and deep inelastic scattering are estimated

Identification of microorganisms using superconducting tunnel junctions and time-of-flight mass spectrometry

Science.gov (United States)

Ullom, J. N.; Frank, M.; Horn, J. M.; Labov, S. E.; Langry, K.; Benner, W. H.

2000-04-01

We present time-of-flight measurements of biological material ejected from bacterial spores following laser irradiation. Ion impacts are registered on a microchannel plate detector and on a Superconducting Tunnel Junction (STJ) detector. We compare mass spectra obtained with the two detectors. The STJ has better sensitivity to massive ions and also measures the energy of each ion. We show evidence that spores of different bacillus species produce distinctive mass spectra and associate the observed mass peaks with coat proteins.

Identification of microorganisms using superconducting tunnel junctions and time-of-flight mass spectrometry

International Nuclear Information System (INIS)

Ullom, J.N.; Frank, M.; Horn, J.M.; Labov, S.E.; Langry, K.; Benner, W.H.

2000-01-01

We present time-of-flight measurements of biological material ejected from bacterial spores following laser irradiation. Ion impacts are registered on a microchannel plate detector and on a Superconducting Tunnel Junction (STJ) detector. We compare mass spectra obtained with the two detectors. The STJ has better sensitivity to massive ions and also measures the energy of each ion. We show evidence that spores of different bacillus species produce distinctive mass spectra and associate the observed mass peaks with coat proteins

Use of ribosomal proteins as biomarkers for identification of Flavobacterium psychrophilum by MALDI-TOF mass spectrometry.

Science.gov (United States)

Fernández-Álvarez, Clara; Torres-Corral, Yolanda; Santos, Ysabel

2018-01-06

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) is a rapid methodology for identification of bacteria that is increasingly used in diagnostic laboratories. This work aimed at evaluating the potential of MALDI-TOF-MS for identification of the main serotypes of Flavobacterium psychrophilum isolated from salmonids, and its discrimination from closely related Flavobacterium spp. A mass spectra library was constructed by analysing 70 F. psychrophilum strains representing the serotypes O1, O2a, O2b and O3, including reference and clinical isolates. Peak mass lists were examined using the Mass-Up software for the detection of potential biomarkers, similarity and cluster analysis. Fourteen species-identifying biomarkers were detected in all the F. psychrophilum isolates tested, moreover, sets of serotype-identifying biomarkers ions were selected. F. psychrophilum-specific biomarkers were identified as ribosomal proteins by matching with protein databases. Furthermore, sequence variation corresponding to amino acid exchanges in several biomarker proteins were tentatively assigned. Closely related Flavobacterium species (F. flevense, F. succinicans, F. columnare, F. branchiophilum and F. johnsoniae) could be differentiated from F. psychrophilum by defining species identifying biomarkers and hierarchical cluster analysis. These results demonstrated that MALDI-TOF spectrometry represents a powerful tool for an accurate identification of the fish pathogen F. psychrophilum as well as for epidemiological studies. The results obtained in this study demonstrated that MALDI-TOF mass spectrometry represents a powerful tool that can be used by diagnostic laboratories for rapid identification of the fish pathogen Flavobacterium psychrophilum and its differentiation from other Flavobacterium-related species. Analysis of mass peak lists revealed the potential of the MALDI-TOF technique to identify epidemiologically important serotypes affecting

Combining metal oxide affinity chromatography (MOAC and selective mass spectrometry for robust identification of in vivo protein phosphorylation sites

Directory of Open Access Journals (Sweden)

Weckwerth Wolfram

2005-11-01

Full Text Available Abstract Background Protein phosphorylation is accepted as a major regulatory pathway in plants. More than 1000 protein kinases are predicted in the Arabidopsis proteome, however, only a few studies look systematically for in vivo protein phosphorylation sites. Owing to the low stoichiometry and low abundance of phosphorylated proteins, phosphorylation site identification using mass spectrometry imposes difficulties. Moreover, the often observed poor quality of mass spectra derived from phosphopeptides results frequently in uncertain database hits. Thus, several lines of evidence have to be combined for a precise phosphorylation site identification strategy. Results Here, a strategy is presented that combines enrichment of phosphoproteins using a technique termed metaloxide affinity chromatography (MOAC and selective ion trap mass spectrometry. The complete approach involves (i enrichment of proteins with low phosphorylation stoichiometry out of complex mixtures using MOAC, (ii gel separation and detection of phosphorylation using specific fluorescence staining (confirmation of enrichment, (iii identification of phosphoprotein candidates out of the SDS-PAGE using liquid chromatography coupled to mass spectrometry, and (iv identification of phosphorylation sites of these enriched proteins using automatic detection of H3PO4 neutral loss peaks and data-dependent MS3-fragmentation of the corresponding MS2-fragment. The utility of this approach is demonstrated by the identification of phosphorylation sites in Arabidopsis thaliana seed proteins. Regulatory importance of the identified sites is indicated by conservation of the detected sites in gene families such as ribosomal proteins and sterol dehydrogenases. To demonstrate further the wide applicability of MOAC, phosphoproteins were enriched from Chlamydomonas reinhardtii cell cultures. Conclusion A novel phosphoprotein enrichment procedure MOAC was applied to seed proteins of A. thaliana and to

Yeast-expressed human membrane protein aquaporin-1 yields excellent resolution of solid-state MAS NMR spectra

International Nuclear Information System (INIS)

Emami, Sanaz; Fan Ying; Munro, Rachel; Ladizhansky, Vladimir; Brown, Leonid S.

2013-01-01

One of the biggest challenges in solid-state NMR studies of membrane proteins is to obtain a homogeneous natively folded sample giving high spectral resolution sufficient for structural studies. Eukaryotic membrane proteins are especially difficult and expensive targets in this respect. Methylotrophic yeast Pichia pastoris is a reliable producer of eukaryotic membrane proteins for crystallography and a promising economical source of isotopically labeled proteins for NMR. We show that eukaryotic membrane protein human aquaporin 1 can be doubly ( 13 C/ 15 N) isotopically labeled in this system and functionally reconstituted into phospholipids, giving excellent resolution of solid-state magic angle spinning NMR spectra.

Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer.

Science.gov (United States)

Wei, Wei; Luo, Weijia; Wu, Feilin; Peng, Xuehui; Zhang, Yao; Zhang, Manli; Zhao, Yan; Su, Na; Qi, YingZi; Chen, Lingsheng; Zhang, Yangjun; Wen, Bo; He, Fuchu; Xu, Ping

2016-11-04

Since 2012, missing proteins (MPs) investigation has been one of the critical missions of Chromosome-Centric Human Proteome Project (C-HPP) through various biochemical strategies. On the basis of our previous testis MPs study, faster scanning and higher resolution mass-spectrometry-based proteomics might be conducive to MPs exploration, especially for low-abundance proteins. In this study, Q-Exactive HF (HF) was used to survey proteins from the same testis tissues separated by two separating methods (tricine- and glycine-SDS-PAGE), as previously described. A total of 8526 proteins were identified, of which more low-abundance proteins were uniquely detected in HF data but not in our previous LTQ Orbitrap Velos (Velos) reanalysis data. Further transcriptomics analysis showed that these uniquely identified proteins by HF also had lower expression at the mRNA level. Of the 81 total identified MPs, 74 and 39 proteins were listed as MPs in HF and Velos data sets, respectively. Among the above MPs, 47 proteins (43 neXtProt PE2 and 4 PE3) were ranked as confirmed MPs after verifying with the stringent spectra match and isobaric and single amino acid variants filtering. Functional investigation of these 47 MPs revealed that 11 MPs were testis-specific proteins and 7 MPs were involved in spermatogenesis process. Therefore, we concluded that higher scanning speed and resolution of HF might be factors for improving the low-abundance MP identification in future C-HPP studies. All mass-spectrometry data from this study have been deposited in the ProteomeXchange with identifier PXD004092.

Detection of irradiated food by the changes in protein molecular mass distribution

International Nuclear Information System (INIS)

Niciforovic, A.; Radojcic, M.; Milosavljevic, B.H.

1998-01-01

Complete text of publication follows. The present work deals with the radiation-induced damage of proteins, which is followed by the change in the molecular mass. The phenomenon was studied on protein rich samples, i.e., chicken meat and dehydrated egg white. The radiation dose applied was in the range of the ones used for food microbial control. Chicken drumstick and chicken white meat proteins were separated according to their molecular mass. The protein profile was compared to the meat samples irradiated in the frozen state with 5 kGy at 60 Co source. In the case of chicken white meat, irradiation produces both nonselective protein scission (e.g. the amount of proteins of molecular mass larger than 30 kDa decreases, while the amount of proteins of molecular mass smaller than 30 kDa increases), and selective protein scission (e.g. appearance of a protein fragment of molecular mass equal to 18 kDa). In the case of chicken drumstick proteins the irradiation induces both the protein scission and the aggregation. The changes are nonspecific as well as specific and the generation of Mm = 18 kDa protein fragment was observed again. Irradiation of aerated dehydrated egg white proteins produces only nonselective protein scission. The results are discussed in view of the routine application of SDS-PAGE method for the detection of irradiated foodstuff

Excited state mass spectra of doubly heavy baryons Ω{sub cc}, Ω{sub bb} and Ω{sub bc}

Energy Technology Data Exchange (ETDEWEB)

Shah, Zalak; Rai, Ajay Kumar [Sardar Vallabhbhai National Institute of Technology, Department of Applied Physics, Surat, Gujarat (India); Thakkar, Kaushal [GIDC Degree Engineering college, Department of Applied Sciences and Humanities, Abrama, Navsari (India)

2016-10-15

We discuss the mass spectrum of Ω baryon with two heavy quarks and one light quark (ccs, bbs, and bcs). The main goal of the paper is to calculate the ground state masses and after that, the positive and negative parity excited states masses are also obtained within a hypercentral constituent quark model, using Coulomb plus linear potential framework. We also added a first order correction to the potential. The mass spectra up to 5S for radial excited states and 1P-5P, 1D-4D, and 1F-2F states for orbital excited states are computed for Ω{sub cc}, Ω{sub bb} and Ω{sub bc} baryons. Our obtained results are compared with other theoretical predictions, which could be a useful complementary tool for the interpretation of experimentally unknown heavy baryon spectra. The Regge trajectory is constructed in both the (n{sub r}, M{sup 2}) and the (J, M{sup 2}) planes for Ω{sub cc}, Ω{sub bb} and Ω{sub bc} baryons and their slopes and intercepts are also determined. Magnetic moments of doubly heavy Ω{sup '}s are also calculated. (orig.) 8.

Facilitated assignment of large protein NMR signals with covariance sequential spectra using spectral derivatives.

Science.gov (United States)

Harden, Bradley J; Nichols, Scott R; Frueh, Dominique P

2014-09-24

Nuclear magnetic resonance (NMR) studies of larger proteins are hampered by difficulties in assigning NMR resonances. Human intervention is typically required to identify NMR signals in 3D spectra, and subsequent procedures depend on the accuracy of this so-called peak picking. We present a method that provides sequential connectivities through correlation maps constructed with covariance NMR, bypassing the need for preliminary peak picking. We introduce two novel techniques to minimize false correlations and merge the information from all original 3D spectra. First, we take spectral derivatives prior to performing covariance to emphasize coincident peak maxima. Second, we multiply covariance maps calculated with different 3D spectra to destroy erroneous sequential correlations. The maps are easy to use and can readily be generated from conventional triple-resonance experiments. Advantages of the method are demonstrated on a 37 kDa nonribosomal peptide synthetase domain subject to spectral overlap.

Mass spectrometry for protein quantification in biomarker discovery.

Science.gov (United States)

Wang, Mu; You, Jinsam

2012-01-01

Major technological advances have made proteomics an extremely active field for biomarker discovery in recent years due primarily to the development of newer mass spectrometric technologies and the explosion in genomic and protein bioinformatics. This leads to an increased emphasis on larger scale, faster, and more efficient methods for detecting protein biomarkers in human tissues, cells, and biofluids. Most current proteomic methodologies for biomarker discovery, however, are not highly automated and are generally labor-intensive and expensive. More automation and improved software programs capable of handling a large amount of data are essential to reduce the cost of discovery and to increase throughput. In this chapter, we discuss and describe mass spectrometry-based proteomic methods for quantitative protein analysis.

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Science.gov (United States)

Villanueva, Josep; Villegas, Virtudes; Querol, Enrique; Avilés, Francesc X; Serrano, Luis

2002-09-01

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability. Copyright 2002 John Wiley & Sons, Ltd.

Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm

International Nuclear Information System (INIS)

Yang, Yu; Fritzsching, Keith J.; Hong, Mei

2013-01-01

A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra (“good connections”), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra (“bad connections”), and minimizing the number of assigned peaks that have no matching peaks in the other spectra (“edges”). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct

Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm.

Science.gov (United States)

Yang, Yu; Fritzsching, Keith J; Hong, Mei

2013-11-01

A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra ("good connections"), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra ("bad connections"), and minimizing the number of assigned peaks that have no matching peaks in the other spectra ("edges"). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct assignment for a

RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database.

Science.gov (United States)

Field, Helen I; Fenyö, David; Beavis, Ronald C

2002-01-01

RADARS, a rapid, automated, data archiving and retrieval software system for high-throughput proteomic mass spectral data processing and storage, is described. The majority of mass spectrometer data files are compatible with RADARS, for consistent processing. The system automatically takes unprocessed data files, identifies proteins via in silico database searching, then stores the processed data and search results in a relational database suitable for customized reporting. The system is robust, used in 24/7 operation, accessible to multiple users of an intranet through a web browser, may be monitored by Virtual Private Network, and is secure. RADARS is scalable for use on one or many computers, and is suited to multiple processor systems. It can incorporate any local database in FASTA format, and can search protein and DNA databases online. A key feature is a suite of visualisation tools (many available gratis), allowing facile manipulation of spectra, by hand annotation, reanalysis, and access to all procedures. We also described the use of Sonar MS/MS, a novel, rapid search engine requiring 40 MB RAM per process for searches against a genomic or EST database translated in all six reading frames. RADARS reduces the cost of analysis by its efficient algorithms: Sonar MS/MS can identifiy proteins without accurate knowledge of the parent ion mass and without protein tags. Statistical scoring methods provide close-to-expert accuracy and brings robust data analysis to the non-expert user.

Null-plane formulation of Bethe-Salpeter qqq dynamics: Baryon mass spectra

International Nuclear Information System (INIS)

Kulshreshtha, D.S.; Mitra, A.N.

1988-01-01

The Bethe-Salpeter (BS) equation for a qqq system is formulated in the null-plane approximation (NPA) for the BS wave function, as a direct generalization of a corresponding QCD-motivated formalism developed earlier for qq-bar systems. The confinement kernel is assumed vector type (γ/sub μ//sup (1)/γ/sub μ//sup (2)/) for both qq-bar and qq pairs, with identical harmonic structures, and with the spring constant proportional, among other things, to the running coupling constant α/sub s/ (for an explicit QCD motivation). The harmonic kernel is given a suitable Lorentz-invariant definition [not D'Alembertian 2 δ 4 (q)], which is amenable to NPA reduction in a covariant form. The reduced qqq equation in NPA is solved algebraically in a six-dimensional harmonic-oscillator (HO) basis, using the techniques of SO(2,1) algebra interlinked with S 3 symmetry. The results on the nonstrange baryon mass spectra agree well with the data all the way up to N = 6, thus confirming the asymptotic prediction M∼N/sup 2/3/ characteristic of vector confinement in HO form. There are no extra parameters beyond the three basic constants (ω 0 ,C 0 ,m/sub u//sub d/) which were earlier found to provide excellent fits to meson spectra (qq-bar)

CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO

International Nuclear Information System (INIS)

Guerry, Paul; Duong, Viet Dung; Herrmann, Torsten

2015-01-01

UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involved—including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge (CASD-NMR 2), we participated in two categories of CASD-NMR 2, namely using either raw NMR spectra or unrefined NOE peak lists as input. A total of 15 resulting NMR structure bundles were submitted for 9 out of 10 blind protein targets. All submitted UNIO structures accurately coincided with the corresponding blind targets as documented by an average backbone root mean-square deviation to the reference proteins of only 1.2 Å. Also, the precision of the UNIO structure bundles was virtually identical to the ensemble of reference structures. By assessing the quality of all UNIO structures submitted to the two categories, we find throughout that only the UNIO–ATNOS/CANDID approach using raw NMR spectra consistently yielded structure bundles of high quality for direct deposition in the Protein Data Bank. In conclusion, the results obtained in CASD-NMR 2 are another vital proof for robust, accurate and unsupervised NMR data analysis by UNIO for real-world applications

Protein Charge and Mass Contribute to the Spatio-temporal Dynamics of Protein-Protein Interactions in a Minimal Proteome

Science.gov (United States)

Xu, Yu; Wang, Hong; Nussinov, Ruth; Ma, Buyong

2013-01-01

We constructed and simulated a ‘minimal proteome’ model using Langevin dynamics. It contains 206 essential protein types which were compiled from the literature. For comparison, we generated six proteomes with randomized concentrations. We found that the net charges and molecular weights of the proteins in the minimal genome are not random. The net charge of a protein decreases linearly with molecular weight, with small proteins being mostly positively charged and large proteins negatively charged. The protein copy numbers in the minimal genome have the tendency to maximize the number of protein-protein interactions in the network. Negatively charged proteins which tend to have larger sizes can provide large collision cross-section allowing them to interact with other proteins; on the other hand, the smaller positively charged proteins could have higher diffusion speed and are more likely to collide with other proteins. Proteomes with random charge/mass populations form less stable clusters than those with experimental protein copy numbers. Our study suggests that ‘proper’ populations of negatively and positively charged proteins are important for maintaining a protein-protein interaction network in a proteome. It is interesting to note that the minimal genome model based on the charge and mass of E. Coli may have a larger protein-protein interaction network than that based on the lower organism M. pneumoniae. PMID:23420643

One-dimensional power spectrum and neutrino mass in the spectra of BOSS

International Nuclear Information System (INIS)

Borde, Arnaud

2014-01-01

The framework of the studies presented in this thesis is the one-dimensional power spectrum of the transmitted flux in the Lyman-alpha forests. The Lyman-alpha forest is an absorption pattern seen in the spectra of high redshift quasars corresponding to the absorption of the quasar light by the hydrogen clouds along the line of sight. It is a powerful cosmological tool as it probes relatively small scales, of the order of a few Mpc. It is also sensible to small non-linear effects such as the one induced by massive neutrinos. First, we have developed two independent methods to measure the one-dimensional power spectrum of the transmitted flux in the Lyman-alpha forest. The first method is based on a Fourier transform, and the second on a maximum likelihood estimator. The two methods are independent and have different systematic uncertainties. The determination of the noise level in the data spectra was subject to a novel treatment, because of its significant impact on the derived power spectrum. We applied the two methods to 13,821 quasar spectra from SDSS-III/BOSS DR9 selected from a larger sample of over 60,000 spectra on the basis of their high quality, large signal-to-noise ratio, and good spectral resolution. The power spectra measured using either approach are in good agreement over all twelve redshift bins from =2.2 to =4.4, and scales from 0.001 (km/s)"-"1 to 0.02 (km/s)"-"1. We carefully determined the methodological and instrumental systematic uncertainties of our measurements. Then, we present a suite of cosmological N-body simulations with cold dark matter, baryons and neutrinos aiming at modeling the low-density regions of the IGM as probed by the Lyman-alpha forests at high redshift. The simulations are designed to match the requirements imposed by the quality of BOSS and eBOSS data. They are made using either 768"3 or 192"3 particles of each type, spanning volumes ranging from (25 Mpc/h)"3 for high-resolution simulations to (100 Mpc/h)"3 for large

Analysis of COSIMA spectra: Bayesian approach

Directory of Open Access Journals (Sweden)

H. J. Lehto

2015-06-01

secondary ion mass spectrometer (TOF-SIMS spectra. The method is applied to the COmetary Secondary Ion Mass Analyzer (COSIMA TOF-SIMS mass spectra where the analysis can be broken into subgroups of lines close to integer mass values. The effects of the instrumental dead time are discussed in a new way. The method finds the joint probability density functions of measured line parameters (number of lines, and their widths, peak amplitudes, integrated amplitudes and positions. In the case of two or more lines, these distributions can take complex forms. The derived line parameters can be used to further calibrate the mass scaling of TOF-SIMS and to feed the results into other analysis methods such as multivariate analyses of spectra. We intend to use the method, first as a comprehensive tool to perform quantitative analysis of spectra, and second as a fast tool for studying interesting targets for obtaining additional TOF-SIMS measurements of the sample, a property unique to COSIMA. Finally, we point out that the Bayesian method can be thought of as a means to solve inverse problems but with forward calculations, only with no iterative corrections or other manipulation of the observed data.

Capillary zone electrophoresis-mass spectromet of intact proteins

NARCIS (Netherlands)

Domínguez-Vega, Elena; Haselberg, Rob; Somsen, Govert W.

2016-01-01

Capillary electrophoresis (CE) coupled with mass spectrometry (MS) has proven to be a powerful analytical tool for the characterization of intact proteins. It combines the high separation efficiency, short analysis time, and versatility of CE with the mass selectivity and sensitivity offered by MS

Softening and re-hardening of hadron transverse mass spectra in relativistic heavy-ion collisions

International Nuclear Information System (INIS)

Isse, M.; Otuka, N.; Ohnishi, A.; Sahu, P.K.; Nara, Y.

2002-01-01

At RHIC experiments, started at 2000, the data obtained recently seem to exhibit QGP formation, but the conclusion is not drawn yet. Here, we pay out attention to the collective motion at hadronic freeze-out as an evidence of QGP formation. The transverse mass spectra may show softening to re-hardening with increasing incident energy. We compare simulated results obtained in JAM' - a hadronic cascade model - with experimental data, and discuss weather the QGP is formed or not. (author)

Analysis of steranes and triterpanes in geolipid extracts by automatic classification of mass spectra

Science.gov (United States)

Wardroper, A. M. K.; Brooks, P. W.; Humberston, M. J.; Maxwell, J. R.

1977-01-01

A computer method is described for the automatic classification of triterpanes and steranes into gross structural type from their mass spectral characteristics. The method has been applied to the spectra obtained by gas-chromatographic/mass-spectroscopic analysis of two mixtures of standards and of hydrocarbon fractions isolated from Green River and Messel oil shales. Almost all of the steranes and triterpanes identified previously in both shales were classified, in addition to a number of new components. The results indicate that classification of such alkanes is possible with a laboratory computer system. The method has application to diagenesis and maturation studies as well as to oil/oil and oil/source rock correlations in which rapid screening of large numbers of samples is required.

Direct Detection of Biotinylated Proteins by Mass Spectrometry

Science.gov (United States)

2015-01-01

Mass spectrometric strategies to identify protein subpopulations involved in specific biological functions rely on covalently tagging biotin to proteins using various chemical modification methods. The biotin tag is primarily used for enrichment of the targeted subpopulation for subsequent mass spectrometry (MS) analysis. A limitation of these strategies is that MS analysis does not easily discriminate unlabeled contaminants from the labeled protein subpopulation under study. To solve this problem, we developed a flexible method that only relies on direct MS detection of biotin-tagged proteins called “Direct Detection of Biotin-containing Tags” (DiDBiT). Compared with conventional targeted proteomic strategies, DiDBiT improves direct detection of biotinylated proteins ∼200 fold. We show that DiDBiT is applicable to several protein labeling protocols in cell culture and in vivo using cell permeable NHS-biotin and incorporation of the noncanonical amino acid, azidohomoalanine (AHA), into newly synthesized proteins, followed by click chemistry tagging with biotin. We demonstrate that DiDBiT improves the direct detection of biotin-tagged newly synthesized peptides more than 20-fold compared to conventional methods. With the increased sensitivity afforded by DiDBiT, we demonstrate the MS detection of newly synthesized proteins labeled in vivo in the rodent nervous system with unprecedented temporal resolution as short as 3 h. PMID:25117199

Proposal and Evaluation of Subordinate Standard Solar Irradiance Spectra: Preprint

Energy Technology Data Exchange (ETDEWEB)

Habte, Aron M [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Wilbert, Stefan [German Aerospace Center (DLR); Jessen, Wilko [German Aerospace Center (DLR); Gueymard, Chris [Solar Consulting Services; Polo, Jesus [CIEMAT; Bian, Zeqiang [China Meteorological Administration; Driesse, Anton [Photovoltaic Performance Labs; Marzo, Aitor [University of Antofagasta; Armstrong, Peter [Masdar Institute of Science & Technology; Vignola, Frank [University of Oregon; Ramirez, Lourdes [CIEMAT

2018-04-12

This paper introduces a concept for global tilted irradiance (GTI) subordinate standard spectra to supplement the current standard spectra used in solar photovoltaic applications as defined in ASTM G173 and IEC60904. The proposed subordinate standard spectra correspond to atmospheric conditions and tilt angles that depart significantly from the main standard spectrum, and they can be used to more accurately represent various local conditions. For the definition of subordinate standard spectra cases with an elevation 1.5 km above sea level, the question arises whether the air mass should be calculated including a pressure correction or not. This study focuses on the impact of air mass used in standard spectra, and it uses data from 29 locations to examine which air mass is most appropriate for GTI and direct normal irradiance (DNI) spectra. Overall, it is found that the pressure-corrected air mass of 1.5 is most appropriate for DNI spectra. For GTI, a non-pressure-corrected air mass of 1.5 was found to be more appropriate.

Role of protein and amino acids in promoting lean mass accretion with resistance exercise and attenuating lean mass loss during energy deficit in humans.

Science.gov (United States)

Churchward-Venne, Tyler A; Murphy, Caoileann H; Longland, Thomas M; Phillips, Stuart M

2013-08-01

Amino acids are major nutrient regulators of muscle protein turnover. After protein ingestion, hyperaminoacidemia stimulates increased rates of skeletal muscle protein synthesis, suppresses muscle protein breakdown, and promotes net muscle protein accretion for several hours. These acute observations form the basis for strategized protein intake to promote lean mass accretion, or prevent lean mass loss over the long term. However, factors such as protein dose, protein source, and timing of intake are important in mediating the anabolic effects of amino acids on skeletal muscle and must be considered within the context of evaluating the reported efficacy of long-term studies investigating protein supplementation as part of a dietary strategy to promote lean mass accretion and/or prevent lean mass loss. Current research suggests that dietary protein supplementation can augment resistance exercise-mediated gains in skeletal muscle mass and strength and can preserve skeletal muscle mass during periods of diet-induced energy restriction. Perhaps less appreciated, protein supplementation can augment resistance training-mediated gains in skeletal muscle mass even in individuals habitually consuming 'adequate' (i.e., >0.8 g kg⁻¹ day⁻¹) protein. Additionally, overfeeding energy with moderate to high-protein intake (15-25 % protein or 1.8-3.0 g kg⁻¹ day⁻¹) is associated with lean, but not fat mass accretion, when compared to overfeeding energy with low protein intake (5 % protein or ~0.68 g kg⁻¹ day⁻¹). Amino acids represent primary nutrient regulators of skeletal muscle anabolism, capable of enhancing lean mass accretion with resistance exercise and attenuating the loss of lean mass during periods of energy deficit, although factors such as protein dose, protein source, and timing of intake are likely important in mediating these effects.

Effect of Skimmer Cone Material on the Spectra of Inductively Coupled Plasma Mass Spectrometry

International Nuclear Information System (INIS)

Amr, M.A.; Zahran, N.F.; Helal, A.I.

2002-01-01

The inductively coupled plasma ion source for mass spectrometry is very sensitive for multielement analysis with detection limits down to sub part per trillion (ppt). Polyatomic ions which could be formed in the mass spectra may interfere in the analysis of some element. Experimental conditions have great influences on the formation of polyatomic ions. The present work demonstrates that the skimmer materials (Au, Ag, Ni, and Cu) are participating in the formation of polyatomic ions, meanwhile the sampler materials have no real effect. The mechanism of formation of polyatomic ions is explained. Heats of formation of polyatomic species formed from the skimmer materials such as: Au X, Ag X, Ni X and Cu X; where X= Ar, O, N, C and H are calculated by Gaussian program (G 94 W)

Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry—A review

International Nuclear Information System (INIS)

Percy, Andrew J.; Rey, Martial; Burns, Kyle M.; Schriemer, David C.

2012-01-01

Highlights: ► Protein chemistry generates mass shifts useful for structure–function studies. ► H/DX supports a powerful mass shift method for protein interaction analysis. ► H/DX mass shifts are useful for determining binding data (K d , off-rates). ► Improved H/DX–MS workflows can accommodate complex protein systems. - Abstract: Assessing the functional outcome of protein interactions in structural terms is a goal of structural biology, however most techniques have a limited capacity for making structure–function determinations with both high resolution and high throughput. Mass spectrometry can be applied as a reader of protein chemistries in order to fill this void, and enable methodologies whereby protein structure–function determinations may be made on a proteome-wide level. Protein hydrogen/deuterium exchange (H/DX) offers a chemical labeling strategy suitable for tracking changes in “dynamic topography” and thus represents a powerful means of monitoring protein structure–function relationships. This review presents the exchange method in the context of interaction analysis. Applications involving interface detection, quantitation of binding, and conformational responses to ligation are discussed, and commentary on recent analytical developments is provided.

Profiling an electrospray plume by laser-induced fluorescence and Fraunhofer diffraction combined to mass spectrometry: influence of size and composition of droplets on charge-state distributions of electrosprayed proteins.

Science.gov (United States)

Girod, Marion; Dagany, Xavier; Boutou, Véronique; Broyer, Michel; Antoine, Rodolphe; Dugourd, Philippe; Mordehai, Alex; Love, Craig; Werlich, Mark; Fjeldsted, John; Stafford, George

2012-07-14

We investigated how physico-chemical properties of charged droplets are affected by the electrospray process, using simultaneous in situ measurements by laser-induced fluorescence (LIF), Fraunhofer diffraction and mass spectrometry. For this purpose, we implemented a laser-induced-fluorescence profiling setup in conjunction with a fast, high-resolution particle sizing scheme on a modified Agilent Jet Stream electrospray source coupled to a single quadrupole mass analyser. The optical setup permits us to profile the solvent fractionation and the size of the droplets as they evaporate in an electrospray plume by measuring both the angular scattering pattern and emission spectra of a solvatochromic fluorescent dye. Mass spectra are recorded simultaneously. These mass spectrometry and optical spectroscopy investigations allow us to study the relation between the observed charge-state distributions of protein anions and physico-chemical properties of evaporating droplets in the spray plume. By mixing water with methanol, a refolding of cytochrome C is observed as the water percentage increases in the plume due to the preponderant evaporation of volatile methanol.

Main-chain-directed strategy for the assignment of 1H NMR spectra of proteins

International Nuclear Information System (INIS)

Englander, S.W.; Wand, A.J.

1987-01-01

A strategy for assigning the resonances in two-dimensional (2D) NMR spectra of proteins is described. The method emphasizes the analysis of through-space relationships between protons by use of the two-dimensional nuclear Overhauser effect (NOE) experiment. NOE patterns used in the algorithm were derived from a statistical analysis of the combinations of short proton-proton distances observed in the high-resolution crystal structures of 21 proteins. One starts with a search for authentic main-chain NH-C/sub α/H-C/sub β/H J-coupled units, which can be found with high reliability. The many main-chain units of a protein are then placed in their proper juxtaposition by recognition of predefined NOE connectivity patterns. To discover these connectivities, the 2D NOE spectrum is examined, in a prescribed order, for the distinct NOE patterns characteristic of helices, sheets, turns, and extended chain. Finally, the recognition of a few amino acid side-chain types places the discovered secondary structure elements within the polypeptide sequences. Unlike the sequential assignment approach, the main-chain-directed strategy does not rely on the difficult task of recognizing many side-chain spin systems in J-correlated spectra, the assignment process is not in general sequential with the polypeptide chain, and the prescribed connectivity patterns are cyclic rather than linear. The latter characteristic avoids ambiguous branch points in the analysis and imposed an internally confirmatory property on each forward step

Radiative and semi-leptonic B-meson decay spectra: Sudakov resummation beyond logarithmic accuracy and the pole mass

Science.gov (United States)

Gardi, Einan

2004-04-01

The inclusive spectra of radiative and semi-leptonic B-meson decays near the endpoint is computed taking into account renormalons in the Sudakov exponent (Dressed Gluon Exponentiation). In this framework we demonstrate the factorization of decay spectra into hard, jet and soft functions and discuss the universality of the latter two. Going beyond perturbation theory the soft function, which we identify as the longitudinal momentum distribution in an on-shell b quark, is replaced by the b-quark distribution in the B meson. The two differ by power corrections. We show how the resummation of running-coupling effects can be used to perform consistent separation to power accuracy between perturbative and non-perturbative contributions. In particular, we prove that the leading infrared renormalon ambiguity in the Sudakov exponent cancels against the one associated with the definition of the pole mass. This cancellation allows us to identify the non-perturbative parameter that controls the shift of the perturbative spectrum in the heavy-quark limit as the mass difference between the meson and the quark.

Searches of exotic Higgs bosons in general mass spectra of the Georgi-Machacek model at the LHC

International Nuclear Information System (INIS)

Chiang, Cheng-Wei; Kuo, An-Li; Yamada, Toshifumi

2016-01-01

We derive the most general sets of viable mass spectra of the exotic Higgs bosons in the Georgi-Machacek model that are consistent with the theoretical constraints of vacuum stability and perturbative unitarity and the experimental constraints of electroweak precision observables, Zbb̄ coupling and Higgs boson signal strengths. Branching ratios of various cascade decay channels of the doubly-charged Higgs boson in the 5 representation, the singly-charged Higgs boson in 3, and the singlet Higgs boson are further computed. As one of the most promising channels for discovering the model, we study the prospects for detecting the doubly-charged Higgs boson that is produced via the vector boson fusion process and decays into final states containing a pair of same-sign leptons at the 14-TeV LHC and a 100-TeV future pp collider. For this purpose, we evaluate acceptance times efficiency for signals of the doubly-charged Higgs boson with general viable mass spectra and compare it with the standard model background estimates.

Classical electron ionization mass spectra in gas chromatography/mass spectrometry with supersonic molecular beams.

Science.gov (United States)

Gordin, Alexander; Fialkov, Alexander B; Amirav, Aviv

2008-09-01

A major benefit of gas chromatography/mass spectrometry (GC/MS) with a supersonic molecular beam (SMB) interface and its fly-through ion source is the ability to obtain electron ionization of vibrationally cold molecules (cold EI), which show enhanced molecular ions. However, GC/MS with an SMB also has the flexibility to perform 'classical EI' mode of operation which provides mass spectra to mimic those in commercial 70 eV electron ionization MS libraries. Classical EI in SMB is obtained through simple reduction of the helium make-up gas flow rate, which reduces the SMB cooling efficiency; hence the vibrational temperatures of the molecules are similar to those in traditional EI ion sources. In classical EI-SMB mode, the relative abundance of the molecular ion can be tuned and, as a result, excellent identification probabilities and very good matching factors to the NIST MS library are obtained. Classical EI-SMB with the fly-through dual cage ion source has analyte sensitivity similar to that of the standard EI ion source of a basic GC/MS system. The fly-through EI ion source in combination with the SMB interface can serve for cold EI, classical EI-SMB, and cluster chemical ionization (CCI) modes of operation, all easily exchangeable through a simple and quick change (not involving hardware). Furthermore, the fly-through ion source eliminates sample scattering from the walls of the ion source, and thus it offers full sample inertness, tailing-free operation, and no ion-molecule reaction interferences. It is also robust and enables increased column flow rate capability without affecting the sensitivity.

Temperature dependence of Q-band electron paramagnetic resonance spectra of nitrosyl heme proteins

Energy Technology Data Exchange (ETDEWEB)

Flores, Marco; Wajnberg, Eliane; Bemski, George

1997-11-01

The Q-band (35 GHz) electron paramagnetic resonance (EPR) spectra of nitrosyl hemoglobin (Hb N O) and nitrosyl myoglobin (Mb NO) were studied as a function of temperature between 19 K and 200 K. The spectra of both heme proteins show classes of variations as a function of temperature. The first one has previously been associated with the existence of two paramagnetic species, one with rhombic and the other with axial symmetry. The second one manifests itself in changes in the g-factors and linewidths of each species. These changes are correlated with the conformational substates model and associate the variations of g-values with changes in the angle of the N(his)-Fe-N (NO) bond in the rhombic species and with changes in the distance between Fe and N of the proximal (F8) histidine in the axial species. (author) 24 refs., 6 figs.

The Higgs boson mass and SUSY spectra in 10D SYM theory with magnetized extra dimensions

Directory of Open Access Journals (Sweden)

Hiroyuki Abe

2014-11-01

Full Text Available We study the Higgs boson mass and the spectrum of supersymmetric (SUSY particles in the well-motivated particle physics model derived from a ten-dimensional supersymmetric Yang–Mills theory compactified on three factorizable tori with magnetic fluxes. This model was proposed in a previous work, where the flavor structures of the standard model including the realistic Yukawa hierarchies are obtained from non-hierarchical input parameters on the magnetized background. Assuming moduli- and anomaly-mediated contributions dominate the soft SUSY breaking terms, we study the precise SUSY spectra and analyze the Higgs boson mass in this mode, which are compared with the latest experimental data.

Formation of truncated proteins and high-molecular-mass aggregates upon soft illumination of photosynthetic proteins

DEFF Research Database (Denmark)

Rinalducci, Sara; Campostrini, Natascia; Antonioli, Paolo

2005-01-01

Different spot profiles were observed in 2D gel electrophoresis of thylakoid membranes performed either under complete darkness or by leaving the sample for a short time to low visible light. In the latter case, a large number of new spots with lower molecular masses, ranging between 15,000 and 25......,000 Da, were observed, and high-molecular-mass aggregates, seen as a smearing in the upper part of the gel, appeared in the region around 250 kDa. Identification of protein(s) contained in these new spots by MS/MS revealed that most of them are simply truncated proteins deriving from native ones...

Influence of secondary structure on in-source decay of protein in matrix-assisted laser desorption/ionization mass spectrometry.

Science.gov (United States)

Takayama, Mitsuo; Osaka, Issey; Sakakura, Motoshi

2012-01-01

The susceptibility of the N-Cα bond of the peptide backbone to specific cleavage by in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was studied from the standpoint of the secondary structure of three proteins. A naphthalene derivative, 5-amino-1-naphtol (5,1-ANL), was used as the matrix. The resulting c'-ions, which originate from the cleavage at N-Cα bonds in flexible secondary structures such as turn and bend, and are free from intra-molecular hydrogen-bonded α-helix structure, gave relatively intense peaks. Furthermore, ISD spectra of the proteins showed that the N-Cα bonds of specific amino acid residues, namely Gly-Xxx, Xxx-Asp, and Xxx-Asn, were more susceptible to MALDI-ISD than other amino acid residues. This is in agreement with the observation that Gly, Asp and Asn residues usually located in turns, rather than α-helix. The results obtained indicate that protein molecules embedded into the matrix crystal in the MALDI experiments maintain their secondary structures as determined by X-ray crystallography, and that MALDI-ISD has the capability for providing information concerning the secondary structure of protein.

Short communication: Evaluation of MALDI-TOF mass spectrometry and a custom reference spectra expanded database for the identification of bovine-associated coagulase-negative staphylococci.

Science.gov (United States)

Cameron, M; Perry, J; Middleton, J R; Chaffer, M; Lewis, J; Keefe, G P

2018-01-01

This study evaluated MALDI-TOF mass spectrometry and a custom reference spectra expanded database for the identification of bovine-associated coagulase-negative staphylococci (CNS). A total of 861 CNS isolates were used in the study, covering 21 different CNS species. The majority of the isolates were previously identified by rpoB gene sequencing (n = 804) and the remainder were identified by sequencing of hsp60 (n = 56) and tuf (n = 1). The genotypic identification was considered the gold standard identification. Using a direct transfer protocol and the existing commercial database, MALDI-TOF mass spectrometry showed a typeability of 96.5% (831/861) and an accuracy of 99.2% (824/831). Using a custom reference spectra expanded database, which included an additional 13 in-house created reference spectra, isolates were identified by MALDI-TOF mass spectrometry with 99.2% (854/861) typeability and 99.4% (849/854) accuracy. Overall, MALDI-TOF mass spectrometry using the direct transfer method was shown to be a highly reliable tool for the identification of bovine-associated CNS. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Mass Spectra-Based Framework for Automated Structural Elucidation of Metabolome Data to Explore Phytochemical Diversity

Science.gov (United States)

Matsuda, Fumio; Nakabayashi, Ryo; Sawada, Yuji; Suzuki, Makoto; Hirai, Masami Y.; Kanaya, Shigehiko; Saito, Kazuki

2011-01-01

A novel framework for automated elucidation of metabolite structures in liquid chromatography–mass spectrometer metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method. PMID:22645535

Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity

Directory of Open Access Journals (Sweden)

Fumio eMatsuda

2011-08-01

Full Text Available A novel framework for automated elucidation of metabolite structures in liquid chromatography-mass spectrometer (LC-MS metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method.

Probing the Composition, Assembly and Activity of Protein Molecular Machines using Native Mass Spectrometry

NARCIS (Netherlands)

van de Waterbeemd, M.J.

2017-01-01

Native mass spectrometry and mass spectrometry in general, are powerful analytical tools for studying proteins and protein complexes. Native mass spectrometry may provide accurate mass measurements of large macromolecular assemblies enabling the investigation of their composition and stoichiometry.

On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications

Directory of Open Access Journals (Sweden)

Novák Jiří

2013-12-01

Full Text Available The similarity search in theoretical mass spectra generated from protein sequence databases is a widely accepted approach for identification of peptides from query mass spectra produced by shotgun proteomics. Growing protein sequence databases and noisy query spectra demand database indexing techniques and better similarity measures for the comparison of theoretical spectra against query spectra. We employ a modification of previously proposed parameterized Hausdorff distance for comparisons of mass spectra. The new distance outperforms the original distance, the angle distance and state-of-the-art peptide identification tools OMSSA and X!Tandem in the number of identified peptides even though the q-value is only 0.001. When a precursor mass filter is used as a database indexing technique, our method outperforms OMSSA in the speed of search. When variable modifications are not searched, the search time is similar to X!Tandem. We show that the precursor mass filter is an efficient database indexing technique for high-accuracy data even though many variable modifications are being searched. We demonstrate that the number of identified peptides is bigger when variable modifications are searched separately by more search runs of a peptide identification engine. Otherwise, the false discovery rates are affected by mixing unmodified and modified spectra together resulting in a lower number of identified peptides. Our method is implemented in the freely available application SimTandem which can be used in the framework TOPP based on OpenMS.

Laser ablation aerosol particle time-of-flight mass spectrometer (LAAPTOF): performance, reference spectra and classification of atmospheric samples

Science.gov (United States)

Shen, Xiaoli; Ramisetty, Ramakrishna; Mohr, Claudia; Huang, Wei; Leisner, Thomas; Saathoff, Harald

2018-04-01

The laser ablation aerosol particle time-of-flight mass spectrometer (LAAPTOF, AeroMegt GmbH) is able to identify the chemical composition and mixing state of individual aerosol particles, and thus is a tool for elucidating their impacts on human health, visibility, ecosystem, and climate. The overall detection efficiency (ODE) of the instrument we use was determined to range from ˜ (0.01 ± 0.01) to ˜ (4.23 ± 2.36) % for polystyrene latex (PSL) in the size range of 200 to 2000 nm, ˜ (0.44 ± 0.19) to ˜ (6.57 ± 2.38) % for ammonium nitrate (NH4NO3), and ˜ (0.14 ± 0.02) to ˜ (1.46 ± 0.08) % for sodium chloride (NaCl) particles in the size range of 300 to 1000 nm. Reference mass spectra of 32 different particle types relevant for atmospheric aerosol (e.g. pure compounds NH4NO3, K2SO4, NaCl, oxalic acid, pinic acid, and pinonic acid; internal mixtures of e.g. salts, secondary organic aerosol, and metallic core-organic shell particles; more complex particles such as soot and dust particles) were determined. Our results show that internally mixed aerosol particles can result in spectra with new clusters of ions, rather than simply a combination of the spectra from the single components. An exemplary 1-day ambient data set was analysed by both classical fuzzy clustering and a reference-spectra-based classification method. Resulting identified particle types were generally well correlated. We show how a combination of both methods can greatly improve the interpretation of single-particle data in field measurements.

Vibronic spectra of Gd3+ in metaphosphate glasses: Comparison with Raman and infrared spectra

International Nuclear Information System (INIS)

Hall, D.W.; Brawer, S.A.; Weber, M.J.

1982-01-01

Vibronic sidebands associated with the 6 P/sub 7/2/→ 8 S/sub 7/2/ transition of Gd 3+ -doped metaphosphate glasses are observed using line-narrowed fluorescence techniques. Glasses having metal cations of different mass and charge (La,Al,Mg,Ba) are examined. Vibronic spectra, which probe vibrations about the rare-earth element site, are compared with polarized Raman scattering data and the infrared dielectric constant obtained from near-normal reflectance measurements. Results indicate that in metaphosphate glasses vibronic selection rules are similar to HV (vertical height) Raman selection rules. The wavelengths and relative intensities of peaks in the high-frequency portion of the vibronic spectra change with respect to corresponding peaks in the Raman spectra when the mass and/or charge of Gd 3+ differs significantly from that of the metal cation

Traveling-wave ion mobility mass spectrometry of protein complexes

DEFF Research Database (Denmark)

Salbo, Rune; Bush, Matthew F; Naver, Helle

2012-01-01

The collision cross-section (Ω) of a protein or protein complex ion can be measured using traveling-wave (T-wave) ion mobility (IM) mass spectrometry (MS) via calibration with compounds of known Ω. The T-wave Ω-values depend strongly on instrument parameters and calibrant selection. Optimization ...

Mass spectrometric analyses of organophosphate insecticide oxon protein adducts.

Science.gov (United States)

Thompson, Charles M; Prins, John M; George, Kathleen M

2010-01-01

Organophosphate (OP) insecticides continue to be used to control insect pests. Acute and chronic exposures to OP insecticides have been documented to cause adverse health effects, but few OP-adducted proteins have been correlated with these illnesses at the molecular level. Our aim was to review the literature covering the current state of the art in mass spectrometry (MS) used to identify OP protein biomarkers. We identified general and specific research reports related to OP insecticides, OP toxicity, OP structure, and protein MS by searching PubMed and Chemical Abstracts for articles published before December 2008. A number of OP-based insecticides share common structural elements that result in predictable OP-protein adducts. The resultant OP-protein adducts show an increase in molecular mass that can be identified by MS and correlated with the OP agent. Customized OP-containing probes have also been used to tag and identify protein targets that can be identified by MS. MS is a useful and emerging tool for the identification of proteins that are modified by activated organophosphate insecticides. MS can characterize the structure of the OP adduct and also the specific amino acid residue that forms the key bond with the OP. Each protein that is modified in a unique way by an OP represents a unique molecular biomarker that with further research can lead to new correlations with exposure.

VIRIAL BLACK HOLE MASS ESTIMATES FOR 280,000 AGNs FROM THE SDSS BROADBAND PHOTOMETRY AND SINGLE-EPOCH SPECTRA

Energy Technology Data Exchange (ETDEWEB)

Kozłowski, Szymon, E-mail: simkoz@astrouw.edu.pl [Warsaw University Observatory, Al. Ujazdowskie, 4 00-478 Warszawa (Poland)

2017-01-01

We use the Sloan Digital Sky Survey (SDSS) Quasar Data Release 12 (DR12Q), containing nearly 300,000 active galactic nuclei (AGNs), to calculate the monochromatic luminosities at 5100, 3000, and 1350 Å, derived from the broadband extinction-corrected SDSS magnitudes. After matching these sources to their counterparts from the SDSS Quasar Data Release 7 (DR7Q), we find very high correlations between our luminosities and DR7Q spectra-based luminosities with minute mean offsets (∼0.01 dex) and dispersions of differences of 0.11, 0.10, and 0.12 dex, respectively, across a luminosity range of 2.5 dex. We then estimate the black hole (BH) masses of the AGNs using the broad line region radius–disk luminosity relations and the FWHM of the Mg ii and C iv emission lines, to provide a catalog of 283,033 virial BH mass estimates (132,451 for Mg ii, 213,071 for C iv, and 62,489 for both) along with the estimates of the bolometric luminosity and Eddington ratio for 0.1 <  z  < 5.5 and for roughly a quarter of the sky covered by SDSS. The BH mass estimates from Mg ii turned out to be closely matched to the ones from DR7Q with a dispersion of differences of 0.34 dex across a BH mass range of ∼2 dex. We uncovered a bias in the derived C iv FWHMs from DR12Q as compared to DR7Q, which we correct empirically. The C iv BH mass estimates should be used with caution because the C iv line is known to cause problems in the estimation of BH mass from single-epoch spectra. Finally, after the FWHM correction, the AGN BH mass estimates from C iv closely match the DR7Q ones (with a dispersion of 0.28 dex), and more importantly the Mg ii and C iv BH masses agree internally with a mean offset of 0.07 dex and a dispersion of 0.39 dex.

Physical Activity Modifies the Association between Dietary Protein and Lean Mass of Postmenopausal Women.

Science.gov (United States)

Martinez, Jessica A; Wertheim, Betsy C; Thomson, Cynthia A; Bea, Jennifer W; Wallace, Robert; Allison, Matthew; Snetselaar, Linda; Chen, Zhao; Nassir, Rami; Thompson, Patricia A

2017-02-01

Maintenance of lean muscle mass and related strength is associated with lower risk for numerous chronic diseases of aging in women. Our aim was to evaluate whether the association between dietary protein and lean mass differs by physical activity level, amino acid composition, and body mass index categories. We performed a cross-sectional analysis of a prospective cohort. Participants were postmenopausal women from the Women's Health Initiative with body composition measurements by dual-energy x-ray absorptiometry (n=8,298). Our study measured percent lean mass, percent fat mass, and lean body mass index. Linear regression models adjusted for scanner serial number, age, calibrated energy intake, race/ethnicity, neighborhood socioeconomic status, and recreational physical activity were used to determine the relationship between protein intake and body composition measures. Likelihood ratio tests and stratified analysis were used to investigate physical activity and body mass index as potential effect modifiers. Biomarker-calibrated protein intake was positively associated with percent lean mass; women in the highest protein quintile had 6.3 percentage points higher lean mass than the lowest quintile (Plean body mass index were both inversely related to protein intake (both Plean body mass index (P interaction =0.011). Leucine intake was associated with lean mass, as were branched chain amino acids combined (both Plean mass in postmenopausal women. Importantly, those that also engage in physical activity have the highest lean mass across body mass index categories. Copyright © 2017 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

Application of MALDI-TOF mass spectrometry for study on fibrillar and oligomeric aggregates of alpha-synuclein

NARCIS (Netherlands)

Severinovskaya, O. V.; Kovalska, V B; Losytskyy, M Yu; Cherepanov, V. V.; Subramaniam, V.; Yarmoluk, S M

2014-01-01

Aim. To study the α-synuclein (ASN) aggregates of different structural origin, namely amyloid fibrils and spherical oligomers, in comparison with a native protein. Methods. MALDI TOF mass spectrometry and atomic force microscopy (AFM). Results. The mass spectra of native and fibrillar ASN have

Mass Spectra of Tetraselenafulvalenes, Diselenadithiafulvalenes and Tetrathiafulvalenes

DEFF Research Database (Denmark)

Andersen, Jan Rud; Egsgaard, Helge; Larsen, Elfinn

1978-01-01

fragmentation of the molecular ion, as the selenium fulvalenes lose an alkyne molecule, whereas the sulphur fulvalenes first lose an (SĊR) radical. An important feature of the spectra of the simple heterofulvalenes is the formation of a rearrangement ion by migration of a heteroatom. The mechanism...

Electron impact ionization mass spectra of 3-substituted-2-hydroxy-4(3H)-quinazolinones

International Nuclear Information System (INIS)

El Deen, I. M.; Abd El Fattah, M. E.

2003-01-01

2-Amino-2-hydroxy-4(3H)-quinazolinone (3) was prepared via condensation of 1 with hydrazine hydrate. Treatment of 3 with appropriate acid in POCl 3 , ethyl chloroacetate and activated olefinic compounds in DMF yielded the corresponding 3-(substituted)amino-2-hydroxy-4(3H)-quinazolinones 4,5 and 6. The electron impact ionization mass spectra of compounds 3 and 4 show a weak molecular ion peak and a base peak of m/z 146 resulting from a cleavage fragmentation. The compounds 5 and 6 give a characteristics fragmentation pattern with a very stable fragment of benzopyrazolone (m/z 132)

Protein needs in athletes and dietary-nutrition guidelines to gain muscle mass

Directory of Open Access Journals (Sweden)

Aritz Urdampilleta

2014-05-01

Full Text Available One of the most important effects of strength training is muscular hypertrophy. Athletes should optimize their nutritional management in order to compensate their own genetic limitations. The aim of this review is to analyze the scientific evidence concerning protein intake as a tool to achieve muscle hypertrophy. Depending on the expenditure and energy intake of athlete, a daily protein ranging between 10-15% of total dietary intake is needed. However in sports diets, it is preferable to estimate the amount of protein needed per kilogram of body weight in each individual. In this regard athletes should ingest an amount between 1.2 g and 1.8 g of proteins/kg of body mass/day to maintain their lean mass. In order to increase muscle mass (0.5 kg/week, athletes should take between 1.6 g and 1.8 g of protein/kg/day with an increase of 400-500 kcal in their daily diet. These needs will depend on the sport, muscular catabolic status, the athlete’s lean mass and glycogen stores. Protein needs will increase if muscle and liver glycogen stores are empty. Excess of protein intake (more than 2 g/kg/day, with full glycogen stores, does not benefit the athlete and could cause an increase in circulating ketones and urea, thereby producing an early dehydration.

Laser ablation aerosol particle time-of-flight mass spectrometer (LAAPTOF: performance, reference spectra and classification of atmospheric samples

Directory of Open Access Journals (Sweden)

X. Shen

2018-04-01

Full Text Available The laser ablation aerosol particle time-of-flight mass spectrometer (LAAPTOF, AeroMegt GmbH is able to identify the chemical composition and mixing state of individual aerosol particles, and thus is a tool for elucidating their impacts on human health, visibility, ecosystem, and climate. The overall detection efficiency (ODE of the instrument we use was determined to range from  ∼  (0.01 ± 0.01 to  ∼  (4.23 ± 2.36 % for polystyrene latex (PSL in the size range of 200 to 2000 nm,  ∼  (0.44 ± 0.19 to  ∼  (6.57 ± 2.38 % for ammonium nitrate (NH4NO3, and  ∼  (0.14 ± 0.02 to  ∼  (1.46 ± 0.08 % for sodium chloride (NaCl particles in the size range of 300 to 1000 nm. Reference mass spectra of 32 different particle types relevant for atmospheric aerosol (e.g. pure compounds NH4NO3, K2SO4, NaCl, oxalic acid, pinic acid, and pinonic acid; internal mixtures of e.g. salts, secondary organic aerosol, and metallic core–organic shell particles; more complex particles such as soot and dust particles were determined. Our results show that internally mixed aerosol particles can result in spectra with new clusters of ions, rather than simply a combination of the spectra from the single components. An exemplary 1-day ambient data set was analysed by both classical fuzzy clustering and a reference-spectra-based classification method. Resulting identified particle types were generally well correlated. We show how a combination of both methods can greatly improve the interpretation of single-particle data in field measurements.

[Probabilistic calculations of biomolecule charge states that generate mass spectra of multiply charged ions].

Science.gov (United States)

Raznikova, M O; Raznikov, V V

2015-01-01

In this work, information relating to charge states of biomolecule ions in solution obtained using the electrospray ionization mass spectrometry of different biopolymers is analyzed. The data analyses have mainly been carried out by solving an inverse problem of calculating the probabilities of retention of protons and other charge carriers by ionogenic groups of biomolecules with known primary structures. The approach is a new one and has no known to us analogues. A program titled "Decomposition" was developed and used to analyze the charge distribution of ions of native and denatured cytochrome c mass spectra. The possibility of splitting of the charge-state distribution of albumin into normal components, which likely corresponds to various conformational states of the biomolecule, has been demonstrated. The applicability criterion for using previously described method of decomposition of multidimensional charge-state distributions with two charge carriers, e.g., a proton and a sodium ion, to characterize the spatial structure of biopolymers in solution has been formulated. In contrast to known mass-spectrometric approaches, this method does not require the use of enzymatic hydrolysis or collision-induced dissociation of the biopolymers.

Rapid identification of DNA-binding proteins by mass spectrometry

DEFF Research Database (Denmark)

Nordhoff, E.; Korgsdam, A.-M.; Jørgensen, H.F.

1999-01-01

We report a protocol for the rapid identification of DNA-binding proteins. Immobilized DNA probes harboring a specific sequence motif are incubated with cell or nuclear extract. Proteins are analyzed directly off the solid support by matrix-assisted laser desorption/ionization time-of-flight mass...... was validated by the identification of known prokaryotic and eukaryotic DNA-binding proteins, and its use provided evidence that poly(ADP-ribose) polymerase exhibits DNA sequence-specific binding to DNA....

Rapid identification of fluorochrome modification sites in proteins by LC ESI-Q-TOF mass spectrometry.

Science.gov (United States)

Manikwar, Prakash; Zimmerman, Tahl; Blanco, Francisco J; Williams, Todd D; Siahaan, Teruna J

2011-07-20

Conjugation of either a fluorescent dye or a drug molecule to the ε-amino groups of lysine residues of proteins has many applications in biology and medicine. However, this type of conjugation produces a heterogeneous population of protein conjugates. Because conjugation of fluorochrome or drug molecule to a protein may have deleterious effects on protein function, the identification of conjugation sites is necessary. Unfortunately, the identification process can be time-consuming and laborious; therefore, there is a need to develop a rapid and reliable way to determine the conjugation sites of the fluorescent label or drug molecule. In this study, the sites of conjugation of fluorescein-5'-isothiocyanate and rhodamine-B-isothiocyanate to free amino groups on the insert-domain (I-domain) protein derived from the α-subunit of lymphocyte function-associated antigen-1 (LFA-1) were determined by electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-Q-TOF MS) along with peptide mapping using trypsin digestion. A reporter fragment of the fluorochrome moiety that is generated in the collision cell of the Q-TOF without explicit MS/MS precursor selection was used to identify the conjugation site. Selected ion plots of the reporter ion readily mark modified peptides in chromatograms of the complex digest. Interrogation of theses spectra reveals a neutral loss/precursor pair that identifies the modified peptide. The results show that one to seven fluorescein molecules or one to four rhodamine molecules were attached to the lysine residue(s) of the I-domain protein. No modifications were found in the metal ion-dependent adhesion site (MIDAS), which is an important binding region of the I-domain.

Definition of the mitochondrial proteome by measurement of molecular masses of membrane proteins

Science.gov (United States)

Carroll, Joe; Fearnley, Ian M.; Walker, John E.

2006-01-01

The covalent structure of a protein is incompletely defined by its gene sequence, and mass spectrometric analysis of the intact protein is needed to detect the presence of any posttranslational modifications. Because most membrane proteins are purified in detergents that are incompatible with mass spectrometric ionization techniques, this essential measurement has not been made on many hydrophobic proteins, and so proteomic data are incomplete. We have extracted membrane proteins from bovine mitochondria and detergent-purified NADH:ubiquinone oxidoreductase (complex I) with organic solvents, fractionated the mixtures by hydrophilic interaction chromatography, and measured the molecular masses of the intact membrane proteins, including those of six subunits of complex I that are encoded in mitochondrial DNA. These measurements resolve long-standing uncertainties about the interpretation of the mitochondrial genome, and they contribute significantly to the definition of the covalent composition of complex I. PMID:17060615

Ga+ TOF-SIMS lineshape analysis for resolution enhancement of MALDI MS spectra of a peptide mixture

International Nuclear Information System (INIS)

Malyarenko, D.I.; Chen, H.; Wilkerson, A.L.; Tracy, E.R.; Cooke, W.E.; Manos, D.M.; Sasinowski, M.; Semmes, O.J.

2004-01-01

The use of mass spectrometry to obtain molecular profiles indicative of alteration of concentrations of peptides in body fluids is currently the subject of intense investigation. For surface-based time-of-flight mass spectrometry the reliability and specificity of such profiling methods depend both on the resolution of the measuring instrument and on the preparation of samples. The present work is a part of a program to use Ga + beam TOF-SIMS alone, and as an adjunct to MALDI, in the development of reliable protein and peptide markers for diseases. Here, we describe techniques to prepare samples of relatively high-mass peptides, which serve as calibration standards and proxies for biomarkers. These are: Arg8-vasopressin, human angiotensin II, and somatostatin. Their TOF-SIMS spectra show repeatable characteristic features, with mass resolution exceeding 2000, including parent peaks and chemical adducts. The lineshape analysis for high-resolution parent peaks is shown to be useful for filter construction and deconvolution of inferior resolution SELDI-TOF spectra of calibration peptide mixture

Feed intake, live mass-gain, body composition and protein ...

African Journals Online (AJOL)

Appropriate regression relationships were used to measure the effect of dietary protein level on the patterns of DE intake, daily gain and the deposition rates of protein (PDR) and fat (FDR) over the growth period 30-90 kg live mass. Dietary CP content had no significant effect on mean voluntary DE intakes and daily gains.

Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry

Science.gov (United States)

Belov, Arseniy M.; Viner, Rosa; Santos, Marcia R.; Horn, David M.; Bern, Marshall; Karger, Barry L.; Ivanov, Alexander R.

2017-12-01

Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein-protein and protein-ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes). [Figure not available: see fulltext.

Accelerated identification of proteins by mass spectrometry by employing covalent pre-gel staining with Uniblue A.

Directory of Open Access Journals (Sweden)

Marco A Mata-Gómez

Full Text Available BACKGROUND: The identification of proteins by mass spectrometry is a standard method in biopharmaceutical quality control and biochemical research. Prior to identification by mass spectrometry, proteins are usually pre-separated by electrophoresis. However, current protein staining and de-staining protocols are tedious and time consuming, and therefore prolong the sample preparation time for mass spectrometry. METHODOLOGY AND PRINCIPAL FINDINGS: We developed a 1-minute covalent pre-gel staining protocol for proteins, which does not require de-staining before the mass spectrometry analysis. We investigated the electrophoretic properties of derivatized proteins and peptides and studied their behavior in mass spectrometry. Further, we elucidated the preferred reaction of proteins with Uniblue A and demonstrate the integration of the peptide derivatization into typical informatics tools. CONCLUSIONS AND SIGNIFICANCE: The Uniblue A staining method drastically speeds up the sample preparation for the mass spectrometry based identification of proteins. The application of this chemo-proteomic strategy will be advantageous for routine quality control of proteins and for time-critical tasks in protein analysis.

Feed intake, live mass-gain, body composition and protein ...

African Journals Online (AJOL)

Feed intake, live mass-gain, body composition and protein deposition in pigs fed three protein levels. E.H. Kemm,* F.K. Siebrits, M.N. Ras and H.A. Badenhorst. Animal and Dairy Science Research Institute, Private Bag X2, Irene 1675, Republic of South Africa. A group of 82 genetically lean and 90 obese Landrace pigs was ...

LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise

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Di Nicola Marta

2007-03-01

Full Text Available Abstract Background Mass spectrometry protein profiling is a promising tool for biomarker discovery in clinical proteomics. However, the development of a reliable approach for the separation of protein signals from noise is required. In this paper, LIMPIC, a computational method for the detection of protein peaks from linear-mode MALDI-TOF data is proposed. LIMPIC is based on novel techniques for background noise reduction and baseline removal. Peak detection is performed considering the presence of a non-homogeneous noise level in the mass spectrum. A comparison of the peaks collected from multiple spectra is used to classify them on the basis of a detection rate parameter, and hence to separate the protein signals from other disturbances. Results LIMPIC preprocessing proves to be superior than other classical preprocessing techniques, allowing for a reliable decomposition of the background noise and the baseline drift from the MALDI-TOF mass spectra. It provides lower coefficient of variation associated with the peak intensity, improving the reliability of the information that can be extracted from single spectra. Our results show that LIMPIC peak-picking is effective even in low protein concentration regimes. The analytical comparison with commercial and freeware peak-picking algorithms demonstrates its superior performances in terms of sensitivity and specificity, both on in-vitro purified protein samples and human plasma samples. Conclusion The quantitative information on the peak intensity extracted with LIMPIC could be used for the recognition of significant protein profiles by means of advanced statistic tools: LIMPIC might be valuable in the perspective of biomarker discovery.

Dansyl labeling and bidimensional mass spectrometry to investigate protein carbonylation.

Science.gov (United States)

Palmese, Angelo; De Rosa, Chiara; Marino, Gennaro; Amoresano, Angela

2011-01-15

Carbonylation is a non-enzymatic irreversible post-translational modification. The adduction of carbonyl groups to proteins is due to the presence of excess of ROS in cells. Carbonylation of specific amino acid side chains is one of the most abundant consequences of oxidative stress; therefore, the determination of carbonyl groups content in proteins is regarded as a reliable way to estimate the cellular damage caused by oxidative stress. This paper reports a novel RIGhT (Reporter Ion Generating Tag) (A. Amoresano, G. Monti, C. Cirulli, G. Marino. Rapid Commun. Mass Spectrom. 2006, 20, 1400) approach for selective labeling of carbonyl groups in proteins using dansylhydrazide, coupled with selective analysis by bidimensional mass spectrometry. We first applied this approach to ribonuclease A and lysozyme as model proteins. According to the so-called 'gel-free procedures', the analysis is carried out at the level of peptides following tryptic digest of the whole protein mixture. Modified RNaseA was analyzed in combined MS(2) and MS(3) scan mode, to specifically select the dansylated species taking advantage of the dansyl-specific fragmentation pathways. This combination allowed us to obtain a significant increase in signal/noise ratio and a significant increase in sensitivity of analysis, due to the reduction of duty cycle of the mass spectrometer. The unique signal obtained was correlated to peptide 1-10 of RNaseA carbonylated and labeled by dansylhydrazide. This strategy represents the first method leading to the direct identification of the carbonylation sites in proteins, thus indicating the feasibility of this strategy to investigate protein carbonylation in a proteomic approach. Copyright © 2010 John Wiley & Sons, Ltd.

Mass spectrometry allows direct identification of proteins in large genomes

DEFF Research Database (Denmark)

Küster, B; Mortensen, Peter V.; Andersen, Jens S.

2001-01-01

Proteome projects seek to provide systematic functional analysis of the genes uncovered by genome sequencing initiatives. Mass spectrometric protein identification is a key requirement in these studies but to date, database searching tools rely on the availability of protein sequences derived fro...

The Association between Total Protein and Vegetable Protein Intake and Low Muscle Mass among the Community-Dwelling Elderly Population in Northern Taiwan

Directory of Open Access Journals (Sweden)

Ru-Yi Huang

2016-06-01

Full Text Available Sarcopenia, highly linked with fall, frailty, and disease burden, is an emerging problem in aging society. Higher protein intake has been suggested to maintain nitrogen balance. Our objective was to investigate whether pre-sarcopenia status was associated with lower protein intake. A total of 327 community-dwelling elderly people were recruited for a cross-sectional study. We adopted the multivariate nutrient density model to identify associations between low muscle mass and dietary protein intake. The general linear regression models were applied to estimate skeletal muscle mass index across the quartiles of total protein and vegetable protein density. Participants with diets in the lowest quartile of total protein density (<13.2% were at a higher risk for low muscle mass (odds ratio (OR 3.03, 95% confidence interval (CI 1.37–6.72 than those with diets in the highest quartile (≥17.2%. Similarly, participants with diets in the lowest quartile of vegetable protein density (<5.8% were at a higher risk for low muscle mass (OR 2.34, 95% CI 1.14–4.83 than those with diets in the highest quartile (≥9.4%. Furthermore, the estimated skeletal muscle mass index increased significantly across the quartiles of total protein density (p = 0.023 and vegetable protein density (p = 0.025. Increasing daily intakes of total protein and vegetable protein densities appears to confer protection against pre-sarcopenia status.

reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

Science.gov (United States)

Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

2015-11-01

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website.

Identifying inter-residue resonances in crowded 2D {sup 13}C-{sup 13}C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Miao Yimin; Cross, Timothy A. [Florida State University, Department of Chemistry and Biochemistry (United States); Fu Riqiang, E-mail: rfu@magnet.fsu.edu [National High Magnet Field Lab (United States)

2013-07-15

The feasibility of using difference spectroscopy, i.e. subtraction of two correlation spectra at different mixing times, for substantially enhanced resolution in crowded two-dimensional {sup 13}C-{sup 13}C chemical shift correlation spectra is presented. With the analyses of {sup 13}C-{sup 13}C spin diffusion in simple spin systems, difference spectroscopy is proposed to partially separate the spin diffusion resonances of relatively short intra-residue distances from the longer inter-residue distances, leading to a better identification of the inter-residue resonances. Here solid-state magic-angle-spinning NMR spectra of the full length M2 protein embedded in synthetic lipid bilayers have been used to illustrate the resolution enhancement in the difference spectra. The integral membrane M2 protein of Influenza A virus assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH and is essential for the viral lifecycle. Based on known amino acid resonance assignments from amino acid specific labeled samples of truncated M2 sequences or from time-consuming 3D experiments of uniformly labeled samples, some inter-residue resonances of the full length M2 protein can be identified in the difference spectra of uniformly {sup 13}C labeled protein that are consistent with the high resolution structure of the M2 (22-62) protein (Sharma et al., Science 330(6003):509-512, 2010)

Synthesis and purification of some alkyl phenanthrenes and presentation of their infrared, ultraviolet, nuclear magnetic resonance and mass spectra

International Nuclear Information System (INIS)

Persaud, K.

1965-01-01

We have carried out the synthesis of: - phenanthrene - its five monomethyl derivatives - three dimethyl derivatives - two trimethyl derivatives. We have then purified these products as well as a certain number of others obtained from various sources. We have been able to obtain in the majority of cases, a purity of 99.5 per cent or over, these figures being obtained by low voltage mass spectrometry. Finally we have recorded the infrared, ultraviolet, nuclear magnetic resonance and mass spectra of these products for which an atlas has been drawn up. (author) [fr

Experimental search of structures in missing mass spectra of B=2, T=1 system: possible evidence for narrow states

International Nuclear Information System (INIS)

Tatischeff, B.; Combes, M.P.; Didelez, J.P.

1984-01-01

The missing mass spectra for the transfer reaction p( 3 He,d)X (B=2, T=1) have been measured at Tsub( 3 He) = 2.7 GeV. The data show: 1) a narrow structure lying on top of an important continuum, with a mass M = 2.240+-0.005 GeV and a width GAMMAsub(1/2) = .016 +- .003 GeV; 2) a large structure with centroid location close to Msub(x) approximately equal to 2.170 +- .005 GeV and width GAMMAsub(1/2) approximately .100 +- .005 Gev

Protein Glycation in Diabetes as Determined by Mass Spectrometry

Directory of Open Access Journals (Sweden)

Annunziata Lapolla

2013-01-01

Full Text Available Diabetes is a common endocrine disorder characterized by hyperglycemia leading to nonenzymatic glycation of proteins, responsible for chronic complications. The development of mass spectrometric techniques able to give highly specific and reliable results in proteome field is of wide interest for physicians, giving them new tools to monitor the disease progression and the possible complications related to diabetes, as well as the effectiveness of therapeutic treatments. This paper reports and discusses some of the data pertaining protein glycation in diabetic subjects obtained by matrix-assisted laser desorption ionization (MALDI mass spectrometry (MS. The preliminary studies carried out by in vitro protein glycation experiments show clear differences in molecular weight of glycated and unglycated proteins. Then, the attention was focused on plasma proteins human serum albumin (HSA and immunoglobulin G (IgG. Enzymatic degradation products of in vitro glycated HSA were studied in order to simulate the in vivo enzymatic digestion of glycated species by the immunological system leading to the highly reactive advanced glycation end-products (AGEs peptides. Further studies led to the evaluation of glycated Apo A-I and glycated haemoglobin levels. A different MALDI approach was employed for the identification of markers of disease in urine samples of healthy, diabetic, nephropathic, and diabetic-nephropathic subjects.

Origin of Disagreements in Tandem Mass Spectra Interpretation by Search Engines.

Science.gov (United States)

Tessier, Dominique; Lollier, Virginie; Larré, Colette; Rogniaux, Hélène

2016-10-07

Several proteomic database search engines that interpret LC-MS/MS data do not identify the same set of peptides. These disagreements occur even when the scores of the peptide-to-spectrum matches suggest good confidence in the interpretation. Our study shows that these disagreements observed for the interpretations of a given spectrum are almost exclusively due to the variation of what we call the "peptide space", i.e., the set of peptides that are actually compared to the experimental spectra. We discuss the potential difficulties of precisely defining the "peptide space." Indeed, although several parameters that are generally reported in publications can easily be set to the same values, many additional parameters-with much less straightforward user access-might impact the "peptide space" used by each program. Moreover, in a configuration where each search engine identifies the same candidates for each spectrum, the inference of the proteins may remain quite different depending on the false discovery rate selected.

Enhancing non-refractory aerosol apportionment from an urban industrial site through receptor modeling of complete high time-resolution aerosol mass spectra

Science.gov (United States)

McGuire, M. L.; Chang, R. Y.-W.; Slowik, J. G.; Jeong, C.-H.; Healy, R. M.; Lu, G.; Mihele, C.; Abbatt, J. P. D.; Brook, J. R.; Evans, G. J.

2014-08-01

Receptor modeling was performed on quadrupole unit mass resolution aerosol mass spectrometer (Q-AMS) sub-micron particulate matter (PM) chemical speciation measurements from Windsor, Ontario, an industrial city situated across the Detroit River from Detroit, Michigan. Aerosol and trace gas measurements were collected on board Environment Canada's Canadian Regional and Urban Investigation System for Environmental Research (CRUISER) mobile laboratory. Positive matrix factorization (PMF) was performed on the AMS full particle-phase mass spectrum (PMFFull MS) encompassing both organic and inorganic components. This approach compared to the more common method of analyzing only the organic mass spectra (PMFOrg MS). PMF of the full mass spectrum revealed that variability in the non-refractory sub-micron aerosol concentration and composition was best explained by six factors: an amine-containing factor (Amine); an ammonium sulfate- and oxygenated organic aerosol-containing factor (Sulfate-OA); an ammonium nitrate- and oxygenated organic aerosol-containing factor (Nitrate-OA); an ammonium chloride-containing factor (Chloride); a hydrocarbon-like organic aerosol (HOA) factor; and a moderately oxygenated organic aerosol factor (OOA). PMF of the organic mass spectrum revealed three factors of similar composition to some of those revealed through PMFFull MS: Amine, HOA and OOA. Including both the inorganic and organic mass proved to be a beneficial approach to analyzing the unit mass resolution AMS data for several reasons. First, it provided a method for potentially calculating more accurate sub-micron PM mass concentrations, particularly when unusual factors are present, in this case the Amine factor. As this method does not rely on a priori knowledge of chemical species, it circumvents the need for any adjustments to the traditional AMS species fragmentation patterns to account for atypical species, and can thus lead to more complete factor profiles. It is expected that this

Enhancing non-refractory aerosol apportionment from an urban industrial site through receptor modelling of complete high time-resolution aerosol mass spectra

Science.gov (United States)

McGuire, M. L.; Chang, R. Y.-W.; Slowik, J. G.; Jeong, C.-H.; Healy, R. M.; Lu, G.; Mihele, C.; Abbatt, J. P. D.; Brook, J. R.; Evans, G. J.

2014-02-01

Receptor modelling was performed on quadrupole unit mass resolution aerosol mass spectrometer (Q-AMS) sub-micron particulate matter (PM) chemical speciation measurements from Windsor, Ontario, an industrial city situated across the Detroit River from Detroit, Michigan. Aerosol and trace gas measurements were collected on board Environment Canada's CRUISER mobile laboratory. Positive matrix factorization (PMF) was performed on the AMS full particle-phase mass spectrum (PMFFull MS) encompassing both organic and inorganic components. This approach was compared to the more common method of analysing only the organic mass spectra (PMFOrg MS). PMF of the full mass spectrum revealed that variability in the non-refractory sub-micron aerosol concentration and composition was best explained by six factors: an amine-containing factor (Amine); an ammonium sulphate and oxygenated organic aerosol containing factor (Sulphate-OA); an ammonium nitrate and oxygenated organic aerosol containing factor (Nitrate-OA); an ammonium chloride containing factor (Chloride); a hydrocarbon-like organic aerosol (HOA) factor; and a moderately oxygenated organic aerosol factor (OOA). PMF of the organic mass spectrum revealed three factors of similar composition to some of those revealed through PMFFull MS: Amine, HOA and OOA. Including both the inorganic and organic mass proved to be a beneficial approach to analysing the unit mass resolution AMS data for several reasons. First, it provided a method for potentially calculating more accurate sub-micron PM mass concentrations, particularly when unusual factors are present, in this case, an Amine factor. As this method does not rely on a priori knowledge of chemical species, it circumvents the need for any adjustments to the traditional AMS species fragmentation patterns to account for atypical species, and can thus lead to more complete factor profiles. It is expected that this method would be even more useful for HR-ToF-AMS data, due to the ability

Identification of barley and rye varieties using matrix- assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks

DEFF Research Database (Denmark)

Bloch, H.A.; Petersen, Marianne Kjerstine; Sperotto, Maria Maddalena

2001-01-01

developed, which combines analysis of alcohol-soluble wheat proteins (gliadins) using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks. Here we have applied the same method for the identification of both barley (Hordeum vulgare L.) and rye (Secale cereale L.......) varieties. For barley, 95% of the mass spectra were correctly classified. This is an encouraging result, since in earlier experiments only a grouping into subsets of varieties was possible. However, the method was not useful in the classification of rye, due to the strong similarity between mass spectra...

Search for and study of the effective mass spectra of nucleon clusters produced in relativistic nucleon collisions

International Nuclear Information System (INIS)

Didenko, L.A.; Grishin, V.G.; Kuznetsov, A.A.

1991-01-01

The effective mass spectra of nucleon clusters, produced in p, d, He and C collisions with carbon nuclei at P=4.2xA GeV/c are studied. The results obtained show that clusters with proton multiplicity n p =2 and 3 can be interpreted as decay products of nucleon resonances with a width from a few MeV to a few tens MeV. 11 refs.; 6 figs.; 4 tabs

Sequence-specific capture of protein-DNA complexes for mass spectrometric protein identification.

Directory of Open Access Journals (Sweden)

Cheng-Hsien Wu

Full Text Available The regulation of gene transcription is fundamental to the existence of complex multicellular organisms such as humans. Although it is widely recognized that much of gene regulation is controlled by gene-specific protein-DNA interactions, there presently exists little in the way of tools to identify proteins that interact with the genome at locations of interest. We have developed a novel strategy to address this problem, which we refer to as GENECAPP, for Global ExoNuclease-based Enrichment of Chromatin-Associated Proteins for Proteomics. In this approach, formaldehyde cross-linking is employed to covalently link DNA to its associated proteins; subsequent fragmentation of the DNA, followed by exonuclease digestion, produces a single-stranded region of the DNA that enables sequence-specific hybridization capture of the protein-DNA complex on a solid support. Mass spectrometric (MS analysis of the captured proteins is then used for their identification and/or quantification. We show here the development and optimization of GENECAPP for an in vitro model system, comprised of the murine insulin-like growth factor-binding protein 1 (IGFBP1 promoter region and FoxO1, a member of the forkhead rhabdomyosarcoma (FoxO subfamily of transcription factors, which binds specifically to the IGFBP1 promoter. This novel strategy provides a powerful tool for studies of protein-DNA and protein-protein interactions.

Dietary protein and urinary nitrogen in relation to 6-year changes in fat mass and fat-free mass

DEFF Research Database (Denmark)

Ankarfeldt, Mikkel Zøllner; Gottliebsen, K; Ängquist, L

2015-01-01

Background:In contrast to the physiological expectation, observational studies show that greater protein intake is associated with subsequent body weight (BW) gain. An increase in fat-free mass (FFM) due to anabolic effects of protein could explain this.Objective:To examine associations between...... protein intake and subsequent changes in fat mass (FM) and FFM in longitudinal, observational data.Design:A health examination, including measures of FM and FFM by bioelectrical impedance at baseline and follow-up six years later, was conducted. Diet history interviews (DHI) were performed, and 24-hour...... nitrogen. Estimated from DHI, FM increased 46 gram/year with every 1 E% protein substituted for fat (95%CI: 13, 79; P=0.006) and FFM increased 15 gram/year (1, 30; P=0.046). Results were similar in other substitution models. Estimated from urinary nitrogen, FM increased 53 gram/year with 1 E% protein...

Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output.

Science.gov (United States)

Turewicz, Michael; Deutsch, Eric W

2011-01-01

This chapter describes Mass Spectrometry Markup Language (mzML), an XML-based and vendor-neutral standard data format for storage and exchange of mass spectrometer output like raw spectra and peak lists. It is intended to replace its two precursor data formats (mzData and mzXML), which had been developed independently a few years earlier. Hence, with the release of mzML, the problem of having two different formats for the same purposes is solved, and with it the duplicated effort of maintaining and supporting two data formats. The new format has been developed by a broad-based consortium of major instrument vendors, software vendors, and academic researchers under the aegis of the Human Proteome Organisation (HUPO), Proteomics Standards Initiative (PSI), with full participation of the main developers of the precursor formats. This comprehensive approach helped mzML to become a generally accepted standard. Furthermore, the collaborative development insured that mzML has adopted the best features of its precursor formats. In this chapter, we discuss mzML's development history, its design principles and use cases, as well as its main building components. We also present the available documentation, an example file, and validation software for mzML.

Computational methods for protein identification from mass spectrometry data.

Directory of Open Access Journals (Sweden)

Leo McHugh

2008-02-01

Full Text Available Protein identification using mass spectrometry is an indispensable computational tool in the life sciences. A dramatic increase in the use of proteomic strategies to understand the biology of living systems generates an ongoing need for more effective, efficient, and accurate computational methods for protein identification. A wide range of computational methods, each with various implementations, are available to complement different proteomic approaches. A solid knowledge of the range of algorithms available and, more critically, the accuracy and effectiveness of these techniques is essential to ensure as many of the proteins as possible, within any particular experiment, are correctly identified. Here, we undertake a systematic review of the currently available methods and algorithms for interpreting, managing, and analyzing biological data associated with protein identification. We summarize the advances in computational solutions as they have responded to corresponding advances in mass spectrometry hardware. The evolution of scoring algorithms and metrics for automated protein identification are also discussed with a focus on the relative performance of different techniques. We also consider the relative advantages and limitations of different techniques in particular biological contexts. Finally, we present our perspective on future developments in the area of computational protein identification by considering the most recent literature on new and promising approaches to the problem as well as identifying areas yet to be explored and the potential application of methods from other areas of computational biology.

Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling.

Science.gov (United States)

Politis, Argyris; Schmidt, Carla

2018-03-20

Structural mass spectrometry with its various techniques is a powerful tool for the structural elucidation of medically relevant protein assemblies. It delivers information on the composition, stoichiometries, interactions and topologies of these assemblies. Most importantly it can deal with heterogeneous mixtures and assemblies which makes it universal among the conventional structural techniques. In this review we summarise recent advances and challenges in structural mass spectrometric techniques. We describe how the combination of the different mass spectrometry-based methods with computational strategies enable structural models at molecular levels of resolution. These models hold significant potential for helping us in characterizing the function of protein assemblies related to human health and disease. In this review we summarise the techniques of structural mass spectrometry often applied when studying protein-ligand complexes. We exemplify these techniques through recent examples from literature that helped in the understanding of medically relevant protein assemblies. We further provide a detailed introduction into various computational approaches that can be integrated with these mass spectrometric techniques. Last but not least we discuss case studies that integrated mass spectrometry and computational modelling approaches and yielded models of medically important protein assembly states such as fibrils and amyloids. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Scikit-spectra: Explorative Spectroscopy in Python

Directory of Open Access Journals (Sweden)

Adam Hughes

2015-06-01

Full Text Available Scikit-spectra is an intuitive framework for explorative spectroscopy in Python. Scikit-spectra leverages the Pandas library for powerful data processing to provide datastructures and an API designed for spectroscopy. Utilizing the new IPython Notebook widget system, scikit-spectra is headed towards a GUI when you want it, API when you need it approach to spectral analysis. As an application, analysis is presented of the surface-plasmon resonance shift in a solution of gold nanoparticles induced by proteins binding to the gold’s surface. Please refer to the scikit-spectra website for full documentation and support: http://hugadams.github.io/scikit-spectra/

Detection of intact megadalton protein assemblies of vanillyl-alcohol oxidase by mass spectrometry

NARCIS (Netherlands)

Berkel, van W.J.H.; Heuvel, van den R.H.H.; Versluis, C.; Heck, A.

2000-01-01

Well-resolved ion signals of intact large protein assemblies, with molecular masses extending above one million Dalton, have been detected and mass analyzed using electrospray ionization mass spectrometry, with an uncertainty in mass of <0.2&Eth;The mass spectral data seem to reflect known

Effects of drift gas on collision cross sections of a protein standard in linear drift tube and traveling wave ion mobility mass spectrometry.

Science.gov (United States)

Jurneczko, Ewa; Kalapothakis, Jason; Campuzano, Iain D G; Morris, Michael; Barran, Perdita E

2012-10-16

There has been a significant increase in the use of ion mobility mass spectrometry (IM-MS) to investigate conformations of proteins and protein complexes following electrospray ionization. Investigations which employ traveling wave ion mobility mass spectrometry (TW IM-MS) instrumentation rely on the use of calibrants to convert the arrival times of ions to collision cross sections (CCS) providing "hard numbers" of use to structural biology. It is common to use nitrogen as the buffer gas in TW IM-MS instruments and to calibrate by extrapolating from CCS measured in helium via drift tube (DT) IM-MS. In this work, both DT and TW IM-MS instruments are used to investigate the effects of different drift gases (helium, neon, nitrogen, and argon) on the transport of multiply charged ions of the protein myoglobin, frequently used as a standard in TW IM-MS studies. Irrespective of the drift gas used, recorded mass spectra are found to be highly similar. In contrast, the recorded arrival time distributions and the derived CCS differ greatly. At low charge states (7 ≤ z ≤ 11) where the protein is compact, the CCS scale with the polarizability of the gas; this is also the case for higher charge states (12 ≤ z ≤ 22) where the protein is more unfolded for the heavy gases (neon, argon, and nitrogen) but not the case for helium. This is here interpreted as a different conformational landscape being sampled by the lighter gas and potentially attributable to increased field heating by helium. Under nanoelectrospray ionization (nESI) conditions, where myoglobin is sprayed from an aqueous solution buffered to pH 6.8 with 20 mM ammonium acetate, in the DT IM-MS instrument, each buffer gas can yield a different arrival time distribution (ATD) for any given charge state.

Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

Science.gov (United States)

Trinkle-Mulcahy, Laura; Boulon, Séverine; Lam, Yun Wah; Urcia, Roby; Boisvert, François-Michel; Vandermoere, Franck; Morrice, Nick A.; Swift, Sam; Rothbauer, Ulrich; Leonhardt, Heinrich; Lamond, Angus

2008-01-01

The identification of interaction partners in protein complexes is a major goal in cell biology. Here we present a reliable affinity purification strategy to identify specific interactors that combines quantitative SILAC-based mass spectrometry with characterization of common contaminants binding to affinity matrices (bead proteomes). This strategy can be applied to affinity purification of either tagged fusion protein complexes or endogenous protein complexes, illustrated here using the well-characterized SMN complex as a model. GFP is used as the tag of choice because it shows minimal nonspecific binding to mammalian cell proteins, can be quantitatively depleted from cell extracts, and allows the integration of biochemical protein interaction data with in vivo measurements using fluorescence microscopy. Proteins binding nonspecifically to the most commonly used affinity matrices were determined using quantitative mass spectrometry, revealing important differences that affect experimental design. These data provide a specificity filter to distinguish specific protein binding partners in both quantitative and nonquantitative pull-down and immunoprecipitation experiments. PMID:18936248

Surface-Induced Dissociation of Protein Complexes in a Hybrid Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

Energy Technology Data Exchange (ETDEWEB)

Yan, Jing; Zhou, Mowei; Gilbert, Joshua D.; Wolff, Jeremy J.; Somogyi, Árpád; Pedder, Randall E.; Quintyn, Royston S.; Morrison, Lindsay J.; Easterling, Michael L.; Paša-Tolić, Ljiljana; Wysocki, Vicki H.

2017-01-03

Mass spectrometry continues to develop as a valuable tool in the analysis of proteins and protein complexes. In protein complex mass spectrometry studies, surface-induced dissociation (SID) has been successfully applied in quadrupole time-of-flight (Q-TOF) instruments. SID provides structural information on non-covalent protein complexes that is complementary to other techniques. However, the mass resolution of Q-TOF instruments can limit the information that can be obtained for protein complexes by SID. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provides ultrahigh resolution and ultrahigh mass accuracy measurements. In this study, an SID device was designed and successfully installed in a hybrid FT-ICR instrument in place of the standard gas collision cell. The SID-FT-ICR platform has been tested with several protein complex systems (homooligomers, a heterooligomer, and a protein-ligand complex, ranging from 53 kDa to 85 kDa), and the results are consistent with data previously acquired on Q-TOF platforms, matching predictions from known protein interface information. SID fragments with the same m/z but different charge states are well-resolved based on distinct spacing between adjacent isotope peaks, and the addition of metal cations and ligands can also be isotopically resolved with the ultrahigh mass resolution available in FT-ICR.

Integrative Mass Spectrometry Approaches to Monitor Protein Structures, Modifications, and Interactions

NARCIS (Netherlands)

Lössl, P.

2017-01-01

This thesis illustrates the current standing of mass spectrometry (MS) in molecular and structural biology. The primary aim of the herein described research is to facilitate protein characterization by combining mass spectrometric methods among each other and with complementary analytical

Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.

Science.gov (United States)

Chamrad, Daniel C; Körting, Gerhard; Schäfer, Heike; Stephan, Christian; Thiele, Herbert; Apweiler, Rolf; Meyer, Helmut E; Marcus, Katrin; Blüggel, Martin

2006-09-01

A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM-Explorer was evaluated on excellently manually characterized and evaluated LC-MS/MS data sets from Alpha-A-Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.

Functional proteomics with new mass spectrometric and bioinformatics tools

International Nuclear Information System (INIS)

Kesners, P.W.A.

2001-01-01

A comprehensive range of mass spectrometric tools is required to investigate todays life science applications and a strong focus is on addressing the needs of functional proteomics. Application examples are given showing the streamlined process of protein identification from low femtomole amounts of digests. Sample preparation is achieved with a convertible robot for automated 2D gel picking, and MALDI target dispensing. MALDI-TOF or ESI-MS subsequent to enzymatic digestion. A choice of mass spectrometers including Q-q-TOF with multipass capability, MALDI-MS/MS with unsegmented PSD, Ion Trap and FT-MS are discussed for their respective strengths and applications. Bioinformatics software that allows both database work and novel peptide mass spectra interpretation is reviewed. The automated database searching uses either entire digest LC-MS n ESI Ion Trap data or MALDI MS and MS/MS spectra. It is shown how post translational modifications are interactively uncovered and de-novo sequencing of peptides is facilitated

Deconvolution of mixture spectra and increased throughput of Peptide identification by utilization of intensified complementary ions formed in tandem mass spectrometry

DEFF Research Database (Denmark)

Kryuchkov, Fedor; Verano-Braga, Thiago; Hansen, Thomas Aarup

2013-01-01

-resolution orbitrap mass spectrometry, an increase in the number of peptide identifications was obtained relative to the original CAD MS/MS spectra when intensified golden complementary (+18.6%) and CAD complementary pairs (+17.2%) were submitted to the Mascot search engine. This also exceeded the results obtained...

reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

Science.gov (United States)

Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W; Moritz, Robert L

2015-11-01

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. Graphical Abstract ᅟ.

Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

International Nuclear Information System (INIS)

Bellstedt, Peter; Herbst, Christian; Häfner, Sabine; Leppert, Jörg; Görlach, Matthias; Ramachandran, Ramadurai

2012-01-01

We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC′C and 3D C′NCA with sequential 13 C acquisitions, 3D NHH and 3D NC′H with sequential 1 H acquisitions and 3D CANH and 3D C’NH with broadband 13 C– 15 N mixing are demonstrated using microcrystalline samples of the β1 immunoglobulin binding domain of protein G (GB1) and the chicken α-spectrin SH3 domain.

Reactions and mass spectra of complex particles using Aerosol CIMS

Science.gov (United States)

Hearn, John D.; Smith, Geoffrey D.

2006-12-01

Aerosol chemical ionization mass spectrometry (CIMS) is used both on- and off-line for the analysis of complex laboratory-generated and ambient particles. One of the primary advantages of Aerosol CIMS is the low degree of ion fragmentation, making this technique well suited for investigating the reactivity of complex particles. To demonstrate the usefulness of this "soft" ionization, particles generated from meat cooking were reacted with ozone and the composition was monitored as a function of reaction time. Two distinct kinetic regimes were observed with most of the oleic acid in these particles reacting quickly but with 30% appearing to be trapped in the complex mixture. Additionally, detection limits are measured to be sufficiently low (100-200 ng/m3) to detect some of the more abundant constituents in ambient particles, including sulfate, which is measured in real-time at 1.2 [mu]g/m3. To better characterize complex aerosols from a variety of sources, a novel off-line collection method was also developed in which non-volatile and semi-volatile organics are desorbed from particles and concentrated in a cold U-tube. Desorption from the U-tube followed by analysis with Aerosol CIMS revealed significant amounts of nicotine in cigarette smoke and levoglucosan in oak and pine smoke, suggesting that this may be a useful technique for monitoring particle tracer species. Additionally, secondary organic aerosol formed from the reaction of ozone with R-limonene and volatile organics from orange peel were analyzed off-line showing large molecular weight products (m/z > 300 amu) that may indicate the formation of oligomers. Finally, mass spectra of ambient aerosol collected offline reveal a complex mixture of what appears to be highly processed organics, some of which may contain nitrogen.

Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation

Science.gov (United States)

Riley, Nicholas M.; Westphall, Michael S.; Coon, Joshua J.

2018-01-01

The analysis of intact proteins via mass spectrometry can offer several benefits to proteome characterization, although the majority of top-down experiments focus on proteoforms in a relatively low mass range (AI-ETD) to proteins in the 30-70 kDa range. AI-ETD leverages infrared photo-activation concurrent to ETD reactions to improve sequence-informative product ion generation. This method generates more product ions and greater sequence coverage than conventional ETD, higher-energy collisional dissociation (HCD), and ETD combined with supplemental HCD activation (EThcD). Importantly, AI-ETD provides the most thorough protein characterization for every precursor ion charge state investigated in this study, making it suitable as a universal fragmentation method in top-down experiments. Additionally, we highlight several acquisition strategies that can benefit characterization of larger proteins with AI-ETD, including combination of spectra from multiple ETD reaction times for a given precursor ion, multiple spectral acquisitions of the same precursor ion, and combination of spectra from two different dissociation methods (e.g., AI-ETD and HCD). In all, AI-ETD shows great promise as a method for dissociating larger intact protein ions as top-down proteomics continues to advance into larger mass ranges. [Figure not available: see fulltext.

Getting to the core of protein pharmaceuticals – comprehensive structure analysis by mass spectrometry

DEFF Research Database (Denmark)

Leurs, Ulrike; Mistarz, Ulrik Hvid; Rand, Kasper Dyrberg

2015-01-01

. Mass spectrometry has evolved as a powerful tool for the characterization of both primary and higher order structures of protein pharmaceuticals. Furthermore, the chemical and physical stability of protein drugs, as well as their pharmacokinetics are nowadays routinely determined by mass spectrometry...

Desalting Protein Ions in Native Mass Spectrometry Using Supercharging Reagents

Science.gov (United States)

Cassou, Catherine A.; Williams, Evan R.

2014-01-01

Effects of the supercharging reagents m-NBA and sulfolane on sodium ion adduction to protein ions formed using native mass spectrometry were investigated. There is extensive sodium adduction on protein ions formed by electrospray ionization from aqueous solutions containing millimolar concentrations of NaCl, which can lower sensitivity by distributing the signal of a given charge state over multiple adducted ions and can reduce mass measuring accuracy for large proteins and non-covalent complexes for which individual adducts cannot be resolved. The average number of sodium ions adducted to the most abundant ion formed from ten small (8.6–29 kDa) proteins for which adducts can be resolved is reduced by 58% or 80% on average, respectively, when 1.5% m-NBA or 2.5% sulfolane are added to aqueous solutions containing sodium compared to without the supercharging reagent. Sulfolane is more effective than m-NBA at reducing sodium ion adduction and at preserving non-covalent protein-ligand and protein-protein interactions. Desalting with 2.5% sulfolane enables detection of several glycosylated forms of 79.7 kDa holo-transferrin and NADH bound to the 146 kDa homotetramer LDH, which are otherwise unresolved due to peak broadening from extensive sodium adduction. Although sulfolane is more effective than m-NBA at protein ion desalting, m-NBA reduces salt clusters at high m/z and can increase the signal-to-noise ratios of protein ions by reducing chemical noise. Desalting is likely a result of these supercharging reagents binding sodium ions in solution, thereby reducing the sodium available to adduct to protein ions. PMID:25133273

A hybrid approach to protein differential expression in mass spectrometry-based proteomics

KAUST Repository

Wang, X.; Anderson, G. A.; Smith, R. D.; Dabney, A. R.

2012-01-01

MOTIVATION: Quantitative mass spectrometry-based proteomics involves statistical inference on protein abundance, based on the intensities of each protein's associated spectral peaks. However, typical MS-based proteomics datasets have substantial

Weak cation exchange magnetic beads coupled with matrix-assisted laser desorption ionization-time of flight-mass spectrometry in screening serum protein markers in osteopenia.

Science.gov (United States)

He, Wei-Tao; Liang, Bo-Cheng; Shi, Zhen-Yu; Li, Xu-Yun; Li, Chun-Wen; Shi, Xiao-Lin

2016-01-01

The present study aimed at investigating the weak cation magnetic separation technology and matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) in screening serum protein markers of osteopenia from ten postmenopausal women and ten postmenopausal women without osteopenia as control group, to find a new method for screening biomarkers and establishing a diagnostic model for primary type I osteoporosis. Serum samples were collected from postmenopausal women with osteopenia and postmenopausal women with normal bone mass. Proteins were extracted from serum samples by weak cation exchange magnetic beads technology, and mass spectra acquisition was done by MALDI-TOF-MS. The visualization and comparison of data sets, statistical peak evaluation, model recognition, and discovery of biomarker candidates were handled by the proteinchip data analysis system software(ZJU-PDAS). The diagnostic models were established using genetic arithmetic based support vector machine (SVM). The SVM result with the highest Youden Index was selected as the model. Combinatorial Peaks having the highest accuracy in distinguishing different samples were selected as potential biomarker. From the two group serum samples, a total of 133 differential features were selected. Ten features with significant intensity differences were screened. In the pair-wise comparisons, processing of MALDI-TOF spectra resulted in the identification of ten differential features between postmenopausal women with osteopenia and postmenopausal women with normal bone mass. The difference of features by Youden index showed that the highest features had a mass to charge ratio of 1699 and 3038 Da. A diagnosis model was established with these two peaks as the candidate marker, and the specificity of the model is 100 %, the sensitivity was 90 % by leave-one-out cross validation test. The two groups of specimens in SVM results on the scatter plot could be clearly distinguished. The peak

Mining the human tissue proteome for protein citrullination.

Science.gov (United States)

Lee, Chien-Yun; Wang, Dongxue; Wilhelm, Mathias; Zolg, Daniel Paul; Schmidt, Tobias; Schnatbaum, Karsten; Reimer, Ulf; Pontén, Fredrik; Uhlén, Mathias; Hahne, Hannes; Kuster, Bernhard

2018-04-02

Citrullination is a post-translational modification of arginine catalyzed by five peptidylarginine deiminases (PADs) in humans. The loss of a positive charge may cause structural or functional alterations and while the modification has been linked to several diseases including rheumatoid arthritis and cancer, its physiological or pathophysiological roles remain largely unclear. In part this is owing to limitations in available methodology able to robustly enrich, detect and localize the modification. As a result, only few citrullination sites have been identified on human proteins with high confidence. In this study, we mined data from mass spectrometry-based deep proteomic profiling of 30 human tissues to identify citrullination sites on endogenous proteins. Database searching of ~70 million tandem mass spectra yielded ~13,000 candidate spectra which were further triaged by spectrum quality metrics and the detection of the specific neutral loss of isocyanic acid from citrullinated peptides to reduce false positives. Because citrullination is easily confused with deamidation, we synthetized ~2,200 citrullinated and 1,300 deamidated peptides to build a library of reference spectra. This led to the validation of 375 citrullination sites on 209 human proteins. Further analysis showed that >80% of the identified modifications sites were new and for 56% of the proteins, citrullination was detected for the first time. Sequence motif analysis revealed a strong preference for Asp and Gly, residues around the citrullination site. Interestingly, while the modification was detected in 26 human tissues with the highest levels found in brain and lung, citrullination levels did not correlate well with protein expression of the PAD enzymes. Even though the current work represents the largest survey of protein citrullination to date, the modification was mostly detected on high abundant proteins arguing that the development of specific enrichment methods would be required in order

Diffusive transfer to membranes as an effective interface between gel electrophoresis and mass spectrometry

Science.gov (United States)

Ogorzalek Loo, Rachel R.; Mitchell, Charles; Stevenson, Tracy I.; Loo, Joseph A.; Andrews, Philip C.

1997-12-01

Diffusive transfer was examined as a blotting method to transfer proteins from polyacrylamide gels to membranes for ultraviolet matrix-assisted laser desorption ionization (MALDI) mass spectrometry. The method is well-suited for transfers from isoelectric focusing (IEF) gels. Spectra have been obtained for 11 pmol of 66 kDa albumin loaded onto an IEF gel and subsequently blotted to polyethylene. Similarly, masses of intact carbonic anhydrase and hemoglobin were obtained from 14 and 20 pmol loadings. This methodology is also compatible with blotting high molecular weight proteins, as seen for 6 pmol of the 150 kDa monoclonal antibody anti-[beta]-galactosidase transferred to Goretex. Polypropylene, Teflon, Nafion and polyvinylidene difluoride (PVDF) also produced good spectra following diffusive transfer. Only analysis from PVDF required that the membrane be kept wet prior to application of matrix. Considerations in mass accuracy for analysis from large-area membranes with continuous extraction and delayed extraction were explored, as were remedies for surface charging. Vapor phase CNBr cleavage was applied to membrane-bound samples for peptide mapping.

Synthesis of nanoparticles in helium droplets—A characterization comparing mass-spectra and electron microscopy data

International Nuclear Information System (INIS)

Thaler, Philipp; Volk, Alexander; Lackner, Florian; Steurer, Johannes; Schnedlitz, Martin; Ernst, Wolfgang E.; Knez, Daniel; Haberfehlner, Georg

2015-01-01

Micrometer sized helium droplets provide an extraordinary environment for the growth of nanoparticles. The method promises great potential for the preparation of core-shell particles as well as one-dimensional nanostructures, which agglomerate along quantum vortices, without involving solvents, ligands, or additives. Using a new apparatus, which enables us to record mass spectra of heavy dopant clusters (>10 4 amu) and to produce samples for transmission electron microscopy simultaneously, we synthesize bare and bimetallic nanoparticles consisting of various materials (Au, Ni, Cr, and Ag). We present a systematical study of the growth process of clusters and nanoparticles inside the helium droplets, which can be described with a simple theoretical model

Synthesis of nanoparticles in helium droplets—A characterization comparing mass-spectra and electron microscopy data

Energy Technology Data Exchange (ETDEWEB)

Thaler, Philipp; Volk, Alexander; Lackner, Florian; Steurer, Johannes; Schnedlitz, Martin; Ernst, Wolfgang E., E-mail: wolfgang.ernst@tugraz.at [Institute of Experimental Physics, Graz University of Technology, Petersgasse 16, A-8010 Graz (Austria); Knez, Daniel; Haberfehlner, Georg [Institute for Electron Microscopy and Nanoanalysis & Graz Centre for Electron Microscopy, TU Graz, Steyrergasse 17, A-8010 Graz (Austria)

2015-10-07

Micrometer sized helium droplets provide an extraordinary environment for the growth of nanoparticles. The method promises great potential for the preparation of core-shell particles as well as one-dimensional nanostructures, which agglomerate along quantum vortices, without involving solvents, ligands, or additives. Using a new apparatus, which enables us to record mass spectra of heavy dopant clusters (>10{sup 4} amu) and to produce samples for transmission electron microscopy simultaneously, we synthesize bare and bimetallic nanoparticles consisting of various materials (Au, Ni, Cr, and Ag). We present a systematical study of the growth process of clusters and nanoparticles inside the helium droplets, which can be described with a simple theoretical model.

Imaging mass spectrometry in papillary thyroid carcinoma for the identification and validation of biomarker proteins.

Science.gov (United States)

Min, Kyueng-Whan; Bang, Joo-Young; Kim, Kwang Pyo; Kim, Wan-Seop; Lee, Sang Hwa; Shanta, Selina Rahman; Lee, Jeong Hwa; Hong, Ji Hye; Lim, So Dug; Yoo, Young-Bum; Na, Chan-Hyun

2014-07-01

Direct tissue imaging mass spectrometry (IMS) by matrix-assisted laser desorption ionization and time-of-flight (MALDI-TOF) mass spectrometry has become increasingly important in biology and medicine, because this technology can detect the relative abundance and spatial distribution of interesting proteins in tissues. Five thyroid cancer samples, along with normal tissue, were sliced and transferred onto conductive glass slides. After laser scanning by MALDI-TOF equipped with a smart beam laser, images were created for individual masses and proteins were classified at 200-µm spatial resolution. Based on the spatial distribution, region-specific proteins on a tumor lesion could be identified by protein extraction from tumor tissue and analysis using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Using all the spectral data at each spot, various intensities of a specific peak were detected in the tumor and normal regions of the thyroid. Differences in the molecular weights of expressed proteins between tumor and normal regions were analyzed using unsupervised and supervised clustering. To verify the presence of discovered proteins through IMS, we identified ribosomal protein P2, which is specific for cancer. We have demonstrated the feasibility of IMS as a useful tool for the analysis of tissue sections, and identified the tumor-specific protein ribosomal protein P2.

On-target digestion of collected bacteria for MALDI mass spectrometry.

Science.gov (United States)

Dugas, Alton J; Murray, Kermit K

2008-10-03

An on-target protein digestion system was developed for the identification of microorganisms in collected bioaerosols using off-line matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Bacteria analysis techniques based on MALDI-MS were adapted for use with an orthogonal MALDI quadrupole-time-of-flight mass spectrometer. Bioaerosols were generated using a pneumatic nebulizer and infused into a chamber for sampling. An Andersen N6 single-stage impactor was used to collect the bioaerosols on a MALDI target. On-target digestion was carried out inside temporary mini-wells placed over the impacted samples. The wells served as miniature reactors for proteolysis. Collected test aerosol particles containing the protein cytochrome c and E. coli bacteria were proteolyzed in situ using trypsin or cyanogen bromide. A total of 19 unique proteins were identified for E. coli. Using the TOF-MS spectra of the digested samples, peptide mass mapping was performed using the MASCOT search engine and an iterative search technique.

Study of the transverse mass spectra of strange particles in Pb-Pb collisions at 158 A GeV/c

Czech Academy of Sciences Publication Activity Database

Antinori, F.; Bacon, P. A.; Badala, A.; Staroba, Pavel; Závada, Petr

2004-01-01

Roč. 30, - (2004), s. 823-840 ISSN 0954-3899 R&D Projects: GA AV ČR KSK1048102 Keywords : NA57 experiment * K o s, .XI. and .OMEGA. hyperons * Pb-Pb collisions at 158 A GeV/c * ultrarelativistic heavy-ion collisions * transverse mass spectra * excited nuclear matter * phase transition Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 1.533, year: 2004

Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

Science.gov (United States)

Muth, Thilo; Rapp, Erdmann; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

2016-01-01

Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.

Ultrananocrystalline Diamond Membranes for Detection of High-Mass Proteins

Science.gov (United States)

Kim, H.; Park, J.; Aksamija, Z.; Arbulu, M.; Blick, R. H.

2016-12-01

Mechanical resonators realized on the nanoscale by now offer applications in mass sensing of biomolecules with extraordinary sensitivity. The general idea is that perfect mechanical mass sensors should be of extremely small size to achieve zepto- or yoctogram sensitivity in weighing single molecules similar to a classical scale. However, the small effective size and long response time for weighing biomolecules with a cantilever restricts their usefulness as a high-throughput method. Commercial mass spectrometry (MS), on the other hand, such as electrospray ionization and matrix-assisted laser desorption and ionization (MALDI) time of flight (TOF) and their charge-amplifying detectors are the gold standards to which nanomechanical resonators have to live up to. These two methods rely on the ionization and acceleration of biomolecules and the following ion detection after a mass selection step, such as TOF. The principle we describe here for ion detection is based on the conversion of kinetic energy of the biomolecules into thermal excitation of chemical vapor deposition diamond nanomembranes via phonons followed by phonon-mediated detection via field emission of thermally emitted electrons. We fabricate ultrathin diamond membranes with large lateral dimensions for MALDI TOF MS of high-mass proteins. These diamond membranes are realized by straightforward etching methods based on semiconductor processing. With a minimal thickness of 100 nm and cross sections of up to 400 ×400 μ m2 , the membranes offer extreme aspect ratios. Ion detection is demonstrated in MALDI TOF analysis over a broad range from insulin to albumin. The resulting data in detection show much enhanced resolution as compared to existing detectors, which can offer better sensitivity and overall performance in resolving protein masses.

Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

Energy Technology Data Exchange (ETDEWEB)

Bellstedt, Peter [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Haefner, Sabine; Leppert, Joerg; Goerlach, Matthias; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany)

2012-12-15

We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC Prime C and 3D C Prime NCA with sequential {sup 13}C acquisitions, 3D NHH and 3D NC Prime H with sequential {sup 1}H acquisitions and 3D CANH and 3D C'NH with broadband {sup 13}C-{sup 15}N mixing are demonstrated using microcrystalline samples of the {beta}1 immunoglobulin binding domain of protein G (GB1) and the chicken {alpha}-spectrin SH3 domain.

Quantifying biological samples using Linear Poisson Independent Component Analysis for MALDI-ToF mass spectra

Science.gov (United States)

Deepaisarn, S; Tar, P D; Thacker, N A; Seepujak, A; McMahon, A W

2018-01-01

Abstract Motivation Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI) facilitates the analysis of large organic molecules. However, the complexity of biological samples and MALDI data acquisition leads to high levels of variation, making reliable quantification of samples difficult. We present a new analysis approach that we believe is well-suited to the properties of MALDI mass spectra, based upon an Independent Component Analysis derived for Poisson sampled data. Simple analyses have been limited to studying small numbers of mass peaks, via peak ratios, which is known to be inefficient. Conventional PCA and ICA methods have also been applied, which extract correlations between any number of peaks, but we argue makes inappropriate assumptions regarding data noise, i.e. uniform and Gaussian. Results We provide evidence that the Gaussian assumption is incorrect, motivating the need for our Poisson approach. The method is demonstrated by making proportion measurements from lipid-rich binary mixtures of lamb brain and liver, and also goat and cow milk. These allow our measurements and error predictions to be compared to ground truth. Availability and implementation Software is available via the open source image analysis system TINA Vision, www.tina-vision.net. Contact paul.tar@manchester.ac.uk Supplementary information Supplementary data are available at Bioinformatics online. PMID:29091994

A Higgs at 125.1 GeV and baryon mass spectra derived from a Common U(3) Lie group framework

DEFF Research Database (Denmark)

Trinhammer, Ole; Bohr, Henrik; Jensen, Mogens O Stibius

2015-01-01

Baryons are described by a Hamiltonian on an intrinsic U(3) Lie group configuration space with electroweak degrees of freedom originating in specific Bloch wave factors. By opening the Bloch degrees of freedom pairwise via a U(2) Higgs mechanism, the strong and electroweak energy scales become...... related to yield the Higgs mass 125.085+/-0.017 GeV and the usual gauge boson masses. From the same Hamiltonian we derive both the relative neutron to proton mass ratio and the N and Delta mass spectra. All compare rather well with the experimental values. We predict neutral flavour baryon singlets...... to be sought for in negative pions scattering on protons or in photoproduction on neutrons and in invariant mass like Σ+c(2455)D- from various decays above the open charm threshold, e.g. at 4499, 4652 and 4723 MeV. The fundamental predictions are based on just one length scale and the fine structure coupling...

MALDI FTICR IMS of Intact Proteins: Using Mass Accuracy to Link Protein Images with Proteomics Data

Science.gov (United States)

Spraggins, Jeffrey M.; Rizzo, David G.; Moore, Jessica L.; Rose, Kristie L.; Hammer, Neal D.; Skaar, Eric P.; Caprioli, Richard M.

2015-06-01

MALDI imaging mass spectrometry is a highly sensitive and selective tool used to visualize biomolecules in tissue. However, identification of detected proteins remains a difficult task. Indirect identification strategies have been limited by insufficient mass accuracy to confidently link ion images to proteomics data. Here, we demonstrate the capabilities of MALDI FTICR MS for imaging intact proteins. MALDI FTICR IMS provides an unprecedented combination of mass resolving power (~75,000 at m/z 5000) and accuracy (differentiate a series of oxidation products of S100A8 ( m/z 10,164.03, -2.1ppm), a subunit of the heterodimer calprotectin, in kidney tissue from mice infected with Staphylococcus aureus. S100A8 - M37O/C42O3 ( m/z 10228.00, -2.6ppm) was found to co-localize with bacterial microcolonies at the center of infectious foci. The ability of MALDI FTICR IMS to distinguish S100A8 modifications is critical to understanding calprotectin's roll in nutritional immunity.

Mass spectrometric identification of isoforms of PR proteins in xylem sap of fungus-infected tomato

NARCIS (Netherlands)

Rep, Martijn; Dekker, Henk L.; Vossen, Jack H.; de Boer, Albert D.; Houterman, Petra M.; Speijer, Dave; Back, Jaap W.; de Koster, Chris G.; Cornelissen, Ben J. C.

2002-01-01

The protein content of tomato (Lycopersicon esculentum) xylem sap was found to change dramatically upon infection with the vascular wilt fungus Fusarium oxysporum. Peptide mass fingerprinting and mass spectrometric sequencing were used to identify the most abundant proteins appearing during

Mass spectrometric protein characterization in proteome analysis using GELoader tip micro-columns packed with various chromatographic material

International Nuclear Information System (INIS)

Larsen, M.R.

2001-01-01

In the early 90'ies mass spectrometry (MS) was introduced as a tool for identifying proteins in protein sequence databases. Since then it has become an integrated tool in protein characterization and is today routinely used to identify proteins separated by gel electrophoresis. A two-tiered mass spectrometric protein identification strategy has recently been proposed. In the first strategy peptide mass maps obtained from the protein of interest are compared with theoretically derived peptide mass maps from proteins in protein sequence databases. If the protein cannot be identified by this strategy, tandem mass spectrometric sequencing is used to generate enough sequence data to identify the protein in protein sequence databases or expressed sequence tag (EST) databases. However, the above strategies primarily identify a protein relatively to the DNA sequence, in which no information about e.g. post-translational modifications (PTMs) is stored. PTMs are known to modify the function, location, solubility and activity of proteins in the cell, and they are therefore very important for understanding living cells. More than 200 different PTMs are known, of which glycosylation, phosphorylation and proteolytic processing are the most common ones. Mass spectrometric analysis of PTMs on gel-separated proteins requires a higher amount of protein than for identification only. In addition, higher sequence coverage from the peptide mass maps or pre-purification of the modified peptides prior to MS analysis, is necessary for detection of putative modified peptides. In this study a multi-tiered strategy, in which GELoader tip micro-columns packed with increasingly more hydrophobic chromatographic material are used in combination with mass spectrometry, is described. The ultimate aim was to gain increased sequence coverage from peptide mixtures derived from gel-separated proteins, in order to locate modified peptides. Graphite powder is described as an alternative to traditional

Detection of high molecular weight proteins by MALDI imaging mass spectrometry.

Science.gov (United States)

Mainini, Veronica; Bovo, Giorgio; Chinello, Clizia; Gianazza, Erica; Grasso, Marco; Cattoretti, Giorgio; Magni, Fulvio

2013-06-01

MALDI imaging mass spectrometry (IMS) is a unique technology to explore the spatial distribution of biomolecules directly on tissues. It allows the in situ investigation of a large number of small proteins and peptides. Detection of high molecular weight proteins through MALDI IMS still represents an important challenge, as it would allow the direct investigation of the distribution of more proteins involved in biological processes, such as cytokines, enzymes, neuropeptide precursors and receptors. In this work we compare the traditional method performed with sinapinic acid with a comparable protocol using ferulic acid as the matrix. Data show a remarkable increase of signal acquisition in the mass range of 20k to 150k Th. Moreover, we report molecular images of biomolecules above 70k Th, demonstrating the possibility of expanding the application of this technology both in clinical investigations and basic science.

Plasma cholesteryl ester transfer protein mass and phospholipid transfer protein activity are associated with leptin in type 2 diabetes mellitus

NARCIS (Netherlands)

Dullaart, R. P. F.; de Vries, R.; Dallinga-Thie, G. M.; van Tol, A.; Sluiter, W. J.

Adipose tissue contributes to plasma levels of lipid transfer proteins and is also the major source of plasma adipokines. We hypothesized that plasma cholesteryl ester transfer protein (CETP) mass, phospholipid transfer protein (PLTP) activity and cholesteryl ester transfer (CET, a measure of CETP

Mass Spectrometry of Intact Proteins Reveals +98 u Chemical Artifacts Following Precipitation in Acetone.

Science.gov (United States)

Güray, Melda Z; Zheng, Shi; Doucette, Alan A

2017-02-03

Protein precipitation in acetone is frequently employed ahead of mass spectrometry for sample preconcentration and purification. Unfortunately, acetone is not chemically inert; mass artifacts have previously been observed on glycine-containing peptides when exposed to acetone under acidic conditions. We herein report a distinct chemical modification occurring at the level of intact proteins when incubated in acetone. This artifact manifests as one or more satellite peaks in the MS spectrum of intact protein, spaced 98 u above the mass of the unmodified protein. Other artifacts (+84, +112 u) also appear upon incubation of proteins or peptides in acetone. The reaction is pH-sensitive, being suppressed when proteins are exposed to acetone under acidic conditions. The +98 u artifact is speculated to originate through an intermediate product of aldol condensation of acetone to form diacetone alcohol and mesityl oxide. A +98 u product could originate from nucleophilic attack on mesityl oxide or through condensation with diacetone alcohol. Given the extent of modification possible upon exposure of proteins to acetone, particularly following overnight solvent exposure or incubation at room temperature, an awareness of the variables influencing this novel modification is valued by proteomics researchers who employ acetone precipitation for protein purification.

Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry.

Science.gov (United States)

Asara, John M; Schweitzer, Mary H; Freimark, Lisa M; Phillips, Matthew; Cantley, Lewis C

2007-04-13

Fossilized bones from extinct taxa harbor the potential for obtaining protein or DNA sequences that could reveal evolutionary links to extant species. We used mass spectrometry to obtain protein sequences from bones of a 160,000- to 600,000-year-old extinct mastodon (Mammut americanum) and a 68-million-year-old dinosaur (Tyrannosaurus rex). The presence of T. rex sequences indicates that their peptide bonds were remarkably stable. Mass spectrometry can thus be used to determine unique sequences from ancient organisms from peptide fragmentation patterns, a valuable tool to study the evolution and adaptation of ancient taxa from which genomic sequences are unlikely to be obtained.

QUALITATIVE INTERPRETATION OF GALAXY SPECTRA

Energy Technology Data Exchange (ETDEWEB)

Sanchez Almeida, J.; Morales-Luis, A. B. [Instituto de Astrofisica de Canarias, E-38205 La Laguna, Tenerife (Spain); Terlevich, R.; Terlevich, E. [Instituto Nacional de Astrofisica, Optica y Electronica, Tonantzintla, Puebla (Mexico); Cid Fernandes, R., E-mail: jos@iac.es, E-mail: abml@iac.es, E-mail: rjt@ast.cam.ac.uk, E-mail: eterlevi@inaoep.mx, E-mail: cid@astro.ufsc.br [Departamento de Fisica-CFM, Universidade Federal de Santa Catarina, P.O. Box 476, 88040-900 Florianopolis, SC (Brazil)

2012-09-10

We describe a simple step-by-step guide to qualitative interpretation of galaxy spectra. Rather than an alternative to existing automated tools, it is put forward as an instrument for quick-look analysis and for gaining physical insight when interpreting the outputs provided by automated tools. Though the recipe is for general application, it was developed for understanding the nature of the Automatic Spectroscopic K-means-based (ASK) template spectra. They resulted from the classification of all the galaxy spectra in the Sloan Digital Sky Survey data release 7, thus being a comprehensive representation of the galaxy spectra in the local universe. Using the recipe, we give a description of the properties of the gas and the stars that characterize the ASK classes, from those corresponding to passively evolving galaxies, to H II galaxies undergoing a galaxy-wide starburst. The qualitative analysis is found to be in excellent agreement with quantitative analyses of the same spectra. We compare the mean ages of the stellar populations with those inferred using the code STARLIGHT. We also examine the estimated gas-phase metallicity with the metallicities obtained using electron-temperature-based methods. A number of byproducts follow from the analysis. There is a tight correlation between the age of the stellar population and the metallicity of the gas, which is stronger than the correlations between galaxy mass and stellar age, and galaxy mass and gas metallicity. The galaxy spectra are known to follow a one-dimensional sequence, and we identify the luminosity-weighted mean stellar age as the affine parameter that describes the sequence. All ASK classes happen to have a significant fraction of old stars, although spectrum-wise they are outshined by the youngest populations. Old stars are metal-rich or metal-poor depending on whether they reside in passive galaxies or in star-forming galaxies.

Detection and quantification of proteins and cells by use of elemental mass spectrometry: progress and challenges.

Science.gov (United States)

Yan, Xiaowen; Yang, Limin; Wang, Qiuquan

2013-07-01

Much progress has been made in identification of the proteins in proteomes, and quantification of these proteins has attracted much interest. In addition to popular tandem mass spectrometric methods based on soft ionization, inductively coupled plasma mass spectrometry (ICPMS), a typical example of mass spectrometry based on hard ionization, usually used for analysis of elements, has unique advantages in absolute quantification of proteins by determination of an element with a definite stoichiometry in a protein or attached to the protein. In this Trends article, we briefly describe state-of-the-art ICPMS-based methods for quantification of proteins, emphasizing protein-labeling and element-tagging strategies developed on the basis of chemically selective reactions and/or biospecific interactions. Recent progress from protein to cell quantification by use of ICPMS is also discussed, and the possibilities and challenges of ICPMS-based protein quantification for universal, selective, or targeted quantification of proteins and cells in a biological sample are also discussed critically. We believe ICPMS-based protein quantification will become ever more important in targeted quantitative proteomics and bioanalysis in the near future.

Mass Spectrometry-Based Methods for Identifying Oxidized Proteins in Disease: Advances and Challenges

Directory of Open Access Journals (Sweden)

Ivan Verrastro

2015-04-01

Full Text Available Many inflammatory diseases have an oxidative aetiology, which leads to oxidative damage to biomolecules, including proteins. It is now increasingly recognized that oxidative post-translational modifications (oxPTMs of proteins affect cell signalling and behaviour, and can contribute to pathology. Moreover, oxidized proteins have potential as biomarkers for inflammatory diseases. Although many assays for generic protein oxidation and breakdown products of protein oxidation are available, only advanced tandem mass spectrometry approaches have the power to localize specific oxPTMs in identified proteins. While much work has been carried out using untargeted or discovery mass spectrometry approaches, identification of oxPTMs in disease has benefitted from the development of sophisticated targeted or semi-targeted scanning routines, combined with chemical labeling and enrichment approaches. Nevertheless, many potential pitfalls exist which can result in incorrect identifications. This review explains the limitations, advantages and challenges of all of these approaches to detecting oxidatively modified proteins, and provides an update on recent literature in which they have been used to detect and quantify protein oxidation in disease.

Effects of high protein diets on fat-free mass and muscle protein synthesis following weight loss: a randomized controlled trial

Science.gov (United States)

Context: The benefits of high protein diets for sparing lean body mass and sustaining skeletal muscle protein metabolism during short-term weight loss in normal-weight adults are not well described. Objective: Determine the effects of varying levels of dietary protein intake on body compos...

Prediction of peak overlap in NMR spectra

International Nuclear Information System (INIS)

Hefke, Frederik; Schmucki, Roland; Güntert, Peter

2013-01-01

Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR experiments and chemical shift statistics from the Biological Magnetic Resonance Data Bank. Assuming a normal distribution with characteristic mean value and standard deviation for the chemical shift of each observable atom, an analytic expression was derived for the expected overlap probability of the cross peaks. The analytical approach was verified to agree with the average peak overlap in a large number of individual peak lists simulated using the same chemical shift statistics. The method was applied to eight proteins, including an intrinsically disordered one, for which the prediction results could be compared with the actual overlap based on the experimentally measured chemical shifts. The extent of overlap predicted using only statistical chemical shift information was in good agreement with the overlap that was observed when the measured shifts were used in the virtual spectrum, except for the intrinsically disordered protein. Since the spectral complexity of a protein NMR spectrum is a crucial factor for protein structure determination, analytical overlap prediction can be used to identify potentially difficult proteins before conducting NMR experiments. Overlap predictions can be tailored to particular classes of proteins by preparing statistics from corresponding protein databases. The method is also suitable for optimizing recording parameters and labeling schemes for NMR experiments and improving the reliability of automated spectra analysis and protein structure determination.

Mass spectrometric detection of proteins in non-aqueous media : the case of prion proteins in biodiesel

Energy Technology Data Exchange (ETDEWEB)

Douma, M.D.; Kerr, G.M.; Brown, R.S.; Keller, B.O.; Oleschuk, R.D. [Queen' s Univ., Kingston, ON (Canada). Dept. of Chemistry

2008-08-15

This paper presented a filtration method for detecting protein traces in non-aqueous media. The extraction technique used a mixture of acetonitrile, non-ionic detergent and water along with filter disks with embedded C{sub 8}-modified silica particles to capture the proteins from non-aqueous samples. The extraction process was then followed by an elution of the protein from the filter disk and direct mass spectrometric detection and tryptic digestion with peptide mapping and MS/MS fragmentation of protein-specific peptides. The method was used to detect prion proteins in spiked biodiesel samples. A tryptic peptide with the sequence YGQGSPGGNR was used for unambiguous identification. Results of the study showed that the method is suitable for the large-scale testing of protein impurities in tallow-based biodiesel production processes. 33 refs., 6 figs.

Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification.

Science.gov (United States)

Cho, Jin-Young; Lee, Hyoung-Joo; Jeong, Seul-Ki; Paik, Young-Ki

2017-12-01

Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variable modification options can increase processing time, false-positive errors in large and complicated MS data sets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity. Unfortunately, this technique has less proteome coverage, resulting in limitations in the detection of novel and whole peptide sequences in biological samples. To solve these problems, we previously developed the "Combo-Spec Search" method, which uses manually multiple references and simulated spectral library searching to analyze whole proteomes in a biological sample. In this study, we have developed a new analytical interface tool called "Epsilon-Q" to enhance the functions of both the Combo-Spec Search method and label-free protein quantification. Epsilon-Q performs automatically multiple spectral library searching, class-specific false-discovery rate control, and result integration. It has a user-friendly graphical interface and demonstrates good performance in identifying and quantifying proteins by supporting standard MS data formats and spectrum-to-spectrum matching powered by SpectraST. Furthermore, when the Epsilon-Q interface is combined with the Combo-Spec search method, called the Epsilon-Q system, it shows a synergistic function by outperforming other sequence DB search engines for identifying and quantifying low-abundance proteins in biological samples. The Epsilon-Q system can be a versatile tool for comparative proteome analysis based on multiple spectral libraries and label-free quantification.

Mass spectrometry analysis of proteome-wide proteolytic post-translational degradation of proteins

OpenAIRE

Shen, Yufeng; Hixson, Kim K.; Tolić, Nikola; Camp, David G.; Purvine, Samuel O.; Moore, Ronald J.; Smith, Richard D.

2008-01-01

Protein proteolytic degradation is an essential component to proper cell function and its life cycle. Here, we study the protein degradation in yeast Saccharomyces cerevisiae cells on a proteome-wide scale by detection of the intermediate peptides produced from the intracellular degradation of proteins using sequencing-based tandem mass spectrometry. By tracing the detected ~1,100 peptides and their ~200 protein substrate origins we obtain evidence for new insights into the proteome-wide prot...

A setup for simultaneous measurement of infrared spectra and light scattering signals: Watching amyloid fibrils grow from intact proteins

Energy Technology Data Exchange (ETDEWEB)

Li, Yang; Maurer, Jürgen; Roth, Andreas; Vogel, Vitali; Winter, Ernst; Mäntele, Werner, E-mail: maentele@biophysik.uni-frankfurt.de [Institut für Biophysik, Goethe-Universität Frankfurt am Main, Max-von Laue-Straße 1, D-60438 Frankfurt am Main (Germany)

2014-08-15

A setup for the simultaneous measurement of mid-infrared spectra and static light scattering is described that can be used for the analysis of the formation of nanoscale and microscopic aggregates from smaller molecules to biopolymers. It can be easily integrated into sample chambers of infrared spectrometers or combined with laser beams from tunable infrared lasers. Here, its use for the analysis of the formation of amyloid fibrils from intact proteins is demonstrated. The formation of amyloid fibrils or plaques from proteins is a widespread and pathogenetic relevant process, and a number of diseases are caused and correlated with the deposition of amyloid fibrils in cells and tissues. The molecular mechanisms of these transformations, however, are still unclear. We report here the simultaneous measurement of infrared spectra and static light scattering for the analysis of fibril formation from egg-white lysozyme. The transformation of the native form into non-native forms rich in β-sheet structure is measured by analysis of the amide I spectral region in the infrared spectra, which is sensitive for local structures. At the same time, light scattering signals at forward direction as well as the forward/backward ratio, which are sensitive for the number of scattering centers and their approximate sizes, respectively, are collected for the analysis of fibril growth. Thermodynamic and kinetic parameters as well as mechanistic information are deduced from the combination of the two complementary techniques.

A setup for simultaneous measurement of infrared spectra and light scattering signals: Watching amyloid fibrils grow from intact proteins

Science.gov (United States)

Li, Yang; Maurer, Jürgen; Roth, Andreas; Vogel, Vitali; Winter, Ernst; Mäntele, Werner

2014-08-01

A setup for the simultaneous measurement of mid-infrared spectra and static light scattering is described that can be used for the analysis of the formation of nanoscale and microscopic aggregates from smaller molecules to biopolymers. It can be easily integrated into sample chambers of infrared spectrometers or combined with laser beams from tunable infrared lasers. Here, its use for the analysis of the formation of amyloid fibrils from intact proteins is demonstrated. The formation of amyloid fibrils or plaques from proteins is a widespread and pathogenetic relevant process, and a number of diseases are caused and correlated with the deposition of amyloid fibrils in cells and tissues. The molecular mechanisms of these transformations, however, are still unclear. We report here the simultaneous measurement of infrared spectra and static light scattering for the analysis of fibril formation from egg-white lysozyme. The transformation of the native form into non-native forms rich in β-sheet structure is measured by analysis of the amide I spectral region in the infrared spectra, which is sensitive for local structures. At the same time, light scattering signals at forward direction as well as the forward/backward ratio, which are sensitive for the number of scattering centers and their approximate sizes, respectively, are collected for the analysis of fibril growth. Thermodynamic and kinetic parameters as well as mechanistic information are deduced from the combination of the two complementary techniques.

Missing mass spectra in pp inelastic scattering at total energies of 23 GeV and 31 GeV

CERN Document Server

Albrow, M G; Barber, D P; Bogaerts, A; Bosnjakovic, B; Brooks, J R; Clegg, A B; Erné, F C; Gee, C N P; Locke, D H; Loebinger, F K; Murphy, P G; Rudge, A; Sens, Johannes C; Van der Veen, F

1974-01-01

Results are reported of measurements of the momentum spectra of protons emitted at small angles in inelastic reactions at the CERN ISR. The data are for total energies s/sup 1///sub 2/ of 23 GeV and 31 GeV. The structure of the peak at low values of the missing mass M (of the system recoiling against the observed proton) is studied. The missing mass distributions have the form (M/sup 2/)-/sup B(t)/ where t is the four-momentum transfer squared. B(t) drops from 0.98+or-0.06 at t=-0.15 GeV/sup 2/ to 0.20+or-0.15 at t=-1.65 GeV/sup 2/. The results are compared with a simple triple-Regge formula. (12 refs).

Mass Spectrometry Coupled Experiments and Protein Structure Modeling Methods

Directory of Open Access Journals (Sweden)

Lee Sael

2013-10-01

Full Text Available With the accumulation of next generation sequencing data, there is increasing interest in the study of intra-species difference in molecular biology, especially in relation to disease analysis. Furthermore, the dynamics of the protein is being identified as a critical factor in its function. Although accuracy of protein structure prediction methods is high, provided there are structural templates, most methods are still insensitive to amino-acid differences at critical points that may change the overall structure. Also, predicted structures are inherently static and do not provide information about structural change over time. It is challenging to address the sensitivity and the dynamics by computational structure predictions alone. However, with the fast development of diverse mass spectrometry coupled experiments, low-resolution but fast and sensitive structural information can be obtained. This information can then be integrated into the structure prediction process to further improve the sensitivity and address the dynamics of the protein structures. For this purpose, this article focuses on reviewing two aspects: the types of mass spectrometry coupled experiments and structural data that are obtainable through those experiments; and the structure prediction methods that can utilize these data as constraints. Also, short review of current efforts in integrating experimental data in the structural modeling is provided.

A label-free internal standard method for the differential analysis of bioactive lupin proteins using nano HPLC-Chip coupled with Ion Trap mass spectrometry.

Science.gov (United States)

Brambilla, Francesca; Resta, Donatella; Isak, Ilena; Zanotti, Marco; Arnoldi, Anna

2009-01-01

Quantitative proteomics based on MS is useful for pointing out the differences in some food proteomes relevant to human nutrition. Stable isotope label-free (SIF) techniques are suitable for comparing an unlimited number of samples by the use of relatively simple experimental workflows. We have developed an internal standard label-free method based on the intensities of peptide precursor ions from MS/MS spectra, collected in data dependent runs, for the simultaneous qualitative characterization and relative quantification of storage proteins of Lupinus albus seeds in protein extracts of four lupin cultivars (cv Adam, Arés, Lucky, Multitalia). The use of an innovative microfluidic system, the HPLC-Chip, coupled with a classical IT mass spectrometer, has allowed a complete qualitative characterization of all proteins. In particular, the homology search mode has permitted to identify single amino acid substitutions in the sequences of vicilins (beta-conglutin precursor and vicilin-like protein). The MS/MS sequencing of substituted peptides confirms the high heterogeneity of vicilins according to the peculiar characteristics of the vicilin-encoding gene family. Two suitable bioinformatics parameters were optimized for the differential analyses of the main bioactive proteins: the "normalized protein average of common reproducible peptides" (N-ACRP) for gamma-conglutin, which is a homogeneous protein, and the "normalized protein mean peptide spectral intensity" (N-MEAN) for the highly heterogenous class of the vicilins.

Microwave-assisted acid and base hydrolysis of intact proteins containing disulfide bonds for protein sequence analysis by mass spectrometry.

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Reiz, Bela; Li, Liang

2010-09-01

Controlled hydrolysis of proteins to generate peptide ladders combined with mass spectrometric analysis of the resultant peptides can be used for protein sequencing. In this paper, two methods of improving the microwave-assisted protein hydrolysis process are described to enable rapid sequencing of proteins containing disulfide bonds and increase sequence coverage, respectively. It was demonstrated that proteins containing disulfide bonds could be sequenced by MS analysis by first performing hydrolysis for less than 2 min, followed by 1 h of reduction to release the peptides originally linked by disulfide bonds. It was shown that a strong base could be used as a catalyst for microwave-assisted protein hydrolysis, producing complementary sequence information to that generated by microwave-assisted acid hydrolysis. However, using either acid or base hydrolysis, amide bond breakages in small regions of the polypeptide chains of the model proteins (e.g., cytochrome c and lysozyme) were not detected. Dynamic light scattering measurement of the proteins solubilized in an acid or base indicated that protein-protein interaction or aggregation was not the cause of the failure to hydrolyze certain amide bonds. It was speculated that there were some unknown local structures that might play a role in preventing an acid or base from reacting with the peptide bonds therein. 2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved.

The correlation between hs C-reactive protein and left ventricular mass in obese women

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Idrus Alwi

2006-06-01

Full Text Available Plasma C-reactive protein (CRP concentrations are increased in obese individuals. In this study, we examined the correlation between hsCRP and left ventricular mass (LV mass. Fourty five healthy obese women and fourty five healthy non obese women as the controls group were studied by echocardiography and hsCRP. There was no significant correlation between hsCRP and left ventricular mass in obese women (r = 0.29, p 0.06. There was a significant correlation between hs CRP and body mass index (r = 0.46, p 0,002, and also hsCRP and visceral fat (r= 0.33, p 0.03. (Med J Indones 2006; 15:100-4 Keywords: hs C-reactive protein, LV mass, obese women

Per meal dose and frequency of protein consumption is associated with lean mass and muscle performance.

Science.gov (United States)

Loenneke, Jeremy P; Loprinzi, Paul D; Murphy, Caoileann H; Phillips, Stuart M

2016-12-01

It has been hypothesized that for older adults evenly distributing consumption of protein at 30-40 g per meal throughout the day may result in more favorable retention of lean mass and muscular strength. Such a thesis has not, to our knowledge, been tested outside of short-term studies or acute measures of muscle protein synthesis. To examine whether the number of times an individual consumed a minimum of 30 g of protein at a meal is associated with leg lean mass and knee extensor strength. Data from the 1999-2002 NHANES were used, with 1081 adults (50-85 y) constituting the analytic sample. A "multiple pass" 24-h dietary interview format was used to collect detailed information about the participants' dietary intake. Knee extensor strength was assessed objectively using the Kin Com MP dynamometer. Leg lean mass was estimated from whole-body dual-energy X-ray absorptiometry (DXA) scans. Participants with 1 vs. 0 (β adjusted  = 23.6, p = 0.002) and 2 vs. 0 (β adjusted  = 51.1, p = 0.001) meals of ≥30 g protein/meal had greater strength and leg lean mass (1 vs. 0, β adjusted  = 1160, p frequency with leg lean mass and strength plateaued at ∼45 g protein/meal for those consuming 2 vs. 0 meals above the evaluated protein/meal threshold. However, for those with only 1 meal at or above the evaluated threshold, the response plateaued at 30 g/meal. Leg lean mass mediated the relationship between protein frequency and strength, with the proportion of the total effect mediated being 64%. We found that more frequent consumption of meals containing between 30 and 45 g protein/meal produced the greatest association with leg lean mass and strength. Thus, the consumption of 1-2 daily meals with protein content from 30 to 45 g may be an important strategy for increasing and/or maintaining lean body mass and muscle strength with aging. Copyright © 2016 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

Mass spectrometric identification of proteins that interact through specific domains of the poly(A) binding protein.

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Richardson, Roy; Denis, Clyde L; Zhang, Chongxu; Nielsen, Maria E O; Chiang, Yueh-Chin; Kierkegaard, Morten; Wang, Xin; Lee, Darren J; Andersen, Jens S; Yao, Gang

2012-09-01

Poly(A) binding protein (PAB1) is involved in a number of RNA metabolic functions in eukaryotic cells and correspondingly is suggested to associate with a number of proteins. We have used mass spectrometric analysis to identify 55 non-ribosomal proteins that specifically interact with PAB1 from Saccharomyces cerevisiae. Because many of these factors may associate only indirectly with PAB1 by being components of the PAB1-mRNP structure, we additionally conducted mass spectrometric analyses on seven metabolically defined PAB1 deletion derivatives to delimit the interactions between these proteins and PAB1. These latter analyses identified 13 proteins whose associations with PAB1 were reduced by deleting one or another of PAB1's defined domains. Included in this list of 13 proteins were the translation initiation factors eIF4G1 and eIF4G2, translation termination factor eRF3, and PBP2, all of whose previously known direct interactions with specific PAB1 domains were either confirmed, delimited, or extended. The remaining nine proteins that interacted through a specific PAB1 domain were CBF5, SLF1, UPF1, CBC1, SSD1, NOP77, yGR250c, NAB6, and GBP2. In further study, UPF1, involved in nonsense-mediated decay, was confirmed to interact with PAB1 through the RRM1 domain. We additionally established that while the RRM1 domain of PAB1 was required for UPF1-induced acceleration of deadenylation during nonsense-mediated decay, it was not required for the more critical step of acceleration of mRNA decapping. These results begin to identify the proteins most likely to interact with PAB1 and the domains of PAB1 through which these contacts are made.

SYNTHESIS OF 4’-ALLYLBENZO-3N-CROWN-N ETHERS AND THEIR MASS SPECTRA COMPARED WITH BENZO-3N-CROWN-N ETHERS

OpenAIRE

Anwar, Chairil

2008-01-01

Synthesis of 4’allylbenzo-3n-crown-n ethers was carried out by reacting demethylated eugenol with α,ω-dichloro-oligoethylene glycols in 1-butanol under basic condition. The mass spectra of 4’allylbenzo-3n-crown-n and benzo-3n-crown-n were investigated by mass spectrometry using electron impact under 70 eV of electron bombardment as ionisation method. The difference between the group of compounds is only the present of allyl moiety as a side chain at the other side of benzene ring. The first g...

A new method to discriminate secondary organic aerosols from different sources using high-resolution aerosol mass spectra

Science.gov (United States)

Heringa, M. F.; Decarlo, P. F.; Chirico, R.; Tritscher, T.; Clairotte, M.; Mohr, C.; Crippa, M.; Slowik, J. G.; Pfaffenberger, L.; Dommen, J.; Weingartner, E.; Prévôt, A. S. H.; Baltensperger, U.

2012-02-01

Organic aerosol (OA) represents a significant and often major fraction of the non-refractory PM1 (particulate matter with an aerodynamic diameter da car and a two-stroke Euro 2 scooter were characterized with an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-TOF-AMS) and compared to SOA from α-pinene. The emissions were sampled from the chimney/tailpipe by a heated inlet system and filtered before injection into a smog chamber. The gas phase emissions were irradiated by xenon arc lamps to initiate photo-chemistry which led to nucleation and subsequent particle growth by SOA production. Duplicate experiments were performed for each SOA type, with the averaged organic mass spectra showing Pearson's r values >0.94 for the correlations between the four different SOA types after five hours of aging. High-resolution mass spectra (HR-MS) showed that the dominant peaks in the MS, m/z 43 and 44, are dominated by the oxygenated ions C2H3O+ and CO2+, respectively, similarly to the relatively fresh semi-volatile oxygenated OA (SV-OOA) observed in the ambient aerosol. The atomic O:C ratios were found to be in the range of 0.25-0.55 with no major increase during the first five hours of aging. On average, the diesel SOA showed the lowest O:C ratio followed by SOA from wood burning, α-pinene and the scooter emissions. Grouping the fragment ions revealed that the SOA source with the highest O:C ratio had the largest fraction of small ions. The HR data of the four sources could be clustered and separated using principal component analysis (PCA). The model showed a significant separation of the four SOA types and clustering of the duplicate experiments on the first two principal components (PCs), which explained 79% of the total variance. Projection of ambient SV-OOA spectra resolved by positive matrix factorization (PMF) showed that this approach could be useful to identify large contributions of the tested SOA sources to SV-OOA. The first results from this

Hemoglobin variants as models for investigation of dissociation of intact polypeptide chains by ESI tandem mass spectrometry

International Nuclear Information System (INIS)

Light, K.J.; Loo, J.A.; Edmonds, C.G.; Smith, R.D.

1991-06-01

Electrospray ionization mass spectroscopy (ESI-MS) is rapidly becoming a practical biochemical tool for peptide and protein sequence analysis. The utility of ESI-MS is through use of Collisionally Activated Dissociation (ESI-CAD-MS). Human hemoglobin (Hb, ∼62 kDa) consists of four polypeptide chains and a prosthetic heme group. There are over 400 Hb variants, characterized by amino acid substitutions in either the alpha or beta polypeptide chains. We investigated ESI-CAD-MS as a tool for rapidly analyzing amino acid substitutions, using eight Hb beta chain variants. The approximate location of the modification can be deduced from comparison of the CAD mass spectra and observance of the mass shifts of the fragment ion containing the substitution. Fragmentation occurs preferentially at the amino terminus of proline residues. For most substitutions, differences in CAD mass spectra were not seen. 2 figs

Maize MeJA-responsive proteins identified by high-resolution 2-DE PAGE

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Yuliang Zhang

2015-12-01

Full Text Available Exogenous methyl jasmonate (MeJA is well-known to induce plant defense mechanisms effective against a wide variety of insect and microbial pests. High-resolution 2-DE gel electrophoresis was used to discover changes in the leaf proteome of maize exposed to MeJA. We sequenced 62 MeJA-responsive proteins by tandem mass spectroscopy, and deposited the mass spectra and identities in the EMBL-EBI PRIDE repository under reference number PXD001793. An analysis and discussion of the identified proteins in relation to maize defense against Asian corn borer is published by Zhang et al. (2015 [1].

Measurement of the average mass of proteins adsorbed to a nanoparticle by using a suspended microchannel resonator.

Science.gov (United States)

Nejadnik, M Reza; Jiskoot, Wim

2015-02-01

We assessed the potential of a suspended microchannel resonator (SMR) to measure the adsorption of proteins to nanoparticles. Standard polystyrene beads suspended in buffer were weighed by a SMR system. Particle suspensions were mixed with solutions of bovine serum albumin (BSA) or monoclonal human antibody (IgG), incubated at room temperature for 3 h and weighed again with SMR. The difference in buoyant mass of the bare and protein-coated polystyrene beads was calculated into real mass of adsorbed proteins. The average surface area occupied per protein molecule was calculated, assuming a monolayer of adsorbed protein. In parallel, dynamic light scattering (DLS), nanoparticle tracking analysis (NTA), and zeta potential measurements were performed. SMR revealed a statistically significant increase in the mass of beads because of adsorption of proteins (for BSA and IgG), whereas DLS and NTA did not show a difference between the size of bare and protein-coated beads. The change in the zeta potential of the beads was also measurable. The surface area occupied per protein molecule was in line with their known size. Presented results show that SMR can be used to measure the mass of adsorbed protein to nanoparticles with a high precision in the presence of free protein. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

A new method to discriminate secondary organic aerosols from different sources using high-resolution aerosol mass spectra

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M. F. Heringa

2012-02-01

Full Text Available Organic aerosol (OA represents a significant and often major fraction of the non-refractory PM₁ (particulate matter with an aerodynamic diameter d_a < 1 μm mass. Secondary organic aerosol (SOA is an important contributor to the OA and can be formed from biogenic and anthropogenic precursors. Here we present results from the characterization of SOA produced from the emissions of three different anthropogenic sources. SOA from a log wood burner, a Euro 2 diesel car and a two-stroke Euro 2 scooter were characterized with an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-TOF-AMS and compared to SOA from α-pinene.

The emissions were sampled from the chimney/tailpipe by a heated inlet system and filtered before injection into a smog chamber. The gas phase emissions were irradiated by xenon arc lamps to initiate photo-chemistry which led to nucleation and subsequent particle growth by SOA production.

Duplicate experiments were performed for each SOA type, with the averaged organic mass spectra showing Pearson's r values >0.94 for the correlations between the four different SOA types after five hours of aging. High-resolution mass spectra (HR-MS showed that the dominant peaks in the MS, m/z 43 and 44, are dominated by the oxygenated ions C₂H₃O⁺ and CO₂⁺, respectively, similarly to the relatively fresh semi-volatile oxygenated OA (SV-OOA observed in the ambient aerosol. The atomic O:C ratios were found to be in the range of 0.25–0.55 with no major increase during the first five hours of aging. On average, the diesel SOA showed the lowest O:C ratio followed by SOA from wood burning, α-pinene and the scooter emissions. Grouping the fragment ions revealed that the SOA source with the highest O:C ratio had the largest fraction of small ions.

The HR data of the four sources could be clustered and separated using

Reproducibility of mass spectrometry based protein profiles for diagnosis of breast cancer across clinical studies

DEFF Research Database (Denmark)

Callesen, Anne Kjærgaard; Vach, Werner; Jørgensen, Per E

2008-01-01

Serum protein profiling by mass spectrometry has achieved attention as a promising technology in oncoproteomics. We performed a systematic review of published reports on protein profiling as a diagnostic tool for breast cancer. The MEDLINE, EMBASE, and COCHRANE databases were searched for original...... studies reporting discriminatory protein peaks for breast cancer as either protein identity or as m/ z values in the period from January 1995 to October 2006. To address the important aspect of reproducibility of mass spectrometry data across different clinical studies, we compared the published lists...... of potential discriminatory peaks with those peaks detected in an original MALDI MS protein profiling study performed by our own research group. A total of 20 protein/peptide profiling studies were eligible for inclusion in the systematic review. Only 3 reports included information on protein identity...

Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry

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Pramod Kumar Singh

2016-01-01

Full Text Available Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE across a broad range 3.0–10.0 immobilized pH gradient (IPG strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS which showed 45% amino acid homology of chickpea seed storage proteins with Arabidopsis thaliana.

A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments

International Nuclear Information System (INIS)

Schubert, Mario; Labudde, Dirk; Leitner, Dietmar; Oschkinat, Hartmut; Schmieder, Peter

2005-01-01

The determination of the three-dimensional structure of a protein or the study of protein-ligand interactions requires the assignment of all relevant nuclei as an initial step. This is nowadays almost exclusively performed using triple-resonance experiments. The conventional strategy utilizes one or more pairs of three dimensional spectra to obtain redundant information and thus reliable assignments. Here, a modified strategy for obtaining sequence specific assignments based on two dimensional amino acid type selective triple-resonance experiments is proposed. These experiments can be recorded with good resolution in a relatively short time. They provide very specific and redundant information, in particular on sequential connectivities, that drastically increases the ease and reliability of the assignment procedure, done either manually or in an automated fashion. The new strategy is demonstrated with the protein domain PB1 from yeast CDC24p

Strategies in protein sequencing and characterization: Multi-enzyme digestion coupled with alternate CID/ETD tandem mass spectrometry

Energy Technology Data Exchange (ETDEWEB)

Nardiello, Donatella; Palermo, Carmen, E-mail: carmen.palermo@unifg.it; Natale, Anna; Quinto, Maurizio; Centonze, Diego

2015-01-07

Highlights: • Multi-enzyme digestion for protein sequencing and characterization by CID/ETD. • Simultaneous use of trypsin/chymotrypsin for the maximization of sequence. • Identification of PTMs, sequence variants and species-specific residues. • Increase of accuracy in sequence assignments by orthogonal fragmentation techniques. - Abstract: A strategy based on a simultaneous multi-enzyme digestion coupled with electron transfer dissociation (ETD) and collision-induced dissociation (CID) was developed for protein sequencing and characterization, as a valid alternative platform in ion-trap based proteomics. The effect of different proteolytic procedures using chymotrypsin, trypsin, a combination of both, and Lys-C, was carefully evaluated in terms of number of identified peptides, protein coverage, and score distribution. A systematic comparison between CID and ETD is shown for the analysis of peptides originating from the in-solution digestion of standard caseins. The best results were achieved with a trypsin/chymotrypsin mix combined with CID and ETD operating in alternating mode. A post-database search validation of MS/MS dataset was performed, then, the matched peptides were cross checked by the evaluation of ion scores, rank, number of experimental product ions, and their relative abundances in the MS/MS spectrum. By integrated CID/ETD experiments, high quality-spectra have been obtained, thus allowing a confirmation of spectral information and an increase of accuracy in peptide sequence assignments. Overlapping peptides, produced throughout the proteins, reduce the ambiguity in mapping modifications between natural variants and animal species, and allow the characterization of post translational modifications. The advantages of using the enzymatic mix trypsin/chymotrypsin were confirmed by the nanoLC and CID/ETD tandem mass spectrometry of goat milk proteins, previously separated by two-dimensional gel electrophoresis.

Supplementing an energy adequate, higher protein diet with protein does not enhance fat-free mass restoration after short-term severe negative energy balance.

Science.gov (United States)

Berryman, C E; Sepowitz, J J; McClung, H L; Lieberman, H R; Farina, E K; McClung, J P; Ferrando, A A; Pasiakos, S M

2017-06-01

Negative energy balance during military operations can be severe and result in significant reductions in fat-free mass (FFM). Consuming supplemental high-quality protein following such military operations may accelerate restoration of FFM. Body composition (dual-energy X-ray absorptiometry) and whole body protein turnover (single-pool [ 15 N]alanine method) were determined before (PRE) and after 7 days (POST) of severe negative energy balance during military training in 63 male US Marines (means ± SD, 25 ± 3 yr, 84 ± 9 kg). After POST measures were collected, volunteers were randomized to receive higher protein (HIGH: 1,103 kcal/day, 133 g protein/day), moderate protein (MOD: 974 kcal/day, 84 g protein/day), or carbohydrate-based low protein control (CON: 1,042 kcal/day, 7 g protein/day) supplements, in addition to a self-selected, ad libitum diet, for the 27-day intervention (REFED). Measurements were repeated POST-REFED. POST total body mass (TBM; -5.8 ± 1.0 kg, -7.0%), FFM (-3.1 ± 1.6 kg, -4.7%), and net protein balance (-1.7 ± 1.1 g protein·kg -1 ·day -1 ) were lower and proteolysis (1.1 ± 1.9 g protein·kg -1 ·day -1 ) was higher compared with PRE ( P energy (4,498 ± 725 kcal/day). All volunteers, independent of group assignment, achieved positive net protein balance (0.4 ± 1.0 g protein·kg -1 ·day -1 ) and gained TBM (5.9 ± 1.7 kg, 7.8%) and FFM (3.6 ± 1.8 kg, 5.7%) POST-REFED compared with POST ( P energy-adequate, higher protein diets with additional protein may not be necessary to restore FFM after short-term severe negative energy balance. NEW & NOTEWORTHY This article demonstrates 1 ) the majority of physiological decrements incurred during military training (e.g., total and fat-free mass loss), with the exception of net protein balance, resolve and return to pretraining values after 27 days and 2 ) protein supplementation, in addition to an ad libitum, higher protein (~2.0 g·kg -1 ·day -1 ), energy adequate diet, is not necessary to

Process and apparatus for determining molecular spectra

International Nuclear Information System (INIS)

Boesl, U.; Neusser, H.J.; Schlag, E.W.

1984-01-01

A process for determining molecular spectra in unseparated mixtures, in particular unseparated isotopic mixtures, which comprises allowing said mixture to successively flow through a photoreactor which is irradiated by an adjustable-wavelength laser and then through a mass spectrometer wherein the concentration of particles of specified mass is determined by variation of the wavelength of the laser or variation of the mass setting of the mass spectrometer in such a manner that a two-dimensional spectrum results having the parameters of wavelength and mass

Increasing Protein Charge State When Using Laser Electrospray Mass Spectrometry

Science.gov (United States)

Karki, Santosh; Flanigan, Paul M.; Perez, Johnny J.; Archer, Jieutonne J.; Levis, Robert J.

2015-05-01

Femtosecond (fs) laser vaporization is used to transfer cytochrome c, myoglobin, lysozyme, and ubiquitin from the condensed phase into an electrospray (ES) plume consisting of a mixture of a supercharging reagent, m-nitrobenzyl alcohol ( m-NBA), and trifluoroacetic acid (TFA), acetic acid (AA), or formic acid (FA). Interaction of acid-sensitive proteins like cytochrome c and myoglobin with the highly charged ES droplets resulted in a shift to higher charge states in comparison with acid-stable proteins like lysozyme and ubiquitin. Laser electrospray mass spectrometry (LEMS) measurements showed an increase in both the average charge states (Zavg) and the charge state with maximum intensity (Zmode) for acid-sensitive proteins compared with conventional electrospray ionization mass spectrometry (ESI-MS) under equivalent solvent conditions. A marked increase in ion abundance of higher charge states was observed for LEMS in comparison with conventional electrospray for cytochrome c (ranging from 19+ to 21+ versus 13+ to 16+) and myoglobin (ranging from 19+ to 26+ versus 18+ to 21+) using an ES solution containing m-NBA and TFA. LEMS measurements as a function of electrospray flow rate yielded increasing charge states with decreasing flow rates for cytochrome c and myoglobin.

Increased protein intake reduces lean body mass loss during weight loss in athletes.

Science.gov (United States)

Mettler, Samuel; Mitchell, Nigel; Tipton, Kevin D

2010-02-01

To examine the influence of dietary protein on lean body mass loss and performance during short-term hypoenergetic weight loss in athletes. In a parallel design, 20 young healthy resistance-trained athletes were examined for energy expenditure for 1 wk and fed a mixed diet (15% protein, 100% energy) in the second week followed by a hypoenergetic diet (60% of the habitual energy intake), containing either 15% (approximately 1.0 g x kg(-1)) protein (control group, n = 10; CP) or 35% (approximately 2.3 g x kg(-1)) protein (high-protein group, n = 10; HP) for 2 wk. Subjects continued their habitual training throughout the study. Total, lean body, and fat mass, performance (squat jump, maximal isometric leg extension, one-repetition maximum (1RM) bench press, muscle endurance bench press, and 30-s Wingate test) and fasting blood samples (glucose, nonesterified fatty acids (NEFA), glycerol, urea, cortisol, free testosterone, free Insulin-like growth factor-1 (IGF-1), and growth hormone), and psychologic measures were examined at the end of each of the 4 wk. Total (-3.0 +/- 0.4 and -1.5 +/- 0.3 kg for the CP and HP, respectively, P = 0.036) and lean body mass loss (-1.6 +/- 0.3 and -0.3 +/- 0.3 kg, P = 0.006) were significantly larger in the CP compared with those in the HP. Fat loss, performance, and most blood parameters were not influenced by the diet. Urea was higher in HP, and NEFA and urea showed a group x time interaction. Fatigue ratings and "worse than normal" scores on the Daily Analysis of Life Demands for Athletes were higher in HP. These results indicate that approximately 2.3 g x kg(-1) or approximately 35% protein was significantly superior to approximately 1.0 g x kg(-1) or approximately 15% energy protein for maintenance of lean body mass in young healthy athletes during short-term hypoenergetic weight loss.

MSX-3D: a tool to validate 3D protein models using mass spectrometry.

Science.gov (United States)

Heymann, Michaël; Paramelle, David; Subra, Gilles; Forest, Eric; Martinez, Jean; Geourjon, Christophe; Deléage, Gilbert

2008-12-01

The technique of chemical cross-linking followed by mass spectrometry has proven to bring valuable information about the protein structure and interactions between proteic subunits. It is an effective and efficient way to experimentally investigate some aspects of a protein structure when NMR and X-ray crystallography data are lacking. We introduce MSX-3D, a tool specifically geared to validate protein models using mass spectrometry. In addition to classical peptides identifications, it allows an interactive 3D visualization of the distance constraints derived from a cross-linking experiment. Freely available at http://proteomics-pbil.ibcp.fr

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

DEFF Research Database (Denmark)

Ho, Yuen; Gruhler, Albrecht; Heilbut, Adrian

2002-01-01

The recent abundance of genome sequence data has brought an urgent need for systematic proteomics to decipher the encoded protein networks that dictate cellular function. To date, generation of large-scale protein-protein interaction maps has relied on the yeast two-hybrid system, which detects...... as a test case, an example of this approach, which we term high-throughput mass spectrometric protein complex identification (HMS-PCI). Beginning with 10% of predicted yeast proteins as baits, we detected 3,617 associated proteins covering 25% of the yeast proteome. Numerous protein complexes were...... identified, including many new interactions in various signalling pathways and in the DNA damage response. Comparison of the HMS-PCI data set with interactions reported in the literature revealed an average threefold higher success rate in detection of known complexes compared with large-scale two...

A fragmentation study of kaempferol using electrospray quadrupole time-of-flight mass spectrometry at high mass resolution

Science.gov (United States)

March, Raymond E.; Miao, Xiu-Sheng

2004-02-01

A mass spectrometric method based on the combined use of electrospray ionization, collision-induced dissociation and tandem mass spectrometry at high mass resolution has been applied to an investigation of the structural characterization of protonated and deprotonated kaempferol (3,5,7,4'-tetrahydroxyflavone). Low-energy product ion mass spectra of [M+H]+ ions showed simple fragmentations of the C ring that permitted characterization of the substituents in the A and B rings. In addition, four rearrangement reactions accompanied by losses of C2H2O, CHO[radical sign], CO, and H2O were observed. Low-energy product ion mass spectra of [M-H]- ions showed only four rearrangement reactions accompanied by losses of OH[radical sign], CO, CH2O, and C2H2O. The use of elevated cone voltages permitted observation of product ion mass spectra of selected primary and secondary fragment ions so that each fragment ion reported was observed as a direct product of its immediate precursor ion. Product ion mass spectra examined at high mass resolution allowed unambiguous determination of the elemental composition of fragment ions and resolution of two pairs of isobars. Fragmentation mechanisms and ion structures have been proposed.

Mass spectrometry compatible surfactant for optimized in-gel protein digestion.

Science.gov (United States)

Saveliev, Sergei V; Woodroofe, Carolyn C; Sabat, Grzegorz; Adams, Christopher M; Klaubert, Dieter; Wood, Keith; Urh, Marjeta

2013-01-15

Identification of proteins resolved by SDS-PAGE depends on robust in-gel protein digestion and efficient peptide extraction, requirements that are often difficult to achieve. A lengthy and laborious procedure is an additional challenge of protein identification in gel. We show here that with the use of the mass spectrometry compatible surfactant sodium 3-((1-(furan-2-yl)undecyloxy)carbonylamino)propane-1-sulfonate, the challenges of in-gel protein digestion are effectively addressed. Peptide quantitation based on stable isotope labeling showed that the surfactant induced 1.5-2 fold increase in peptide recovery. Consequently, protein sequence coverage was increased by 20-30%, on average, and the number of identified proteins saw a substantial boost. The surfactant also accelerated the digestion process. Maximal in-gel digestion was achieved in as little as one hour, depending on incubation temperature, and peptides were readily recovered from gel eliminating the need for postdigestion extraction. This study shows that the surfactant provides an efficient means of improving protein identification in gel and streamlining the in-gel digestion procedure requiring no extra handling steps or special equipment.

Assessment of meat authenticity using bioinformatics, targeted peptide biomarkers and high-resolution mass spectrometry.

Science.gov (United States)

Ruiz Orduna, Alberto; Husby, Erik; Yang, Charles T; Ghosh, Dipankar; Beaudry, Francis

2015-01-01

In recent years a significant increase of food fraud has been observed, ranging from false label claims to the use of additives and fillers to increase profitability. Recently in 2013 horse and pig DNAs were detected in beef products sold from several retailers. Mass spectrometry (MS) has become the workhorse in protein research, and the detection of marker proteins could serve for both animal species and tissue authentication. Meat species authenticity is performed in this paper using a well-defined proteogenomic annotation, carefully chosen surrogate tryptic peptides and analysis using a hybrid quadrupole-Orbitrap MS. Selected mammalian meat samples were homogenised and proteins were extracted and digested with trypsin. The samples were analysed using a high-resolution MS. Chromatography was achieved using a 30-min linear gradient along with a BioBasic C8 100 × 1 mm column at a flow rate of 75 µl min(-1). The MS was operated in full-scan high resolution and accurate mass. MS/MS spectra were collected for selected proteotypic peptides. Muscular proteins were methodically analysed in silico in order to generate tryptic peptide mass lists and theoretical MS/MS spectra. Following a comprehensive bottom-up proteomic analysis, we detected and identified a proteotypic myoglobin tryptic peptide (120-134) for each species with observed m/z below 1.3 ppm compared with theoretical values. Moreover, proteotypic peptides from myosin-1, myosin-2 and β-haemoglobin were also identified. This targeted method allowed comprehensive meat speciation down to 1% (w/w) of undesired product.

The effects of dietary protein intake on appendicular lean mass and muscle function in elderly men

DEFF Research Database (Denmark)

Mitchell, Cameron J; Milan, Amber M; Mitchell, Sarah M

2017-01-01

Background: The Recommended Daily Allowance (RDA) for protein intake in the adult population is widely promoted as 0.8 g · kg-1 · d-1 Aging may increase protein requirements, particularly to maintain muscle mass.Objective: We investigated whether controlled protein consumption at the current RDA...... or twice the RDA (2RDA) affects skeletal muscle mass and physical function in elderly men.Design: In this parallel-group randomized trial, 29 men aged >70 y [mean ± SD body mass index (in kg/m2): 28.3 ± 4.2] were provided with a complete diet containing either 0.8 (RDA) or 1.6 (2RDA) g protein · kg-1 · d-1...... energy balance (mean ± SD RDA: 209 ± 213 kcal/d; 2RDA 145 ± 214 kcal/d; P= 0.427 for difference between the groups). In comparison with RDA, whole-body lean mass increased in 2RDA (P = 0.001; 1.49 ± 1.30 kg, P

General Notes on Processes and Their Spectra

Directory of Open Access Journals (Sweden)

Gustav Cepciansky

2012-01-01

Full Text Available The frequency spectrum performs one of the main characteristics of a process. The aim of the paper is to show the coherence between the process and its own spectrum and how the behaviour and properties of a process itself can be deduced from its spectrum. Processes are categorized and general principles of their spectra calculation and recognition are given. The main stress is put on power spectra of electric and optic signals, as they also perform a kind of processes. These spectra can be directly measured, observed and examined by means of spectral analyzers and they are very important characteristics which can not be omitted at transmission techniques in telecommunication technologies. Further, the paper also deals with non electric processes, mainly with processes and spectra at mass servicing and how these spectra can be utilised in praxis.

The application of mass-spectrometry-based protein biomarker discovery to theragnostics

OpenAIRE

Street, Jonathan M; Dear, James W

2010-01-01

Over the last decade rapid developments in mass spectrometry have allowed the identification of multiple proteins in complex biological samples. This proteomic approach has been applied to biomarker discovery in the context of clinical pharmacology (the combination of biomarker and drug now being termed ‘theragnostics’). In this review we provide a roadmap for early protein biomarker discovery studies, focusing on some key questions that regularly confront researchers.

Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometry

DEFF Research Database (Denmark)

Steen, Hanno; Jensen, Ole Nørregaard

2002-01-01

. Mass spectrometry (MS) has emerged as a sensitive and efficient analytical technique for determination of such cross-linking sites in proteins. The present review of the field describes a number of MS-based approaches for the characterization of cross-linked protein-nucleic acid complexes...

Identification of species- and tissue-specific proteins using proteomic strategy

Science.gov (United States)

Chernukha, I. M.; Vostrikova, N. L.; Kovalev, L. I.; Shishkin, S. S.; Kovaleva, M. A.; Manukhin, Y. S.

2017-09-01

Proteomic technologies have proven to be very effective for detecting biochemical changes in meat products, such as changes in tissue- and species-specific proteins. In the tissues of cattle, pig, horse and camel M. longissimus dorsi both tissue- and species specific proteins were detected using two dimensional electrophoresis. Species-specific isoforms of several muscle proteins were also identified. The identified and described proteins of cattle, pig, horse and camel skeletal muscles (including mass spectra of the tryptic peptides) were added to the national free access database “Muscle organ proteomics”. This research has enabled the development of new highly sensitive technologies for meat product quality control against food fraud.

Application of electrospray mass spectrometry to the characterization of recombinant proteins up to 44 kDa

NARCIS (Netherlands)

Van Dorsselaer, A.; Bitsch, F.; Green, B.; Jarvis, S.; Lepage, P.; Bischoff, Rainer; Kolbe, V.J.; Roitsch, C.

1990-01-01

Mass measurement by electrospray mass spectrometry (ESMS) is used as a rapid preliminary verification of the identity of various recombinant proteins ranging from 7 to 44 kDa with an accuracy of 0.01-0.03%. ESMS not only improves the speed but also the reliability of the protein structure

Towards a full reference library of MS(n) spectra. II: A perspective from the library of pesticide spectra extracted from the literature/Internet.

Science.gov (United States)

Milman, Boris L; Zhurkovich, Inna K

2011-12-30

To gain perspective on building full transferable libraries of MS(n) spectra from their diverse/numerous collections, a new library was built from 1723 MS(>1) spectra (mainly MS² spectra) of 490 pesticides and related compounds. Spectra acquired on different types of tandem instruments in various experimental conditions were extracted from 168 literature articles and Internet sites. Testing of the library was based on searches where 'unknown' and reference spectra originated from different sources (mainly from different laboratories) were cross-compared. The NIST 05 MS² library was added to the reference spectra. The library searches were performed with all the test spectra or were divided into different subsamples containing (a) various numbers of replicate spectra of test compounds or (b) spectra acquired from different instrument types. Thus, the dependence of true/false search (identification) result rates on different factors was explored. The percentage of 1st rank correct identifications (true positives) for the only 'unknown' mass spectrum and two and more reference spectra and matching precursor ion m/z values was 89%. For qualified matches, above the cut-off match factor, that rate decreased to 80%. The corresponding rates based on the best match for two and more 'unknown' and reference spectral replicates were 89-94%. For quadrupole instruments, the rates were even higher: 91-95% (one 'unknown' spectrum) and 90-100% (two and more such spectra). This study shows that MS² spectral libraries generated from the numerous literature/Internet sources are not less efficient for the goal of identification of unknown compounds including pesticides than very common EI-MS¹ libraries and are almost as efficient as the most productive from current MS² spectral databases. Such libraries may be used as individual reference databases or supplements to large experimental spectral collections covering many groups of abundant compounds and different types of tandem

Identification of hemoglobin variants by top-down mass spectrometry using selected diagnostic product ions.

Science.gov (United States)

Coelho Graça, Didia; Hartmer, Ralf; Jabs, Wolfgang; Beris, Photis; Clerici, Lorella; Stoermer, Carsten; Samii, Kaveh; Hochstrasser, Denis; Tsybin, Yury O; Scherl, Alexander; Lescuyer, Pierre

2015-04-01

Hemoglobin disorder diagnosis is a complex procedure combining several analytical steps. Due to the lack of specificity of the currently used protein analysis methods, the identification of uncommon hemoglobin variants (proteoforms) can become a hard task to accomplish. The aim of this work was to develop a mass spectrometry-based approach to quickly identify mutated protein sequences within globin chain variants. To reach this goal, a top-down electron transfer dissociation mass spectrometry method was developed for hemoglobin β chain analysis. A diagnostic product ion list was established with a color code strategy allowing to quickly and specifically localize a mutation in the hemoglobin β chain sequence. The method was applied to the analysis of rare hemoglobin β chain variants and an (A)γ-β fusion protein. The results showed that the developed data analysis process allows fast and reliable interpretation of top-down electron transfer dissociation mass spectra by nonexpert users in the clinical area.

Laboratory Measurements of Mass Specific Absorption Spectra for Suites of Black Carbon-like, Biomass Burning and Mineral Dust Aerosols

Science.gov (United States)

Radney, J.; Zangmeister, C.

2017-12-01

Light-absorbing atmospheric aerosols can be grouped into three categories: black carbon (BC), brown carbon (BrC) or mineral dust (MD). In many cases, the absorption of these species is best quantified using a mass-specific absorption cross section (MAC) since the particles are in the Rayleigh regime (BC) or optically thin (BrC and MD); notably, MAC values are both traceable to the SI and transferrable between photoacoustic spectroscopy and filter-based absorption measurements. Here, we present laboratory measurements of MAC for all three light-absorbing aerosol classes. Particles were size- and mass-selected using a differential mobility analyzer and aerosol particle mass analyzer, respectively, with absorption coefficients (αabs) and number concentrations (N) being measured by a broadband photoacoustic spectrometer and condensation particle counter, respectively. This suite of instrumentation allows for direct quantification of MAC from the measured parameters (MAC = αabs/Nmp). Further, the measurements contained > 8 data points spanning λ = 405 nm to 840 nm allowing for spectral curvatures (i.e. the Absorption Angstrom Exponent or AAE) to be fit from many data points versus the more common 2-point interpolations. For the carbonaceous, BC-like aerosols - five samples generated from flames, spark discharge soot (i.e. fullerene soot), graphene, reduced graphene oxide (rGO), and fullerene (C60) - we found: 1) measured MAC ranged between 2.4 m2 g-1 and 8.6 m2 g-1 at λ = 550 nm, 2) most AAEs ranged between 0.5 and 1.3; C60 AAE was 7.5 ± 0.9 and 3) MAC spectra were dependent on fuel type and formation conditions. For BrC particles generated from smoldering combustion of 3 hardwood (Oak, Hickory and Mesquite) and 3 softwood species (Western redcedar, Blue spruce and Baldcypress), we found: 1) median MAC values ranged from 1.4 x 10-2 m2 g-1 to 7.9 x 10-2 m2 g-1 at λ = 550 nm, 2) AAE values ranged between 3.5 and 6.2, and 3) Oak, Western redcedar and Blue spruce

Comparison between simplified load spectra in accordance with Germanische Lloyd guidelines, and load spectra derived from time domain simulations

Energy Technology Data Exchange (ETDEWEB)

Rees, M [Aerodyn Energiesysteme gmbH, Rendsburg (Germany)

1996-09-01

The Germanische Lloyd guideline allows calculations of load spectra in two fundamentally different ways. In the case of the so-called `simplified load spectra` the maximum amplitude of fluctuation of a load component is formed as {+-}75% of the average value of the purely aerodynamic loads of this component at rated wind conditions, together with an overlay of mass-related loads. The second method allowed in the GL guideline is the calculation of load spectra from simulation results in the time domain. For a number of average wind speeds the time-dependent characteristics of the load components are calculated taking account of the natural spatial turbulence of the wind. These are converted into load spectra using the rainflow method. In a parametric study the load spectra are calculated according to both methods and compared. The calculations are performed for turbines with rated powers of 100 kW to 2000 kW, with two and three blades, and also for stall-controlled and pitch-controlled turbines. The calculated load spectra are compared with each by means of 1 P fatigue equivalent load spectra. The influence of individual parameters is presented, as is the validity of the simplified load spectra. (au)

New regularities in mass spectra of hadrons

International Nuclear Information System (INIS)

Kajdalov, A.B.

1989-01-01

The properties of bosonic and baryonic Regge trajectories for hadrons composed of light quarks are considered. Experimental data agree with an existence of daughter trajectories consistent with string models. It is pointed out that the parity doubling for baryonic trajectories, observed experimentally, is not understood in the existing quark models. Mass spectrum of bosons and baryons indicates to an approximate supersymmetry in the mass region M>1 GeV. These regularities indicates to a high degree of symmetry for the dynamics in the confinement region. 8 refs.; 5 figs

Matrix-assisted laser desorption/ionisation mass spectrometry imaging and its development for plant protein imaging

Directory of Open Access Journals (Sweden)

Millar A Harvey

2011-07-01

Full Text Available Abstract Matrix-Assisted Laser Desorption/Ionisation (MALDI mass spectrometry imaging (MSI uses the power of high mass resolution time of flight (ToF mass spectrometry coupled to the raster of lasers shots across the cut surface of tissues to provide new insights into the spatial distribution of biomolecules within biological tissues. The history of this technique in animals and plants is considered and the potential for analysis of proteins by this technique in plants is discussed. Protein biomarker identification from MALDI-MSI is a challenge and a number of different approaches to address this bottleneck are discussed. The technical considerations needed for MALDI-MSI are reviewed and these are presented alongside examples from our own work and a protocol for MALDI-MSI of proteins in plant samples.

Increased Protein Structural Resolution from Diethylpyrocarbonate-based Covalent Labeling and Mass Spectrometric Detection

Science.gov (United States)

Zhou, Yuping; Vachet, Richard W.

2012-04-01

Covalent labeling and mass spectrometry are seeing increased use together as a way to obtain insight into the 3-dimensional structure of proteins and protein complexes. Several amino acid specific (e.g., diethylpyrocarbonate) and non-specific (e.g., hydroxyl radicals) labeling reagents are available for this purpose. Diethylpyrocarbonate (DEPC) is a promising labeling reagent because it can potentially probe up to 30% of the residues in the average protein and gives only one reaction product, thereby facilitating mass spectrometric analysis. It was recently reported, though, that DEPC modifications are labile for some amino acids. Here, we show that label loss is more significant and widespread than previously thought, especially for Ser, Thr, Tyr, and His residues, when relatively long protein digestion times are used. Such label loss ultimately decreases the amount of protein structural information that is obtainable with this reagent. We find, however, that the number of DEPC modified residues and, thus, protein structural information, can be significantly increased by decreasing the time between the covalent labeling reaction and the mass spectrometric analysis. This is most effectively accomplished using short (e.g., 2 h) proteolytic digestions with enzymes such as immobilized chymotrypsin or Glu-C rather than using methods (e.g., microwave or ultrasonic irradiation) that accelerate proteolysis in other ways. Using short digestion times, we show that the percentage of solvent accessible residues that can be modified by DEPC increases from 44% to 67% for cytochrome c, 35% to 81% for myoglobin, and 76% to 95% for β-2-microglobulin. In effect, these increased numbers of modified residues improve the protein structural resolution available from this covalent labeling method. Compared with typical overnight digestion conditions, the short digestion times decrease the average distance between modified residues from 11 to 7 Å for myoglobin, 13 to 10 Å for

High Whey Protein Intake Delayed the Loss of Lean Body Mass in Healthy Old Rats, whereas Protein Type and Polyphenol/Antioxidant Supplementation Had No Effects

Science.gov (United States)

Mosoni, Laurent; Gatineau, Eva; Gatellier, Philippe; Migné, Carole; Savary-Auzeloux, Isabelle; Rémond, Didier; Rocher, Emilie; Dardevet, Dominique

2014-01-01

Our aim was to compare and combine 3 nutritional strategies to slow down the age-related loss of muscle mass in healthy old rats: 1) increase protein intake, which is likely to stimulate muscle protein anabolism; 2) use leucine rich, rapidly digested whey proteins as protein source (whey proteins are recognized as the most effective proteins to stimulate muscle protein anabolism). 3) Supplement animals with a mixture of chamomile extract, vitamin E, vitamin D (reducing inflammation and oxidative stress is also effective to improve muscle anabolism). Such comparisons and combinations were never tested before. Nutritional groups were: casein 12% protein, whey 12% protein, whey 18% protein and each of these groups were supplemented or not with polyphenols/antioxidants. During 6 months, we followed changes of weight, food intake, inflammation (plasma fibrinogen and alpha-2-macroglobulin) and body composition (DXA). After 6 months, we measured muscle mass, in vivo and ex-vivo fed and post-absorptive muscle protein synthesis, ex-vivo muscle proteolysis, and oxidative stress parameters (liver and muscle glutathione, SOD and total antioxidant activities, muscle carbonyls and TBARS). We showed that although micronutrient supplementation reduced inflammation and oxidative stress, the only factor that significantly reduced the loss of lean body mass was the increase in whey protein intake, with no detectable effect on muscle protein synthesis, and a tendency to reduce muscle proteolysis. We conclude that in healthy rats, increasing protein intake is an effective way to delay sarcopenia. PMID:25268515

Development of a dedicated peptide tandem mass spectral library for conservation science.

Science.gov (United States)

Fremout, Wim; Dhaenens, Maarten; Saverwyns, Steven; Sanyova, Jana; Vandenabeele, Peter; Deforce, Dieter; Moens, Luc

2012-05-30

In recent years, the use of liquid chromatography tandem mass spectrometry (LC-MS/MS) on tryptic digests of cultural heritage objects has attracted much attention. It allows for unambiguous identification of peptides and proteins, and even in complex mixtures species-specific identification becomes feasible with minimal sample consumption. Determination of the peptides is commonly based on theoretical cleavage of known protein sequences and on comparison of the expected peptide fragments with those found in the MS/MS spectra. In this approach, complex computer programs, such as Mascot, perform well identifying known proteins, but fail when protein sequences are unknown or incomplete. Often, when trying to distinguish evolutionarily well preserved collagens of different species, Mascot lacks the required specificity. Complementary and often more accurate information on the proteins can be obtained using a reference library of MS/MS spectra of species-specific peptides. Therefore, a library dedicated to various sources of proteins in works of art was set up, with an initial focus on collagen rich materials. This paper discusses the construction and the advantages of this spectral library for conservation science, and its application on a number of samples from historical works of art. Copyright © 2012 Elsevier B.V. All rights reserved.

ARTSY-J: Convenient and precise measurement of 3JHNHα couplings in medium-size proteins from TROSY-HSQC spectra

Science.gov (United States)

Roche, Julien; Ying, Jinfa; Shen, Yang; Torchia, Dennis A.; Bax, Ad

2016-07-01

A new and convenient method, named ARTSY-J, is introduced that permits extraction of the 3JHNHα couplings in proteins from the relative intensities in a pair of 15N-1H TROSY-HSQC spectra. The pulse scheme includes 3JHNHα dephasing of the narrower TROSY 1HN-{15N} doublet component during a delay, integrated into the regular two-dimensional TROSY-HSQC pulse scheme, and compares the obtained intensity with a reference spectrum where 3JHNHα dephasing is suppressed. The effect of passive 1Hα spin flips downscales the apparent 3JHNHα coupling by a uniform factor that depends approximately linearly on both the duration of the 3JHNHα dephasing delay and the 1H-1H cross relaxation rate. Using such a correction factor, which accounts for the effects of both inhomogeneity of the radiofrequency field and 1Hα spin flips, agreement between prior and newly measured values for the small model protein GB3 is better than 0.3 Hz. Measurement for the HIV-1 protease homodimer (22 kDa) yields 3JHNHα values that agree to better than 0.7 Hz with predictions made on the basis of a previously parameterized Karplus equation. Although for Gly residues the two individual 3JHNHα couplings cannot be extracted from a single set of ARTSY-J spectra, the measurement provides valuable ϕ angle information.

Profiling of integral membrane proteins and their post translational modifications using high-resolution mass spectrometry

Science.gov (United States)

Souda, Puneet; Ryan, Christopher M.; Cramer, William A.; Whitelegge, Julian

2011-01-01

Integral membrane proteins pose challenges to traditional proteomics approaches due to unique physicochemical properties including hydrophobic transmembrane domains that limit solubility in aqueous solvents. A well resolved intact protein molecular mass profile defines a protein’s native covalent state including post-translational modifications, and is thus a vital measurement toward full structure determination. Both soluble loop regions and transmembrane regions potentially contain post-translational modifications that must be characterized if the covalent primary structure of a membrane protein is to be defined. This goal has been achieved using electrospray-ionization mass spectrometry (ESI-MS) with low-resolution mass analyzers for intact protein profiling, and high-resolution instruments for top-down experiments, toward complete covalent primary structure information. In top-down, the intact protein profile is supplemented by gas-phase fragmentation of the intact protein, including its transmembrane regions, using collisionally activated and/or electroncapture dissociation (CAD/ECD) to yield sequence-dependent high-resolution MS information. Dedicated liquid chromatography systems with aqueous/organic solvent mixtures were developed allowing us to demonstrate that polytopic integral membrane proteins are amenable to ESI-MS analysis, including top-down measurements. Covalent post-translational modifications are localized regardless of their position in transmembrane domains. Top-down measurements provide a more detail oriented high-resolution description of post-transcriptional and post-translational diversity for enhanced understanding beyond genomic translation. PMID:21982782

Evaluation of the site specific protein glycation and antioxidant capacity of rare sugar-protein/peptide conjugates.

Science.gov (United States)

Sun, Yuanxia; Hayakawa, Shigeru; Ogawa, Masahiro; Izumori, Ken

2005-12-28

Protein-sugar conjugates generated in nonenzymatic glycation of alpha-lactalbumin (LA) with rare sugars [D-allose (All) and D-psicose (Psi)] and alimentary sugars as controls [D-glucose (Glc) and D-fructose (Fru)] were qualitatively determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Mass spectra revealed that the extent of glycation at lysine residues on LA with D-aldose molecules was very much higher than that of glycation with d-ketose molecules. To identify the specific site of glycation, the peptide mapping was established from protease V8 digestion, using a combination of computational cutting of proteins and MALDI-TOF-MS. As compared to peptide mapping, three and seven glycation sites were located in the primary structure of LA-ketose and LA-aldose conjugates, respectively. On the other hand, the antioxidant activities of protein-sugar conjugates and their peptic hydrolysates were investigated by 1,1-diphenyl-2-picrylhydrazyl radical scavenging method. The antioxidant activities of proteins/peptides glycated with rare sugars were significantly higher than those modified with the control sugars. The results indicated that the glycation degree and position were not markedly different between rare sugar and corresponding control sugar, but the antioxidant properties of protein and its hydrolysate were significantly enhanced by modifying with rare sugar.

CONFIRMATION OF ENHANCED DWARF-SENSITIVE ABSORPTION FEATURES IN THE SPECTRA OF MASSIVE ELLIPTICAL GALAXIES: FURTHER EVIDENCE FOR A NON-UNIVERSAL INITIAL MASS FUNCTION

International Nuclear Information System (INIS)

Van Dokkum, Pieter G.; Conroy, Charlie

2011-01-01

We recently found that massive cluster elliptical galaxies have strong Na I λ8183, 8195 and FeH λ9916 Wing-Ford band absorption, indicating the presence of a very large population of stars with masses ∼ sun . Here we test this result by comparing the elliptical galaxy spectra to those of luminous globular clusters associated with M31. These globular clusters have similar metallicities, abundance ratios, and ages as massive elliptical galaxies but their low dynamical mass-to-light ratios rule out steep stellar initial mass functions (IMFs). From high-quality Keck spectra we find that the dwarf-sensitive absorption lines in globular clusters are significantly weaker than in elliptical galaxies and consistent with normal IMFs. The differences in the Na I and Wing-Ford indices are 0.027 ± 0.007 mag and 0.017 ± 0.006 mag, respectively. We directly compare the two classes of objects by subtracting the averaged globular cluster spectrum from the averaged elliptical galaxy spectrum. The difference spectrum is well fit by the difference between a stellar population synthesis model with a bottom-heavy IMF and one with a bottom-light IMF. We speculate that the slope of the IMF may vary with velocity dispersion, although it is not yet clear what physical mechanism would be responsible for such a relation.

An Automated, High-Throughput Method for Interpreting the Tandem Mass Spectra of Glycosaminoglycans

Science.gov (United States)

Duan, Jiana; Jonathan Amster, I.

2018-05-01

The biological interactions between glycosaminoglycans (GAGs) and other biomolecules are heavily influenced by structural features of the glycan. The structure of GAGs can be assigned using tandem mass spectrometry (MS2), but analysis of these data, to date, requires manually interpretation, a slow process that presents a bottleneck to the broader deployment of this approach to solving biologically relevant problems. Automated interpretation remains a challenge, as GAG biosynthesis is not template-driven, and therefore, one cannot predict structures from genomic data, as is done with proteins. The lack of a structure database, a consequence of the non-template biosynthesis, requires a de novo approach to interpretation of the mass spectral data. We propose a model for rapid, high-throughput GAG analysis by using an approach in which candidate structures are scored for the likelihood that they would produce the features observed in the mass spectrum. To make this approach tractable, a genetic algorithm is used to greatly reduce the search-space of isomeric structures that are considered. The time required for analysis is significantly reduced compared to an approach in which every possible isomer is considered and scored. The model is coded in a software package using the MATLAB environment. This approach was tested on tandem mass spectrometry data for long-chain, moderately sulfated chondroitin sulfate oligomers that were derived from the proteoglycan bikunin. The bikunin data was previously interpreted manually. Our approach examines glycosidic fragments to localize SO3 modifications to specific residues and yields the same structures reported in literature, only much more quickly.

The Effect of a Whey Protein Supplement on Bone Mass in Older Caucasian Adults

Science.gov (United States)

Kerstetter, Jane E.; Brindisi, Jennifer; Sullivan, Rebecca R.; Mangano, Kelsey M.; Larocque, Sarah; Kotler, Belinda M.; Simpson, Christine A.; Cusano, Anna Maria; Gaffney-Stomberg, Erin; Kleppinger, Alison; Reynolds, Jesse; Dziura, James; Kenny, Anne M.; Insogna, Karl L.

2015-01-01

Context: It has been assumed that the increase in urine calcium (Ca) that accompanies an increase in dietary protein was due to increased bone resorption. However, studies using stable Ca isotopes have found that dietary protein increases Ca absorption without increasing bone resorption. Objective: The objective of the study was to investigate the impact of a moderately high protein diet on bone mineral density (BMD). Design: This was a randomized, double-blind, placebo-controlled trial of protein supplementation daily for 18 months. Setting: The study was conducted at two institutional research centers. Participants: Two hundred eight older women and men with a body mass index between 19 and 32 kg/m2 and a self-reported protein intake between 0.6 and 1.0 g/kg participated in the study. Intervention: Subjects were asked to incorporate either a 45-g whey protein or isocaloric maltodextrin supplement into their usual diet for 18 months. Main Outcome Measure: BMD by dual-energy x-ray absorptiometry, body composition, and markers of skeletal and mineral metabolism were measured at baseline and at 9 and 18 months. Results: There were no significant differences between groups for changes in L-spine BMD (primary outcome) or the other skeletal sites of interest. Truncal lean mass was significantly higher in the protein group at 18 months (P = .048). C-terminal telopeptide (P = .0414), IGF-1 (P = .0054), and urinary urea (P < .001) were also higher in the protein group at the end of the study period. There was no difference in estimated glomerular filtration rate at 18 months. Conclusion: Our data suggest that protein supplementation above the recommended dietary allowance (0.8 g/kg) may preserve fat-free mass without adversely affecting skeletal health or renal function in healthy older adults. PMID:25844619

Nutritional Status of Maintenance Dialysis Patients: Low Lean Body Mass Index and Obesity Are Common, Protein-Energy Wasting Is Uncommon.

Directory of Open Access Journals (Sweden)

Mette Koefoed

Full Text Available Maintenance dialysis patients are at increased risk of abnormal nutritional status due to numerous causative factors, both nutritional and non-nutritional. The present study assessed the current prevalence of protein-energy wasting, low lean body mass index and obesity in maintenance dialysis patients, and compared different methods of nutritional assessment.In a cross-sectional study conducted in 2014 at Roskilde Hospital, Denmark, we performed anthropometry (body weight, skinfolds, mid-arm, waist, and hip circumferences, and determined plasma albumin and normalized protein catabolic rate in order to assess the prevalence of protein-energy wasting, low lean body mass index and obesity in these patients.Seventy-nine eligible maintenance dialysis patients participated. The prevalence of protein-energy wasted patients was 4% (95% CI: 2-12 as assessed by the coexistence of low lean body mass index and low fat mass index. Low lean body mass index was seen in 32% (95% CI: 22-44. Obesity prevalence as assessed from fat mass index was 43% (95% CI: 32-55. Coexistence of low lean body mass index and obesity was seen in 10% (95% CI: 5-19. The prevalence of protein-energy wasting and obesity varied considerably, depending on nutritional assessment methodology.Our data indicate that protein-energy wasting is uncommon, whereas low lean body mass index and obesity are frequent conditions among patients in maintenance dialysis. A focus on how to increase and preserve lean body mass in dialysis patients is suggested in the future. In order to clearly distinguish between shortage, sufficiency and abundance of protein and/or fat deposits in maintenance dialysis patients, we suggest the simple measurements of lean body mass index and fat mass index.

Nutritional Status of Maintenance Dialysis Patients: Low Lean Body Mass Index and Obesity Are Common, Protein-Energy Wasting Is Uncommon.

Science.gov (United States)

Koefoed, Mette; Kromann, Charles Boy; Juliussen, Sophie Ryberg; Hvidtfeldt, Danni; Ekelund, Bo; Frandsen, Niels Erik; Marckmann, Peter

2016-01-01

Maintenance dialysis patients are at increased risk of abnormal nutritional status due to numerous causative factors, both nutritional and non-nutritional. The present study assessed the current prevalence of protein-energy wasting, low lean body mass index and obesity in maintenance dialysis patients, and compared different methods of nutritional assessment. In a cross-sectional study conducted in 2014 at Roskilde Hospital, Denmark, we performed anthropometry (body weight, skinfolds, mid-arm, waist, and hip circumferences), and determined plasma albumin and normalized protein catabolic rate in order to assess the prevalence of protein-energy wasting, low lean body mass index and obesity in these patients. Seventy-nine eligible maintenance dialysis patients participated. The prevalence of protein-energy wasted patients was 4% (95% CI: 2-12) as assessed by the coexistence of low lean body mass index and low fat mass index. Low lean body mass index was seen in 32% (95% CI: 22-44). Obesity prevalence as assessed from fat mass index was 43% (95% CI: 32-55). Coexistence of low lean body mass index and obesity was seen in 10% (95% CI: 5-19). The prevalence of protein-energy wasting and obesity varied considerably, depending on nutritional assessment methodology. Our data indicate that protein-energy wasting is uncommon, whereas low lean body mass index and obesity are frequent conditions among patients in maintenance dialysis. A focus on how to increase and preserve lean body mass in dialysis patients is suggested in the future. In order to clearly distinguish between shortage, sufficiency and abundance of protein and/or fat deposits in maintenance dialysis patients, we suggest the simple measurements of lean body mass index and fat mass index.

Determining Membrane Protein-Lipid Binding Thermodynamics Using Native Mass Spectrometry.

Science.gov (United States)

Cong, Xiao; Liu, Yang; Liu, Wen; Liang, Xiaowen; Russell, David H; Laganowsky, Arthur

2016-04-06

Membrane proteins are embedded in the biological membrane where the chemically diverse lipid environment can modulate their structure and function. However, the thermodynamics governing the molecular recognition and interaction of lipids with membrane proteins is poorly understood. Here, we report a method using native mass spectrometry (MS), to determine thermodynamics of individual ligand binding events to proteins. Unlike conventional methods, native MS can resolve individual ligand binding events and, coupled with an apparatus to control the temperature, determine binding thermodynamic parameters, such as for protein-lipid interactions. We validated our approach using three soluble protein-ligand systems (maltose binding protein, lysozyme, and nitrogen regulatory protein) and obtained similar results to those using isothermal titration calorimetry and surface plasmon resonance. We also determined for the first time the thermodynamics of individual lipid binding to the ammonia channel (AmtB), an integral membrane protein from Escherichia coli. Remarkably, we observed distinct thermodynamic signatures for the binding of different lipids and entropy-enthalpy compensation for binding lipids of variable chain length. Additionally, using a mutant form of AmtB that abolishes a specific phosphatidylglycerol (PG) binding site, we observed distinct changes in the thermodynamic signatures for binding PG, implying these signatures can identify key residues involved in specific lipid binding and potentially differentiate between specific lipid binding sites.

CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.

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Courcelles, Mathieu; Coulombe-Huntington, Jasmin; Cossette, Émilie; Gingras, Anne-Claude; Thibault, Pierre; Tyers, Mike

2017-07-07

Protein cross-linking mass spectrometry (CL-MS) enables the sensitive detection of protein interactions and the inference of protein complex topology. The detection of chemical cross-links between protein residues can identify intra- and interprotein contact sites or provide physical constraints for molecular modeling of protein structure. Recent innovations in cross-linker design, sample preparation, mass spectrometry, and software tools have significantly improved CL-MS approaches. Although a number of algorithms now exist for the identification of cross-linked peptides from mass spectral data, a dearth of user-friendly analysis tools represent a practical bottleneck to the broad adoption of the approach. To facilitate the analysis of CL-MS data, we developed CLMSVault, a software suite designed to leverage existing CL-MS algorithms and provide intuitive and flexible tools for cross-platform data interpretation. CLMSVault stores and combines complementary information obtained from different cross-linkers and search algorithms. CLMSVault provides filtering, comparison, and visualization tools to support CL-MS analyses and includes a workflow for label-free quantification of cross-linked peptides. An embedded 3D viewer enables the visualization of quantitative data and the mapping of cross-linked sites onto PDB structural models. We demonstrate the application of CLMSVault for the analysis of a noncovalent Cdc34-ubiquitin protein complex cross-linked under different conditions. CLMSVault is open-source software (available at https://gitlab.com/courcelm/clmsvault.git ), and a live demo is available at http://democlmsvault.tyerslab.com/ .

Amide or Amine: Determining the Origin of the 3300 cm−1 NH Mode in Protein SFG Spectra Using 15N Isotope Labels

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Weidner, Tobias; Breen, Nicholas F.; Drobny, Gary P.; Castner, David G.

2009-01-01

Sum frequency generation (SFG) vibrational spectroscopy has been employed in biomaterials research and protein adsorption studies with growing success in recent years. A number of studies focusing on understanding SFG spectra of proteins and peptides at different interfaces have laid the foundation for future, more complex studies. In many cases a strong NH mode near 3300 cm−1 is observed in the SFG spectra, but the relationship of this mode to the peptide structure is uncertain since it has been assigned to either a backbone amide mode or a side chain related amine resonance. A thorough understanding of the SFG spectra of these first model systems is an important first step for future experiments. To clarify the origin of the NH SFG mode we studied 15N isotopically labeled 14-amino acid amphiphilic model peptides composed of lysine (K) and leucine (L) in an α-helical secondary structure (LKα14) that were adsorbed onto charged surfaces in situ at the solid-liquid interface. 15N substitution at the terminal amine group of the lysine side chains resulted in a red-shift of the NH mode of 9 cm−1 on SiO2 and 13 cm−1 on CaF2. This clearly shows the 3300 cm−1 NH feature is associated with side chain NH stretches and not with backbone amide modes. PMID:19873996

Amide or amine: determining the origin of the 3300 cm(-1) NH mode in protein SFG spectra using 15N isotope labels.

Science.gov (United States)

Weidner, Tobias; Breen, Nicholas F; Drobny, Gary P; Castner, David G

2009-11-26

Sum frequency generation (SFG) vibrational spectroscopy has been employed in biomaterials research and protein adsorption studies with growing success in recent years. A number of studies focusing on understanding SFG spectra of proteins and peptides at different interfaces have laid the foundation for future, more complex studies. In many cases, a strong NH mode near 3300 cm(-1) is observed in the SFG spectra, but the relationship of this mode to the peptide structure is uncertain, since it has been assigned to either a backbone amide mode or a side chain related amine resonance. A thorough understanding of the SFG spectra of these first model systems is an important first step for future experiments. To clarify the origin of the NH SFG mode, we studied (15)N isotopically labeled 14-amino acid amphiphilic model peptides composed of lysine (K) and leucine (L) in an alpha-helical secondary structure (LKalpha14) that were adsorbed onto charged surfaces in situ at the solid-liquid interface. (15)N substitution at the terminal amine group of the lysine side chains resulted in a red-shift of the NH mode of 9 cm(-1) on SiO(2) and 13 cm(-1) on CaF(2). This clearly shows the 3300 cm(-1) NH feature is associated with side chain NH stretches and not with backbone amide modes.

Matrix-assisted laser desorption/ionization coupled with quadrupole/orthogonal acceleration time-of-flight mass spectrometry for protein discovery, identification, and structural analysis.

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Baldwin, M A; Medzihradszky, K F; Lock, C M; Fisher, B; Settineri, T A; Burlingame, A L

2001-04-15

The design and operation of a novel UV-MALDI ionization source on a commercial QqoaTOF mass spectrometer (Applied Biosystem/MDS Sciex QSTAR Pulsar) is described. Samples are loaded on a 96-well target plate, the movement of which is under software control and can be readily automated. Unlike conventional high-energy MALDI-TOF, the ions are produced with low energies (5-10 eV) in a region of relatively low vacuum (8 mTorr). Thus, they are cooled by extensive low-energy collisions before selection in the quadrupole mass analyzer (Q1), potentially giving a quasi-continuous ion beam ideally suited to the oaTOF used for mass analysis of the fragment ions, although ion yields from individual laser shots may vary widely. Ion dissociation is induced by collisions with argon in an rf-only quadrupole cell, giving typical low-energy CID spectra for protonated peptide ions. Ions separated in the oaTOF are registered by a four-anode detector and time-to-digital converter and accumulated in "bins" that are 625 ps wide. Peak shapes depend upon the number of ion counts in adjacent bins. As expected, the accuracy of mass measurement is shown to be dependent upon the number of ions recorded for a particular peak. With internal calibration, mass accuracy better than 10 ppm is attainable for peaks that contain sufficient ions to give well-defined Gaussian profiles. By virtue of its high resolution, capability for accurate mass measurements, and sensitivity in the low-femotomole range, this instrument is ideally suited to protein identification for proteomic applications by generation of peptide tags, manual sequence interpretation, identification of modifications such as phosphorylation, and protein structural elucidation. Unlike the multiply charged ions typical of electrospray ionization, the singly charged MALDI-generated peptide ions show a linear dependence of optimal collision energy upon molecular mass, which is advantageous for automated operation. It is shown that the novel

Analysis of secreted proteins from Aspergillus flavus.

Science.gov (United States)

Medina, Martha L; Haynes, Paul A; Breci, Linda; Francisco, Wilson A

2005-08-01

MS/MS techniques in proteomics make possible the identification of proteins from organisms with little or no genome sequence information available. Peptide sequences are obtained from tandem mass spectra by matching peptide mass and fragmentation information to protein sequence information from related organisms, including unannotated genome sequence data. This peptide identification data can then be grouped and reconstructed into protein data. In this study, we have used this approach to study protein secretion by Aspergillus flavus, a filamentous fungus for which very little genome sequence information is available. A. flavus is capable of degrading the flavonoid rutin (quercetin 3-O-glycoside), as the only source of carbon via an extracellular enzyme system. In this continuing study, a proteomic analysis was used to identify secreted proteins from A. flavus when grown on rutin. The growth media glucose and potato dextrose were used to identify differentially expressed secreted proteins. The secreted proteins were analyzed by 1- and 2-DE and MS/MS. A total of 51 unique A. flavus secreted proteins were identified from the three growth conditions. Ten proteins were unique to rutin-, five to glucose- and one to potato dextrose-grown A. flavus. Sixteen secreted proteins were common to all three media. Fourteen identifications were of hypothetical proteins or proteins of unknown functions. To our knowledge, this is the first extensive proteomic study conducted to identify the secreted proteins from a filamentous fungus.

Ammonium Bicarbonate Addition Improves the Detection of Proteins by Desorption Electrospray Ionization Mass Spectrometry

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Honarvar, Elahe; Venter, Andre R.

2017-06-01

The analysis of protein by desorption electrospray ionization mass spectrometry (DESI-MS) is considered impractical due to a mass-dependent loss in sensitivity with increase in protein molecular weights. With the addition of ammonium bicarbonate to the DESI-MS analysis the sensitivity towards proteins by DESI was improved. The signal to noise ratio (S/N) improvement for a variety of proteins increased between 2- to 3-fold relative to solvent systems containing formic acid and more than seven times relative to aqueous methanol spray solvents. Three methods for ammonium bicarbonate addition during DESI-MS were investigated. The additive delivered improvements in S/N whether it was mixed with the analyte prior to sample deposition, applied over pre-prepared samples, or simply added to the desorption spray solvent. The improvement correlated well with protein pI but not with protein size. Other ammonium or bicarbonate salts did not produce similar improvements in S/N, nor was this improvement in S/N observed for ESI of the same samples. As was previously described for ESI, DESI also caused extensive protein unfolding upon the addition of ammonium bicarbonate. [Figure not available: see fulltext.

Probing Interfacial Processes on Graphene Surface by Mass Detection

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Kakenov, Nurbek; Kocabas, Coskun

2013-03-01

In this work we studied the mass density of graphene, probed interfacial processes on graphene surface and examined the formation of graphene oxide by mass detection. The graphene layers were synthesized by chemical vapor deposition method on copper foils and transfer-printed on a quartz crystal microbalance (QCM). The mass density of single layer graphene was measured by investigating the mechanical resonance of the QCM. Moreover, we extended the developed technique to probe the binding dynamics of proteins on the surface of graphene, were able to obtain nonspecific binding constant of BSA protein of graphene surface in aqueous solution. The time trace of resonance signal showed that the BSA molecules rapidly saturated by filling the available binding sites on graphene surface. Furthermore, we monitored oxidation of graphene surface under oxygen plasma by tracing the changes of interfacial mass of the graphene controlled by the shifts in Raman spectra. Three regimes were observed the formation of graphene oxide which increases the interfacial mass, the release of carbon dioxide and the removal of small graphene/graphene oxide flakes. Scientific and Technological Research Council of Turkey (TUBITAK) grant no. 110T304, 109T209, Marie Curie International Reintegration Grant (IRG) grant no 256458, Turkish Academy of Science (TUBA-Gebip).

A multi-angular mass spectrometric view at cyclic nucleotide signaling proteins : Structure/function and protein interactions of cAMP- and cGMP-dependent protein kinase

NARCIS (Netherlands)

Scholten, A.

2006-01-01

The primary focus of this thesis is the two kinases PKA and PKG, cAMP and cGMP dependent protein kinase respectively. PKA and PKG are studied both at structure/function level as well as at the level of interaction with other proteins in tissue. Our primary methods are all based on mass spectrometry.

The structure of BPS spectra

Science.gov (United States)

Longhi, Pietro

In this thesis we develop and apply novel techniques for analyzing BPS spectra of supersymmetric quantum field theories of class S. By a combination of wall-crossing, spectral networks and quiver methods we explore the BPS spectra of higher rank four-dimensional N = 2 super Yang-Mills, uncovering surprising new phenomena. Focusing on the SU(3) case, we prove the existence of wild BPS spectra in field theory, featuring BPS states of higher spin whose degeneracies grow exponentially with the energy. The occurrence of wild BPS states is surprising because it appears to be in tension with physical expectations on the behavior of the entropy as a function of the energy scale. The solution to this puzzle comes from realizing that the size of wild BPS states grows rapidly with their mass, and carefully analyzing the volume-dependence of the entropy of BPS states. We also find some interesting structures underlying wild BPS spectra, such as a Regge-like relation between the maximal spin of a BPS multiplet and the square of its mass, and the existence of a universal asymptotic distribution of spin-j irreps within a multiplet of given charge. We also extend the spectral networks construction by introducing a refinement in the topological classification of 2d-4d BPS states, and identifying their spin with a topological invariant known as the "writhe of soliton paths". A careful analysis of the 2d-4d wall-crossing behavior of this refined data reveals that it is described by motivic Kontsevich-Soibelman transformations, controlled by the Protected Spin Character, a protected deformation of the BPS index encoding the spin of BPS states. Our construction opens the way for the systematic study of refined BPS spectra in class S theories. We apply it to several examples, including ones featuring wild BPS spectra, where we find an interesting relation between spectral networks and certain functional equations. For class S theories of A 1 type, we derive an alternative technique for

In Cell Footprinting Coupled with Mass Spectrometry for the Structural Analysis of Proteins in Live Cells.

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Espino, Jessica A; Mali, Vishaal S; Jones, Lisa M

2015-08-04

Protein footprinting coupled with mass spectrometry has become a widely used tool for the study of protein-protein and protein-ligand interactions and protein conformational change. These methods provide residue-level analysis on protein interaction sites and have been successful in studying proteins in vitro. The extension of these methods for in cell footprinting would open an avenue to study proteins that are not amenable for in vitro studies and would probe proteins in their native environment. Here we describe the application of an oxidative-based footprinting approach inside cells in which hydroxyl radicals are used to oxidatively modify proteins. Mass spectrometry is used to detect modification sites and to calculate modification levels. The method is probing biologically relevant proteins in live cells, and proteins in various cellular compartments can be oxdiatively modified. Several different amino acid residues are modified making the method a general labeling strategy for the study of a variety of proteins. Further, comparison of the extent of oxidative modification with solvent accessible surface area reveals the method successfully probes solvent accessibility. This marks the first time protein footprinting has been performed in live cells.

Differential screening and mass mapping of proteins from premalignant and cancer cell lines using nonporous reversed-phase HPLC coupled with mass spectrometric analysis.

Science.gov (United States)

Chong, B E; Hamler, R L; Lubman, D M; Ethier, S P; Rosenspire, A J; Miller, F R

2001-03-15

Nonporous (NPS) RP-HPLC has been used to rapidly separate proteins from whole cell lysates of human breast cell lines. The nonporous separation involves the use of hard-sphere silica beads of 1.5-microm diameter coated with C18, which can be used to separate proteins ranging from 5 to 90 kDa. Using only 30-40 microg of total protein, the protein molecular weights are detectable on-line using an ESI-oaTOF MS. Of hundreds of proteins detected in this mass range, approxinately 75-80 are more highly expressed. The molecular weight profiles can be displayed as a mass map analogous to a virtual "1-D gel" and differentially expressed proteins can be compared by image analysis. The separated proteins can also be detected by UV absorption and differentially expressed proteins quantified. The eluting proteins can be collected in the liquid phase and the molecular weight and peptide maps determined by MALDI-TOF MS for identification. It is demonstrated that the expressed protein profiles change during neoplastic progression and that many oncoproteins are readily detected. It is also shown that the response of premalignant cancer cells to estradiol can be rapidly screened by this method, demonstrating significant changes in response to an external agent. Ultimately, the proteins can be studied by peptide mapping to search for posttranslational modifications of the oncoproteins accompanying progression.

Quantum synchrotron spectra from semirelativistic electrons in teragauss magnetic fields

International Nuclear Information System (INIS)

Brainerd, J.J.

1987-01-01

Synchrotron spectra are calculated from quantum electrodynamic transition rates for thermal and power-law electron distributions. It is shown that quantum effects appear in thermal spectra when the photon energy is greater than the electron temperature, and in power-law spectra when the electron energy in units of the electron rest mass times the magnetic field strength in units of the critical field strength is of order unity. These spectra are compared with spectra calculated from the ultrarelativistic approximation for synchrotron emission. It is found that the approximation for the power-law spectra is good, and the approximation for thermal spectra produces the shape of the spectrum accurately but fails to give the correct normalization. Single photon pair creation masks the quantum effects for power-law distributions, so only modifications to thermal spectra are important for gamma-ray bursts. 13 references

2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments.

Science.gov (United States)

Allmer, Jens; Kuhlgert, Sebastian; Hippler, Michael

2008-07-07

The amount of information stemming from proteomics experiments involving (multi dimensional) separation techniques, mass spectrometric analysis, and computational analysis is ever-increasing. Data from such an experimental workflow needs to be captured, related and analyzed. Biological experiments within this scope produce heterogenic data ranging from pictures of one or two-dimensional protein maps and spectra recorded by tandem mass spectrometry to text-based identifications made by algorithms which analyze these spectra. Additionally, peptide and corresponding protein information needs to be displayed. In order to handle the large amount of data from computational processing of mass spectrometric experiments, automatic import scripts are available and the necessity for manual input to the database has been minimized. Information is in a generic format which abstracts from specific software tools typically used in such an experimental workflow. The software is therefore capable of storing and cross analysing results from many algorithms. A novel feature and a focus of this database is to facilitate protein identification by using peptides identified from mass spectrometry and link this information directly to respective protein maps. Additionally, our application employs spectral counting for quantitative presentation of the data. All information can be linked to hot spots on images to place the results into an experimental context. A summary of identified proteins, containing all relevant information per hot spot, is automatically generated, usually upon either a change in the underlying protein models or due to newly imported identifications. The supporting information for this report can be accessed in multiple ways using the user interface provided by the application. We present a proteomics database which aims to greatly reduce evaluation time of results from mass spectrometric experiments and enhance result quality by allowing consistent data handling

2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments

Directory of Open Access Journals (Sweden)

Hippler Michael

2008-07-01

Full Text Available Abstract Background The amount of information stemming from proteomics experiments involving (multi dimensional separation techniques, mass spectrometric analysis, and computational analysis is ever-increasing. Data from such an experimental workflow needs to be captured, related and analyzed. Biological experiments within this scope produce heterogenic data ranging from pictures of one or two-dimensional protein maps and spectra recorded by tandem mass spectrometry to text-based identifications made by algorithms which analyze these spectra. Additionally, peptide and corresponding protein information needs to be displayed. Results In order to handle the large amount of data from computational processing of mass spectrometric experiments, automatic import scripts are available and the necessity for manual input to the database has been minimized. Information is in a generic format which abstracts from specific software tools typically used in such an experimental workflow. The software is therefore capable of storing and cross analysing results from many algorithms. A novel feature and a focus of this database is to facilitate protein identification by using peptides identified from mass spectrometry and link this information directly to respective protein maps. Additionally, our application employs spectral counting for quantitative presentation of the data. All information can be linked to hot spots on images to place the results into an experimental context. A summary of identified proteins, containing all relevant information per hot spot, is automatically generated, usually upon either a change in the underlying protein models or due to newly imported identifications. The supporting information for this report can be accessed in multiple ways using the user interface provided by the application. Conclusion We present a proteomics database which aims to greatly reduce evaluation time of results from mass spectrometric experiments and enhance

Null-plane Bethe-Salpeter dynamics: Mass spectra, decay constants of pseudoscalar mesons, and the pion form factor

International Nuclear Information System (INIS)

Gupta, K.K.; Mitra, A.N.; Singh, N.N.

1990-01-01

A new relativistic definition of the reduced mass (μ 12 ) of a q bar q pair, so as to be in conformity with the standard Wightman-Garding definition of its relative four-momenta q μ , is introduced into the kernel of an ongoing Bethe-Salpeter (BS) program on a two-tier basis. The new definition of μ 12 (involving the hadron mass M) is found to produce a natural Regge asymptotic behavior (M 2 ∼N) in the hadron mass spectra, while retaining the property of an asymptotically linear (∼r) confinement in the three-dimensional structure of the BS kernel. The relativistic structure of μ 12 is responsible for a significant improvement in the fits to the ground-state masses of q bar q and Q bar q mesons as compared to its nonrelativistic definition m 1 m 2 /(m 1 +m 2 ). The leptonic decay constants f p and the charge radii thus calculated are also in excellent agreement with data (π,k) where available, while f p predictions for Q bar q mesons have good overlap with recent lattice predictions. Further, the scaling property (∼k μ -2 ) of the hadron's electromagnetic form factor at large k 2 is a consequence of the ''on-shell'' form of its null-plane wave function. All these results (which are indicated in the barest outline) are preceded by a perspective summary of the theoretical premises and practical working of the BS equation with a four-fermion interaction kernel as a necessary background on a two-tier basis

What can we learn from inclusive spectra

International Nuclear Information System (INIS)

Nagamiya, S.

1981-05-01

The present experimental status on single particle inclusive measurements is described. Then, the geometrical aspect of the collision is discussed from the data of total integrated cross sections of nuclear charge or mass. The dynamical aspect of the collision, especially that for the participating region is discussed in connection with proton spectra, composite fragment spectra, pion production, ratios of π - /π + , n/p and t/ 3 He, and production of strange particles. The spectator physics is described from the data on projectile fragments

ACYLTRANSFERASE ACTIVITIES OF THE HIGH-MOLECULAR-MASS ESSENTIAL PENICILLIN-BINDING PROTEINS

NARCIS (Netherlands)

ADAM, M; DAMBLON, C; JAMIN, M; ZORZI, W; DUSART, [No Value; GALLENI, M; ELKHARROUBI, A; PIRAS, G; SPRATT, BG; KECK, W; COYETTE, J; GHUYSEN, JM; NGUYENDISTECHE, M; FRERE, JM

1991-01-01

The high-molecular-mass penicillin-binding proteins (HMM-PBPs), present in the cytoplasmic membranes of all eubacteria, are involved in important physiological events such as cell elongation, septation or shape determination. Up to now it has, however, been very difficult or impossible to study the

Next-generation technologies for spatial proteomics: Integrating ultra-high speed MALDI-TOF and high mass resolution MALDI FTICR imaging mass spectrometry for protein analysis.

Science.gov (United States)

Spraggins, Jeffrey M; Rizzo, David G; Moore, Jessica L; Noto, Michael J; Skaar, Eric P; Caprioli, Richard M

2016-06-01

MALDI imaging mass spectrometry is a powerful analytical tool enabling the visualization of biomolecules in tissue. However, there are unique challenges associated with protein imaging experiments including the need for higher spatial resolution capabilities, improved image acquisition rates, and better molecular specificity. Here we demonstrate the capabilities of ultra-high speed MALDI-TOF and high mass resolution MALDI FTICR IMS platforms as they relate to these challenges. High spatial resolution MALDI-TOF protein images of rat brain tissue and cystic fibrosis lung tissue were acquired at image acquisition rates >25 pixels/s. Structures as small as 50 μm were spatially resolved and proteins associated with host immune response were observed in cystic fibrosis lung tissue. Ultra-high speed MALDI-TOF enables unique applications including megapixel molecular imaging as demonstrated for lipid analysis of cystic fibrosis lung tissue. Additionally, imaging experiments using MALDI FTICR IMS were shown to produce data with high mass accuracy (z 5000) for proteins up to ∼20 kDa. Analysis of clear cell renal cell carcinoma using MALDI FTICR IMS identified specific proteins localized to healthy tissue regions, within the tumor, and also in areas of increased vascularization around the tumor. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional Polymers in Protein Detection Platforms: Optical, Electrochemical, Electrical, Mass-Sensitive, and Magnetic Biosensors

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Jong-in Hahm

2011-03-01

Full Text Available The rapidly growing field of proteomics and related applied sectors in the life sciences demands convenient methodologies for detecting and measuring the levels of specific proteins as well as for screening and analyzing for interacting protein systems. Materials utilized for such protein detection and measurement platforms should meet particular specifications which include ease-of-mass manufacture, biological stability, chemical functionality, cost effectiveness, and portability. Polymers can satisfy many of these requirements and are often considered as choice materials in various biological detection platforms. Therefore, tremendous research efforts have been made for developing new polymers both in macroscopic and nanoscopic length scales as well as applying existing polymeric materials for protein measurements. In this review article, both conventional and alternative techniques for protein detection are overviewed while focusing on the use of various polymeric materials in different protein sensing technologies. Among many available detection mechanisms, most common approaches such as optical, electrochemical, electrical, mass-sensitive, and magnetic methods are comprehensively discussed in this article. Desired properties of polymers exploited for each type of protein detection approach are summarized. Current challenges associated with the application of polymeric materials are examined in each protein detection category. Difficulties facing both quantitative and qualitative protein measurements are also identified. The latest efforts on the development and evaluation of nanoscale polymeric systems for improved protein detection are also discussed from the standpoint of quantitative and qualitative measurements. Finally, future research directions towards further advancements in the field are considered.

High-throughput peptide mass fingerprinting and protein macroarray analysis using chemical printing strategies

International Nuclear Information System (INIS)

Sloane, A.J.; Duff, J.L.; Hopwood, F.G.; Wilson, N.L.; Smith, P.E.; Hill, C.J.; Packer, N.H.; Williams, K.L.; Gooley, A.A.; Cole, R.A.; Cooley, P.W.; Wallace, D.B.

2001-01-01

We describe a 'chemical printer' that uses piezoelectric pulsing for rapid and accurate microdispensing of picolitre volumes of fluid for proteomic analysis of 'protein macroarrays'. Unlike positive transfer and pin transfer systems, our printer dispenses fluid in a non-contact process that ensures that the fluid source cannot be contaminated by substrate during a printing event. We demonstrate automated delivery of enzyme and matrix solutions for on-membrane protein digestion and subsequent peptide mass fingerprinting (pmf) analysis directly from the membrane surface using matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). This approach bypasses the more commonly used multi-step procedures, thereby permitting a more rapid procedure for protein identification. We also highlight the advantage of printing different chemistries onto an individual protein spot for multiple microscale analyses. This ability is particularly useful when detailed characterisation of rare and valuable sample is required. Using a combination of PNGase F and trypsin we have mapped sites of N-glycosylation using on-membrane digestion strategies. We also demonstrate the ability to print multiple serum samples in a micro-ELISA format and rapidly screen a protein macroarray of human blood plasma for pathogen-derived antigens. We anticipate that the 'chemical printer' will be a major component of proteomic platforms for high-throughput protein identification and characterisation with widespread applications in biomedical and diagnostic discovery

Soy versus whey protein bars: Effects on exercise training impact on lean body mass and antioxidant status

Directory of Open Access Journals (Sweden)

Babaknia Ari

2004-12-01

Full Text Available Abstract Background Although soy protein may have many health benefits derived from its associated antioxidants, many male exercisers avoid soy protein. This is due partly to a popular, but untested notion that in males, soy is inferior to whey in promoting muscle weight gain. This study provided a direct comparison between a soy product and a whey product. Methods Lean body mass gain was examined in males from a university weight training class given daily servings of micronutrient-fortified protein bars containing soy or whey protein (33 g protein/day, 9 weeks, n = 9 for each protein treatment group. Training used workouts with fairly low repetition numbers per set. A control group from the class (N = 9 did the training, but did not consume either type protein bar. Results Both the soy and whey treatment groups showed a gain in lean body mass, but the training-only group did not. The whey and training only groups, but not the soy group, showed a potentially deleterious post-training effect on two antioxidant-related related parameters. Conclusions Soy and whey protein bar products both promoted exercise training-induced lean body mass gain, but the soy had the added benefit of preserving two aspects of antioxidant function.

Health issues of whey proteins: 1. Protection of lean body mass

NARCIS (Netherlands)

Schaafsma, G.

2006-01-01

Loss of muscle mass as a consequence of changes in protein metabolism during periods of catabolic stress is a serious complication in a variety of conditions. These conditions are weight loss programs, sarcopenia in the elderly and several clinical states. It appears from many studies that improved

Suspected-target pesticide screening using gas chromatography-quadrupole time-of-flight mass spectrometry with high resolution deconvolution and retention index/mass spectrum library.

Science.gov (United States)

Zhang, Fang; Wang, Haoyang; Zhang, Li; Zhang, Jing; Fan, Ruojing; Yu, Chongtian; Wang, Wenwen; Guo, Yinlong

2014-10-01

A strategy for suspected-target screening of pesticide residues in complicated matrices was exploited using gas chromatography in combination with hybrid quadrupole time-of-flight mass spectrometry (GC-QTOF MS). The screening workflow followed three key steps of, initial detection, preliminary identification, and final confirmation. The initial detection of components in a matrix was done by a high resolution mass spectrum deconvolution; the preliminary identification of suspected pesticides was based on a special retention index/mass spectrum (RI/MS) library that contained both the first-stage mass spectra (MS(1) spectra) and retention indices; and the final confirmation was accomplished by accurate mass measurements of representative ions with their response ratios from the MS(1) spectra or representative product ions from the second-stage mass spectra (MS(2) spectra). To evaluate the applicability of the workflow in real samples, three matrices of apple, spinach, and scallion, each spiked with 165 test pesticides in a set of concentrations, were selected as the models. The results showed that the use of high-resolution TOF enabled effective extractions of spectra from noisy chromatograms, which was based on a narrow mass window (5 mDa) and suspected-target compounds identified by the similarity match of deconvoluted full mass spectra and filtering of linear RIs. On average, over 74% of pesticides at 50 ng/mL could be identified using deconvolution and the RI/MS library. Over 80% of pesticides at 5 ng/mL or lower concentrations could be confirmed in each matrix using at least two representative ions with their response ratios from the MS(1) spectra. In addition, the application of product ion spectra was capable of confirming suspected pesticides with specificity for some pesticides in complicated matrices. In conclusion, GC-QTOF MS combined with the RI/MS library seems to be one of the most efficient tools for the analysis of suspected-target pesticide residues

Absolute nutrient concentration measurements in cell culture media: 1H q-NMR spectra and data to compare the efficiency of pH-controlled protein precipitation versus CPMG or post-processing filtering approaches

Directory of Open Access Journals (Sweden)

Luca Goldoni

2016-09-01

Full Text Available The NMR spectra and data reported in this article refer to the research article titled “A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using q-NMR” [1]. We provide the 1H q-NMR spectra of cell culture media (DMEM after removal of serum proteins, which show the different efficiency of various precipitating solvents, the solvent/DMEM ratios, and pH of the solution. We compare the data of the absolute nutrient concentrations, measured by PULCON external standard method, before and after precipitation of serum proteins and those obtained using CPMG (Carr-Purcell-Meiboom-Gill sequence or applying post-processing filtering algorithms to remove, from the 1H q-NMR spectra, the proteins signal contribution. For each of these approaches, the percent error in the absolute value of every measurement for all the nutrients is also plotted as accuracy assessment. Keywords: 1H NMR, pH-controlled serum removal, PULCON, Accuracy, CPMG, Deconvolution

Alterations in the nuclear matrix protein mass correlate with heat-induced inhibition of DNA single-strand-break repair

International Nuclear Information System (INIS)

Warters, R.L.; Brizgys, L.M.; Lyons, B.W.

1987-01-01

The total protein mass co-isolating with the nuclear matrix or nucleoid from Chinese hamster ovary (CHO) cells was observed to increase in heated cells as a function of increasing exposure temperature between 43 0 C and 45 0 C or of exposure time at any temperature. The sedimentation distance of the CHO cell nucleoid in sucrose gradients increased with increasing exposure time at 45 0 C. Both these nuclear alterations correlated in a log-linear manner with heat-induced inhibition of DNA strand break repair. A two-fold threshold increase in nuclear matrix protein mass preceded any substantial inhibition of repair of DNA single-strand breaks. When preheated cells were incubated at 37 0 C the nuclear matrix protein mass and nucleoid sedimentation recovered with a half-time of about 5 h, while DNA single-strand-break repair recovered with a half-time of about 2 h. When preheated cells were placed at 41 0 C a further increase was observed in the nuclear matrix protein mass and the half-time of DNA strand break repair, while nucleoid sedimentation recovered toward control values. These results implicate alterations in the protein mass of the nuclear matrix in heat-induced inhibition of repair of DNA single-strand breaks. (author)

Statistical analysis of fragmentation patterns of electron ionization mass spectra of enolized-trimethylsilylated anabolic androgenic steroids

Science.gov (United States)

Fragkaki, A. G.; Angelis, Y. S.; Tsantili-Kakoulidou, A.; Koupparis, M.; Georgakopoulos, C.

2009-08-01

Anabolic androgenic steroids (AAS) are included in the List of prohibited substances of the World Anti-Doping Agency (WADA) as substances abused to enhance athletic performance. Gas chromatography coupled to mass spectrometry (GC-MS) plays an important role in doping control analyses identifying AAS as their enolized-trimethylsilyl (TMS)-derivatives using the electron ionization (EI) mode. This paper explores the suitability of complementary GC-MS mass spectra and statistical analysis (principal component analysis, PCA and partial least squares-discriminant analysis, PLS-DA) to differentiate AAS as a function of their structural and conformational features expressed by their fragment ions. The results obtained showed that the application of PCA yielded a classification among the AAS molecules which became more apparent after applying PLS-DA to the dataset. The application of PLS-DA yielded a clear separation among the AAS molecules which were, thus, classified as: 1-ene-3-keto, 3-hydroxyl with saturated A-ring, 1-ene-3-hydroxyl, 4-ene-3-keto, 1,4-diene-3-keto and 3-keto with saturated A-ring anabolic steroids. The study of this paper also presents structurally diagnostic fragment ions and dissociation routes providing evidence for the presence of unknown AAS or chemically modified molecules known as designer steroids.

A hybrid approach to protein differential expression in mass spectrometry-based proteomics

KAUST Repository

Wang, X.

2012-04-19

MOTIVATION: Quantitative mass spectrometry-based proteomics involves statistical inference on protein abundance, based on the intensities of each protein\\'s associated spectral peaks. However, typical MS-based proteomics datasets have substantial proportions of missing observations, due at least in part to censoring of low intensities. This complicates intensity-based differential expression analysis. RESULTS: We outline a statistical method for protein differential expression, based on a simple Binomial likelihood. By modeling peak intensities as binary, in terms of \\'presence/absence,\\' we enable the selection of proteins not typically amenable to quantitative analysis; e.g. \\'one-state\\' proteins that are present in one condition but absent in another. In addition, we present an analysis protocol that combines quantitative and presence/absence analysis of a given dataset in a principled way, resulting in a single list of selected proteins with a single-associated false discovery rate. AVAILABILITY: All R code available here: http://www.stat.tamu.edu/~adabney/share/xuan_code.zip.

Decision peptide-driven: a free software tool for accurate protein quantification using gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry.

Science.gov (United States)

Santos, Hugo M; Reboiro-Jato, Miguel; Glez-Peña, Daniel; Nunes-Miranda, J D; Fdez-Riverola, Florentino; Carvallo, R; Capelo, J L

2010-09-15

The decision peptide-driven tool implements a software application for assisting the user in a protocol for accurate protein quantification based on the following steps: (1) protein separation through gel electrophoresis; (2) in-gel protein digestion; (3) direct and inverse (18)O-labeling and (4) matrix assisted laser desorption ionization time of flight mass spectrometry, MALDI analysis. The DPD software compares the MALDI results of the direct and inverse (18)O-labeling experiments and quickly identifies those peptides with paralleled loses in different sets of a typical proteomic workflow. Those peptides are used for subsequent accurate protein quantification. The interpretation of the MALDI data from direct and inverse labeling experiments is time-consuming requiring a significant amount of time to do all comparisons manually. The DPD software shortens and simplifies the searching of the peptides that must be used for quantification from a week to just some minutes. To do so, it takes as input several MALDI spectra and aids the researcher in an automatic mode (i) to compare data from direct and inverse (18)O-labeling experiments, calculating the corresponding ratios to determine those peptides with paralleled losses throughout different sets of experiments; and (ii) allow to use those peptides as internal standards for subsequent accurate protein quantification using (18)O-labeling. In this work the DPD software is presented and explained with the quantification of protein carbonic anhydrase. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Heavy components coupling effect on building response spectra generation

International Nuclear Information System (INIS)

Liu, T.H.; Johnson, E.R.

1985-01-01

This study investigates the dynamic coupling effect on the floor response spectra between the heavy components and the Reactor Interior (R/I) building in a PWR. The following cases were studied: (I) simplified models of one and two lump mass models representing building and heavy components, and (II) actual plant building and heavy component models. Response spectra are developed at building nodes for all models, using time-history analysis methods. Comparisons of response spectra from various models are made to observe the coupling effects. In some cases, this study found that the coupling would reduce the response spectra values in certain frequency regions even if the coupling is not required according to the above criteria. (orig./HP)

Mining Proteomic Data to Expose Protein Modifications in Methanosarcina mazei strain Gö1

Directory of Open Access Journals (Sweden)

Deborah eLeon

2015-03-01

Full Text Available Proteomic tools identify constituents of complex mixtures, often delivering long lists of identified proteins. The high-throughput methods excel at matching tandem mass spectrometry data to spectra predicted from sequence databases. Unassigned mass spectra are ignored, but could, in principle, provide valuable information on unanticipated modifications and improve protein annotations while consuming limited quantities of material. Strategies to mine information from these discards are presented, along with discussion of features that, when present, provide strong support for modifications. In this study we mined LC-MS/MS datasets of proteolytically-digested concanavalin A pull down fractions from Methanosarcina mazei Gö1 cell lysates. Analyses identified 154 proteins. Many of the observed proteins displayed post-translationally modified forms, including O-formylated and methyl-esterified segments that appear biologically relevant (i.e., not artifacts of sample handling. Interesting cleavages and modifications (e.g., S-cyanylation and trimethylation were observed near catalytic sites of methanogenesis enzymes. Of 31 Methanosarcina protein N-termini recovered by concanavalin A binding or from a previous study, only M. mazei S-layer protein MM1976 and its M. acetivorans C2A orthologue, MA0829, underwent signal peptide excision. Experimental results contrast with predictions from algorithms SignalP 3.0 and Exprot, which were found to over-predict the presence of signal peptides. Proteins MM0002, MM0716, MM1364, and MM1976 were found to be glycosylated, and employing chromatography tailored specifically for glycopeptides will likely reveal more.This study supplements limited, existing experimental datasets of mature archaeal N-termini, including presence or absence of signal peptides, translation initiation sites, and other processing. Methanosarcina surface and membrane proteins are richly modified.

Effect of isospin degree of freedom on transverse momentum spectra

International Nuclear Information System (INIS)

Kaur, Sukhjit; Swati

2013-01-01

We study the effect of isospin degree of freedom, incident energy as well as system mass on the behavior of transverse momentum spectra, dN/p t dp t , of neutrons and protons. We find that most of the nucleons suffer soft collisions. The effect of isospin degree of freedom on transverse spectra diminishes with the increase in the incident energy. In Fermi energy region, transverse momentum spectra of both protons and neutrons show sensitivity toward the density dependence of symmetry energy. (author)

Native Liquid Extraction Surface Analysis Mass Spectrometry: Analysis of Noncovalent Protein Complexes Directly from Dried Substrates

Science.gov (United States)

Martin, Nicholas J.; Griffiths, Rian L.; Edwards, Rebecca L.; Cooper, Helen J.

2015-08-01

Liquid extraction surface analysis (LESA) mass spectrometry is a promising tool for the analysis of intact proteins from biological substrates. Here, we demonstrate native LESA mass spectrometry of noncovalent protein complexes of myoglobin and hemoglobin from a range of surfaces. Holomyoglobin, in which apomyoglobin is noncovalently bound to the prosthetic heme group, was observed following LESA mass spectrometry of myoglobin dried onto glass and polyvinylidene fluoride surfaces. Tetrameric hemoglobin [(αβ)2 4H] was observed following LESA mass spectrometry of hemoglobin dried onto glass and polyvinylidene fluoride (PVDF) surfaces, and from dried blood spots (DBS) on filter paper. Heme-bound dimers and monomers were also observed. The `contact' LESA approach was particularly suitable for the analysis of hemoglobin tetramers from DBS.

Identification of toxic cyclopeptides based on mass spectral library matching

Directory of Open Access Journals (Sweden)

Boris L. Milman

2014-08-01

Full Text Available To gain perspective on the use of tandem mass spectral libraries for identification of toxic cyclic peptides, the new library was built from 263 mass spectra (mainly MS2 spectra of 59 compounds of that group, such as microcystins, amatoxins, and some related compounds. Mass spectra were extracted from the literature or specially acquired on ESI-Q-ToF and MALDI-ToF/ToF tandem instruments. ESI-MS2 product-ion mass spectra appeared to be rather close to MALDI-ToF/ToF fragment spectra which are uncommon for mass spectral libraries. Testing of the library was based on searches where reference spectra were in turn cross-compared. The percentage of 1st rank correct identifications (true positives was 70% in a general case and 88–91% without including knowingly defective (‘one-dimension’ spectra as test ones. The percentage of 88–91% is the principal estimate for the overall performance of this library that can be used in a method of choice for identification of individual cyclopeptides and also for group recognition of individual classes of such peptides. The approach to identification of cyclopeptides based on mass spectral library matching proved to be the most effective for abundant toxins. That was confirmed by analysis of extracts from two cyanobacterial strains.

Supplementing Breakfast with a Vitamin D and Leucine-Enriched Whey Protein Medical Nutrition Drink Enhances Postprandial Muscle Protein Synthesis and Muscle Mass in Healthy Older Men.

Science.gov (United States)

Chanet, Audrey; Verlaan, Sjors; Salles, Jérôme; Giraudet, Christophe; Patrac, Véronique; Pidou, Véronique; Pouyet, Corinne; Hafnaoui, Nordine; Blot, Adeline; Cano, Noël; Farigon, Nicolas; Bongers, Anke; Jourdan, Marion; Luiking, Yvette; Walrand, Stéphane; Boirie, Yves

2017-12-01

Background: A promising strategy to help older adults preserve or build muscle mass is to optimize muscle anabolism through providing an adequate amount of high-quality protein at each meal. Objective: This "proof of principle" study investigated the acute effect of supplementing breakfast with a vitamin D and leucine-enriched whey protein medical nutrition drink on postprandial muscle protein synthesis and longer-term effect on muscle mass in healthy older adults. Methods: A randomized, placebo-controlled, double-blind study was conducted in 24 healthy older men [mean ± SD: age 71 ± 4 y; body mass index (in kg/m 2 ) 24.7 ± 2.8] between September 2012 and October 2013 at the Unit of Human Nutrition, University of Auvergne, Clermont-Ferrand, France. Participants received a medical nutrition drink [test group; 21 g leucine-enriched whey protein, 9 g carbohydrates, 3 g fat, 800 IU cholecalciferol (vitamin D 3 ), and 628 kJ] or a noncaloric placebo (control group) before breakfast for 6 wk. Mixed muscle protein fractional synthesis rate (FSR) was measured at week 0 in the basal and postprandial state, after study product intake with a standardized breakfast with the use of l-[ 2 H 5 ]-phenylalanine tracer methodology. The longer-term effect of the medical nutrition drink was evaluated by measurement of appendicular lean mass, representing skeletal muscle mass at weeks 0 and 6, by dual-energy X-ray absorptiometry. Results: Postprandial FSR (0-240 min) was higher in the test group than in the control group [estimate of difference (ED): 0.022%/h; 95% CI: 0.010%/h, 0.035%/h; ANCOVA, P = 0.001]. The test group gained more appendicular lean mass than the control group after 6 wk (ED: 0.37 kg; 95% CI: 0.03, 0.72 kg; ANCOVA, P = 0.035), predominantly as leg lean mass (ED: 0.30 kg; 95% CI: 0.03, 0.57 kg; ANCOVA, P = 0.034). Conclusions: Supplementing breakfast with a vitamin D and leucine-enriched whey protein medical nutrition drink stimulated postprandial muscle protein

The application of an emerging technique for protein-protein interaction interface mapping: the combination of photo-initiated cross-linking protein nanoprobes with mass spectrometry

Czech Academy of Sciences Publication Activity Database

Ptáčková, Renata; Ječmen, Tomáš; Novák, Petr; Šulc, Miroslav; Hudeček, J.; Stiborová, M.

2014-01-01

Roč. 15, č. 6 (2014), s. 9224-9241 E-ISSN 1422-0067 R&D Projects: GA ČR(CZ) GAP207/12/0627 Grant - others:Universita Karlova(CZ) 903413; Magistrát hlavního města Prahy(CZ) CZ.2.16/3.1.00/24023; UNCE(BE) 204025/2012 Institutional support: RVO:61388971 Keywords : nanoprobes * mass spectrometry * protein-protein interactions Subject RIV: CE - Biochemistry Impact factor: 2.862, year: 2014

Absolute quantitation of proteins by Acid hydrolysis combined with amino Acid detection by mass spectrometry

DEFF Research Database (Denmark)

Mirgorodskaya, Olga A; Körner, Roman; Kozmin, Yuri P

2012-01-01

Amino acid analysis is among the most accurate methods for absolute quantification of proteins and peptides. Here, we combine acid hydrolysis with the addition of isotopically labeled standard amino acids and analysis by mass spectrometry for accurate and sensitive protein quantitation...

Mechanistic Links Underlying the Impact of C-Reactive Protein on Muscle Mass in Elderly

Directory of Open Access Journals (Sweden)

Britta Wåhlin-Larsson

2017-11-01

Full Text Available Background/Aims: Mechanisms underlying the relationship between systemic inflammation and age-related decline in muscle mass are poorly defined. The purpose of this work was to investigate the relationship between the systemic inflammatory marker CRP and muscle mass in elderly and to identify mechanisms by which CRP mediates its effects on skeletal muscle, in-vitro. Methods: Muscle mass and serum CRP level were determined in a cohort of 118 older women (67±1.7 years. Human muscle cells were differentiated into myotubes and were exposed to CRP. The size of myotubes was determined after immunofluorescent staining using troponin. Muscle protein synthesis was assessed using stable isotope tracers and key signalling pathways controlling protein synthesis were determined using western-blotting. Results: We observed an inverse relationship between circulating CRP level and muscle mass (β= -0.646 (95% CI: -0.888, -0.405 p<0.05 and demonstrated a reduction (p < 0.05 in the size of human myotubes exposed to CRP for 72 h. We next showed that this morphological change was accompanied by a CRP-mediated reduction (p < 0.05 in muscle protein fractional synthetic rate of human myotubes exposed to CRP for 24 h. We also identified a CRP-mediated increased phosphorylation (p<0.05 of regulators of cellular energy stress including AMPK and downstream targets, raptor and ACC-β, together with decreased phosphorylation of Akt and rpS6, which are important factors controlling protein synthesis. Conclusion: This work established for the first time mechanistic links by which chronic elevation of CRP can contribute to age-related decline in muscle function.

The effects of general anesthetics on ESR spectra of spin labels in phosphatidylcholine vesicles containing purified Na,K-ATPase or microsomal protein

Energy Technology Data Exchange (ETDEWEB)

Shibuya, Makiko, E-mail: shibu@den.hokudai.ac.jp [Department of Dental Anesthesiology, Graduate School of Dental Medicine, Hokkaido University (Japan); Hiraoki, Toshifumi [Division of Applied Physics, Graduate School of Engineering, Hokkaido University (Japan); Kimura, Kunie; Fukushima, Kazuaki [Department of Dental Anesthesiology, Graduate School of Dental Medicine, Hokkaido University (Japan); Suzuki, Kuniaki [Department of Molecular Cell Pharmacology, Graduate School of Dental Medicine, Hokkaido University (Japan)

2012-12-01

Highlights: Black-Right-Pointing-Pointer We studied the effects of general anesthetics on liposome using ESR spectra. Black-Right-Pointing-Pointer Two spin labels, 5-DSA and 16-DSA, were located in different position in liposome. Black-Right-Pointing-Pointer Anesthetics did not change the environment around the spin labels in the liposome. Black-Right-Pointing-Pointer Anesthetics remained on the surface of the lipid bilayer of liposome. Black-Right-Pointing-Pointer Proteins in the liposome did not change the effects of anesthetics on liposome. - Abstract: We investigated the effects of general anesthetics on liposome containing spin labels, 5-doxyl stearic acid (5-DSA) and 16-doxyl stearic acid (16-DSA), and purified Na,K-ATPase or membrane protein of microsome using an electron spin resonance (ESR) spectroscopy. The spectra of 16-DSA in liposomes with both proteins showed three sharp signals compared with 5-DSA. The difference in the order parameter S value of 5-DSA and 16-DSA suggested that the nitroxide radical location of 5-DSA and 16-DSA were different in the membrane bilayer. The results were almost the same as those obtained in liposomes without proteins. The addition of sevoflurane, isoflurane, halothane, ether, ethanol and propofol increased the intensity of the signals, but the clinical concentrations of anesthetics did not significantly alter the S and {tau} values, which are indices of the fluidity of the membrane. These results suggest that anesthetics remain on the surface of the lipid bilayer and do not act on both the inside hydrophobic area and the relatively hydrophilic area near the surface. These results and others also suggest that the existence of Na,K-ATPase and microsomal proteins did not affect the environment around the spin labels in the liposome and the effects of anesthetics on liposome as a model membrane.

Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics.

Science.gov (United States)

Rajabi, Khadijeh

2015-01-01

A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX.

Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins.

Science.gov (United States)

Lakbub, Jude C; Shipman, Joshua T; Desaire, Heather

2018-04-01

Disulfide bonds are important structural moieties of proteins: they ensure proper folding, provide stability, and ensure proper function. With the increasing use of proteins for biotherapeutics, particularly monoclonal antibodies, which are highly disulfide bonded, it is now important to confirm the correct disulfide bond connectivity and to verify the presence, or absence, of disulfide bond variants in the protein therapeutics. These studies help to ensure safety and efficacy. Hence, disulfide bonds are among the critical quality attributes of proteins that have to be monitored closely during the development of biotherapeutics. However, disulfide bond analysis is challenging because of the complexity of the biomolecules. Mass spectrometry (MS) has been the go-to analytical tool for the characterization of such complex biomolecules, and several methods have been reported to meet the challenging task of mapping disulfide bonds in proteins. In this review, we describe the relevant, recent MS-based techniques and provide important considerations needed for efficient disulfide bond analysis in proteins. The review focuses on methods for proper sample preparation, fragmentation techniques for disulfide bond analysis, recent disulfide bond mapping methods based on the fragmentation techniques, and automated algorithms designed for rapid analysis of disulfide bonds from liquid chromatography-MS/MS data. Researchers involved in method development for protein characterization can use the information herein to facilitate development of new MS-based methods for protein disulfide bond analysis. In addition, individuals characterizing biotherapeutics, especially by disulfide bond mapping in antibodies, can use this review to choose the best strategies for disulfide bond assignment of their biologic products. Graphical Abstract This review, describing characterization methods for disulfide bonds in proteins, focuses on three critical components: sample preparation, mass

Electrospray ionization and matrix assisted laser desorption/ionization mass spectrometry: powerful analytical tools in recombinant protein chemistry

DEFF Research Database (Denmark)

Andersen, Jens S.; Svensson, B; Roepstorff, P

1996-01-01

Electrospray ionization and matrix assisted laser desorption/ionization are effective ionization methods for mass spectrometry of biomolecules. Here we describe the capabilities of these methods for peptide and protein characterization in biotechnology. An integrated analytical strategy is presen......Electrospray ionization and matrix assisted laser desorption/ionization are effective ionization methods for mass spectrometry of biomolecules. Here we describe the capabilities of these methods for peptide and protein characterization in biotechnology. An integrated analytical strategy...... is presented encompassing protein characterization prior to and after cloning of the corresponding gene....

Funny hills in pion spectra from heavy-ion collisions

International Nuclear Information System (INIS)

Rasmussen, J.O.

1982-03-01

A discussion of some of the systematic features of the pion spectra in heavy-ions reactions is given. A discussion of the hills and valleys in heavy ion pion spectra that show up at the lower pion energies is given. The following topics are discussed: (1) three kinds of funny hills; (2) π - / + ratios near center of mass; (3) new Monte Carlo studies of charged pion spectra; and (4) pion orbiting about fireballs and Bose-Einstein behavior as explanation for the mid-rapidity P/sub perpendicular to/ approx. = 0.4 to 0.5 m/sub π/c hill

Parallel β-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: quantitative benchmark for the interpretation of amyloid and protein infrared spectra.

Science.gov (United States)

Woys, Ann Marie; Almeida, Aaron M; Wang, Lu; Chiu, Chi-Cheng; McGovern, Michael; de Pablo, Juan J; Skinner, James L; Gellman, Samuel H; Zanni, Martin T

2012-11-21

protected inside the macrocycle. This work provides calculated and experimentally verified couplings for parallel β-sheets that can be used in structure-based models to simulate and interpret the infrared spectra of β-sheet containing proteins and protein assemblies, such as amyloid fibers.

Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry

OpenAIRE

Singh, Pramod Kumar; Shrivastava, Nidhi; Chaturvedi, Krishna; Sharma, Bechan; Bhagyawant, Sameer S.

2016-01-01

Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0–10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected ...

High insulin-like growth factor-binding protein-1 (IGFBP-1) is associated with low relative muscle mass in older women

DEFF Research Database (Denmark)

Stilling, Frej; Wallenius, Sara; Michaëlsson, Karl

2017-01-01

. In the present study we investigate the association between serum IGFBP-1 and muscle mass. Design Cross-sectional analysis of 4908 women, between 55 and 85 years old, participating in the Swedish Mammography Cohort-Clinical. Methods We defined low relative muscle mass (LRMM) as an appendicular lean mass divided...... relative muscle mass. High IGFBP-1 may be a marker of a catabolic state.......Objective Skeletal muscles serve several important roles in maintaining good health. Insulin-like growth factor-1 (IGF-1) is a promoter of protein synthesis in skeletal muscle. Its binding protein, Insulin-like growth factor-binding protein-1 (IGFBP-1) can be one determinant of IGF-1 activity...

Search for electroweak production of supersymmetric states in scenarios with compressed mass spectra at √{s }=13 TeV with the ATLAS detector

Science.gov (United States)

Aaboud, M.; Aad, G.; Abbott, B.; Abdinov, O.; Abeloos, B.; Abidi, S. H.; Abouzeid, O. S.; Abraham, N. L.; Abramowicz, H.; Abreu, H.; Abulaiti, Y.; Acharya, B. S.; Adachi, S.; Adamczyk, L.; Adelman, J.; Adersberger, M.; Adye, T.; Affolder, A. A.; Afik, Y.; Agheorghiesei, C.; Aguilar-Saavedra, J. A.; Ahlen, S. P.; Ahmadov, F.; Aielli, G.; Akatsuka, S.; Åkesson, T. P. A.; Akilli, E.; Akimov, A. V.; Alberghi, G. L.; Albert, J.; Albicocco, P.; Alconada Verzini, M. J.; Alderweireldt, S. C.; Aleksa, M.; Aleksandrov, I. N.; Alexa, C.; Alexander, G.; Alexopoulos, T.; Alhroob, M.; Ali, B.; Aliev, M.; Alimonti, G.; Alison, J.; Alkire, S. P.; Allaire, C.; Allbrooke, B. M. M.; Allen, B. W.; Allport, P. P.; Aloisio, A.; Alonso, A.; Alonso, F.; Alpigiani, C.; Alshehri, A. A.; Alstaty, M. I.; Alvarez Gonzalez, B.; Álvarez Piqueras, D.; Alviggi, M. G.; Amadio, B. T.; Amaral Coutinho, Y.; Ambroz, L.; Amelung, C.; Amidei, D.; Amor Dos Santos, S. P.; Amoroso, S.; Anastopoulos, C.; Ancu, L. S.; Andari, N.; Andeen, T.; Anders, C. F.; Anders, J. K.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Angelidakis, S.; Angelozzi, I.; Angerami, A.; Anisenkov, A. V.; Annovi, A.; Antel, C.; Antonelli, M.; Antonov, A.; Antrim, D. J.; Anulli, F.; Aoki, M.; Aperio Bella, L.; Arabidze, G.; Arai, Y.; Araque, J. P.; Araujo Ferraz, V.; Araujo Pereira, R.; Arce, A. T. H.; Ardell, R. E.; Arduh, F. A.; Arguin, J.-F.; Argyropoulos, S.; Armbruster, A. J.; Armitage, L. J.; Arnaez, O.; Arnold, H.; Arratia, M.; Arslan, O.; Artamonov, A.; Artoni, G.; Artz, S.; Asai, S.; Asbah, N.; Ashkenazi, A.; Asquith, L.; Assamagan, K.; Astalos, R.; Atkin, R. J.; Atkinson, M.; Atlay, N. B.; Augsten, K.; Avolio, G.; Avramidou, R.; Axen, B.; Ayoub, M. K.; Azuelos, G.; Baas, A. E.; Baca, M. J.; Bachacou, H.; Bachas, K.; Backes, M.; Bagnaia, P.; Bahmani, M.; Bahrasemani, H.; Baines, J. T.; Bajic, M.; Baker, O. K.; Bakker, P. J.; Bakshi Gupta, D.; Baldin, E. M.; Balek, P.; Balli, F.; Balunas, W. K.; Banas, E.; Bandyopadhyay, A.; Banerjee, Sw.; Bannoura, A. A. E.; Barak, L.; Barberio, E. L.; Barberis, D.; Barbero, M.; Barillari, T.; Barisits, M.-S.; Barkeloo, J. T.; Barklow, T.; Barlow, N.; Barnes, S. L.; Barnett, B. M.; Barnett, R. M.; Barnovska-Blenessy, Z.; Baroncelli, A.; Barone, G.; Barr, A. J.; Barranco Navarro, L.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Bartoldus, R.; Barton, A. E.; Bartos, P.; Basalaev, A.; Bassalat, A.; Bates, R. L.; Batista, S. J.; Batley, J. R.; Battaglia, M.; Bauce, M.; Bauer, F.; Bauer, K. T.; Bawa, H. S.; Beacham, J. B.; Beattie, M. D.; Beau, T.; Beauchemin, P. H.; Bechtle, P.; Beck, H. P.; Beck, H. C.; Becker, K.; Becker, M.; Becot, C.; Beddall, A. J.; Beddall, A.; Bednyakov, V. A.; Bedognetti, M.; Bee, C. P.; Beermann, T. A.; Begalli, M.; Begel, M.; Behera, A.; Behr, J. K.; Bell, A. S.; Bella, G.; Bellagamba, L.; Bellerive, A.; Bellomo, M.; Belotskiy, K.; Belyaev, N. L.; Benary, O.; Benchekroun, D.; Bender, M.; Benekos, N.; Benhammou, Y.; Benhar Noccioli, E.; Benitez, J.; Benjamin, D. P.; Benoit, M.; Bensinger, J. R.; Bentvelsen, S.; Beresford, L.; Beretta, M.; Berge, D.; Bergeaas Kuutmann, E.; Berger, N.; Bergsten, L. J.; Beringer, J.; Berlendis, S.; Bernard, N. R.; Bernardi, G.; Bernius, C.; Bernlochner, F. U.; Berry, T.; Berta, P.; Bertella, C.; Bertoli, G.; Bertram, I. A.; Bertsche, C.; Besjes, G. J.; Bessidskaia Bylund, O.; Bessner, M.; Besson, N.; Bethani, A.; Bethke, S.; Betti, A.; Bevan, A. J.; Beyer, J.; Bianchi, R. M.; Biebel, O.; Biedermann, D.; Bielski, R.; Bierwagen, K.; Biesuz, N. V.; Biglietti, M.; Billoud, T. R. V.; Bindi, M.; Bingul, A.; Bini, C.; Biondi, S.; Bisanz, T.; Bittrich, C.; Bjergaard, D. M.; Black, J. E.; Black, K. M.; Blair, R. E.; Blazek, T.; Bloch, I.; Blocker, C.; Blue, A.; Blumenschein, U.; Blunier, Dr.; Bobbink, G. J.; Bobrovnikov, V. S.; Bocchetta, S. 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W.; Higashino, S.; Higón-Rodriguez, E.; Hildebrand, K.; Hill, E.; Hill, J. C.; Hiller, K. H.; Hillier, S. J.; Hils, M.; Hinchliffe, I.; Hirose, M.; Hirschbuehl, D.; Hiti, B.; Hladik, O.; Hlaluku, D. R.; Hoad, X.; Hobbs, J.; Hod, N.; Hodgkinson, M. C.; Hoecker, A.; Hoeferkamp, M. R.; Hoenig, F.; Hohn, D.; Hohov, D.; Holmes, T. R.; Holzbock, M.; Homann, M.; Honda, S.; Honda, T.; Hong, T. M.; Hooberman, B. H.; Hopkins, W. H.; Horii, Y.; Horton, A. J.; Horyn, L. A.; Hostachy, J.-Y.; Hostiuc, A.; Hou, S.; Hoummada, A.; Howarth, J.; Hoya, J.; Hrabovsky, M.; Hrdinka, J.; Hristova, I.; Hrivnac, J.; Hryn'ova, T.; Hrynevich, A.; Hsu, P. J.; Hsu, S.-C.; Hu, Q.; Hu, S.; Huang, Y.; Hubacek, Z.; Hubaut, F.; Huegging, F.; Huffman, T. B.; Hughes, E. W.; Huhtinen, M.; Hunter, R. F. H.; Huo, P.; Hupe, A. M.; Huseynov, N.; Huston, J.; Huth, J.; Hyneman, R.; Iacobucci, G.; Iakovidis, G.; Ibragimov, I.; Iconomidou-Fayard, L.; Idrissi, Z.; Iengo, P.; Igonkina, O.; Iizawa, T.; Ikegami, Y.; Ikeno, M.; Iliadis, D.; Ilic, N.; Iltzsche, F.; Introzzi, G.; Iodice, M.; Iordanidou, K.; Ippolito, V.; Isacson, M. F.; Ishijima, N.; Ishino, M.; Ishitsuka, M.; Issever, C.; Istin, S.; Ito, F.; Iturbe Ponce, J. M.; Iuppa, R.; Iwasaki, H.; Izen, J. M.; Izzo, V.; Jabbar, S.; Jacka, P.; Jackson, P.; Jacobs, R. M.; Jain, V.; Jakel, G.; Jakobi, K. B.; Jakobs, K.; Jakobsen, S.; Jakoubek, T.; Jamin, D. O.; Jana, D. K.; Jansky, R.; Janssen, J.; Janus, M.; Janus, P. A.; Jarlskog, G.; Javadov, N.; Javå¯Rek, T.; Javurkova, M.; Jeanneau, F.; Jeanty, L.; Jejelava, J.; Jelinskas, A.; Jenni, P.; Jeske, C.; Jézéquel, S.; Ji, H.; Jia, J.; Jiang, H.; Jiang, Y.; Jiang, Z.; Jiggins, S.; Jimenez Pena, J.; Jin, S.; Jinaru, A.; Jinnouchi, O.; Jivan, H.; Johansson, P.; Johns, K. A.; Johnson, C. A.; Johnson, W. J.; Jon-And, K.; Jones, R. W. L.; Jones, S. D.; Jones, S.; Jones, T. J.; Jongmanns, J.; Jorge, P. M.; Jovicevic, J.; Ju, X.; Juste Rozas, A.; Kaczmarska, A.; Kado, M.; Kagan, H.; Kagan, M.; Kahn, S. J.; Kaji, T.; Kajomovitz, E.; Kalderon, C. W.; Kaluza, A.; Kama, S.; Kamenshchikov, A.; Kanjir, L.; Kano, Y.; Kantserov, V. A.; Kanzaki, J.; Kaplan, B.; Kaplan, L. S.; Kar, D.; Karakostas, K.; Karastathis, N.; Kareem, M. J.; Karentzos, E.; Karpov, S. N.; Karpova, Z. M.; Kartvelishvili, V.; Karyukhin, A. N.; Kasahara, K.; Kashif, L.; Kass, R. D.; Kastanas, A.; Kataoka, Y.; Kato, C.; Katre, A.; Katzy, J.; Kawade, K.; Kawagoe, K.; Kawamoto, T.; Kawamura, G.; Kay, E. F.; Kazanin, V. F.; Keeler, R.; Kehoe, R.; Keller, J. S.; Kellermann, E.; Kempster, J. J.; Kendrick, J.; Keoshkerian, H.; Kepka, O.; Kerševan, B. P.; Kersten, S.; Keyes, R. A.; Khader, M.; Khalil-Zada, F.; Khanov, A.; Kharlamov, A. G.; Kharlamova, T.; Khodinov, A.; Khoo, T. 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E.; Strandberg, J.; Strandberg, S.; Strauss, M.; Strizenec, P.; Ströhmer, R.; Strom, D. M.; Stroynowski, R.; Strubig, A.; Stucci, S. A.; Stugu, B.; Styles, N. A.; Su, D.; Su, J.; Suchek, S.; Sugaya, Y.; Suk, M.; Sulin, V. V.; Sultan, Dms; Sultansoy, S.; Sumida, T.; Sun, S.; Sun, X.; Suruliz, K.; Suster, C. J. E.; Sutton, M. R.; Suzuki, S.; Svatos, M.; Swiatlowski, M.; Swift, S. P.; Sydorenko, A.; Sykora, I.; Sykora, T.; Ta, D.; Tackmann, K.; Taenzer, J.; Taffard, A.; Tafirout, R.; Tahirovic, E.; Taiblum, N.; Takai, H.; Takashima, R.; Takasugi, E. H.; Takeda, K.; Takeshita, T.; Takubo, Y.; Talby, M.; Talyshev, A. A.; Tanaka, J.; Tanaka, M.; Tanaka, R.; Tanioka, R.; Tannenwald, B. B.; Tapia Araya, S.; Tapprogge, S.; Tarek Abouelfadl Mohamed, A. T.; Tarem, S.; Tarna, G.; Tartarelli, G. F.; Tas, P.; Tasevsky, M.; Tashiro, T.; Tassi, E.; Tavares Delgado, A.; Tayalati, Y.; Taylor, A. C.; Taylor, A. J.; Taylor, G. N.; Taylor, P. T. E.; Taylor, W.; Teixeira-Dias, P.; Temple, D.; Ten Kate, H.; Teng, P. K.; Teoh, J. J.; Tepel, F.; Terada, S.; Terashi, K.; Terron, J.; Terzo, S.; Testa, M.; Teuscher, R. J.; Thais, S. J.; Theveneaux-Pelzer, T.; Thiele, F.; Thomas, J. P.; Thompson, P. D.; Thompson, A. S.; Thomsen, L. A.; Thomson, E.; Tian, Y.; Ticse Torres, R. E.; Tikhomirov, V. O.; Tikhonov, Yu. A.; Timoshenko, S.; Tipton, P.; Tisserant, S.; Todome, K.; Todorova-Nova, S.; Todt, S.; Tojo, J.; Tokár, S.; Tokushuku, K.; Tolley, E.; Tomoto, M.; Tompkins, L.; Toms, K.; Tong, B.; Tornambe, P.; Torrence, E.; Torres, H.; Torró Pastor, E.; Toth, J.; Touchard, F.; Tovey, D. R.; Treado, C. J.; Trefzger, T.; Tresoldi, F.; Tricoli, A.; Trigger, I. M.; Trincaz-Duvoid, S.; Tripiana, M. F.; Trischuk, W.; Trocmé, B.; Trofymov, A.; Troncon, C.; Trovatelli, M.; Truong, L.; Trzebinski, M.; Trzupek, A.; Tsang, K. W.; Tseng, J. C.-L.; Tsiareshka, P. V.; Tsirintanis, N.; Tsiskaridze, S.; Tsiskaridze, V.; Tskhadadze, E. G.; Tsukerman, I. I.; Tsulaia, V.; Tsuno, S.; Tsybychev, D.; Tu, Y.; Tudorache, A.; Tudorache, V.; Tulbure, T. T.; Tuna, A. N.; Turchikhin, S.; Turgeman, D.; Turk Cakir, I.; Turra, R.; Tuts, P. M.; Ucchielli, G.; Ueda, I.; Ughetto, M.; Ukegawa, F.; Unal, G.; Undrus, A.; Unel, G.; Ungaro, F. C.; Unno, Y.; Uno, K.; Urban, J.; Urquijo, P.; Urrejola, P.; Usai, G.; Usui, J.; Vacavant, L.; Vacek, V.; Vachon, B.; Vadla, K. O. H.; Vaidya, A.; Valderanis, C.; Valdes Santurio, E.; Valente, M.; Valentinetti, S.; Valero, A.; Valéry, L.; Vallier, A.; Valls Ferrer, J. A.; van den Wollenberg, W.; van der Graaf, H.; van Gemmeren, P.; van Nieuwkoop, J.; van Vulpen, I.; van Woerden, M. C.; Vanadia, M.; Vandelli, W.; Vaniachine, A.; Vankov, P.; Vari, R.; Varnes, E. W.; Varni, C.; Varol, T.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vasquez, J. G.; Vasquez, G. A.; Vazeille, F.; Vazquez Furelos, D.; Vazquez Schroeder, T.; Veatch, J.; Veloce, L. M.; Veloso, F.; Veneziano, S.; Ventura, A.; Venturi, M.; Venturi, N.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, A. T.; Vermeulen, J. C.; Vetterli, M. C.; Viaux Maira, N.; Viazlo, O.; Vichou, I.; Vickey, T.; Vickey Boeriu, O. E.; Viehhauser, G. H. A.; Viel, S.; Vigani, L.; Villa, M.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinogradov, V. B.; Vishwakarma, A.; Vittori, C.; Vivarelli, I.; Vlachos, S.; Vogel, M.; Vokac, P.; Volpi, G.; von Buddenbrock, S. E.; von Toerne, E.; Vorobel, V.; Vorobev, K.; Vos, M.; Vossebeld, J. H.; Vranjes, N.; Vranjes Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Vuillermet, R.; Vukotic, I.; Wagner, P.; Wagner, W.; Wagner-Kuhr, J.; Wahlberg, H.; Wahrmund, S.; Wakamiya, K.; Walder, J.; Walker, R.; Walkowiak, W.; Wallangen, V.; Wang, A. M.; Wang, C.; Wang, F.; Wang, H.; Wang, H.; Wang, J.; Wang, J.; Wang, Q.; Wang, R.-J.; Wang, R.; Wang, S. M.; Wang, T.; Wang, W.; Wang, W.; Wang, Z.; Wanotayaroj, C.; Warburton, A.; Ward, C. P.; Wardrope, D. R.; Washbrook, A.; Watkins, P. M.; Watson, A. T.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, B. M.; Webb, A. F.; Webb, S.; Weber, M. S.; Weber, S. M.; Weber, S. A.; Webster, J. S.; Weidberg, A. R.; Weinert, B.; Weingarten, J.; Weirich, M.; Weiser, C.; Wells, P. S.; Wenaus, T.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M. D.; Werner, P.; Wessels, M.; Weston, T. D.; Whalen, K.; Whallon, N. L.; Wharton, A. M.; White, A. S.; White, A.; White, M. J.; White, R.; Whiteson, D.; Whitmore, B. W.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wiglesworth, C.; Wiik-Fuchs, L. A. M.; Wildauer, A.; Wilk, F.; Wilkens, H. G.; Williams, H. H.; Williams, S.; Willis, C.; Willocq, S.; Wilson, J. A.; Wingerter-Seez, I.; Winkels, E.; Winklmeier, F.; Winston, O. J.; Winter, B. T.; Wittgen, M.; Wobisch, M.; Wolf, A.; Wolf, T. M. H.; Wolff, R.; Wolter, M. W.; Wolters, H.; Wong, V. W. S.; Woods, N. L.; Worm, S. D.; Wosiek, B. K.; Wozniak, K. W.; Wu, M.; Wu, S. L.; Wu, X.; Wu, Y.; Wyatt, T. R.; Wynne, B. M.; Xella, S.; Xi, Z.; Xia, L.; Xu, D.; Xu, L.; Xu, T.; Xu, W.; Yabsley, B.; Yacoob, S.; Yajima, K.; Yallup, D. P.; Yamaguchi, D.; Yamaguchi, Y.; Yamamoto, A.; Yamanaka, T.; Yamane, F.; Yamatani, M.; Yamazaki, T.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, H.; Yang, S.; Yang, Y.; Yang, Z.; Yao, W.-M.; Yap, Y. C.; Yasu, Y.; Yatsenko, E.; Yau Wong, K. H.; Ye, J.; Ye, S.; Yeletskikh, I.; Yigitbasi, E.; Yildirim, E.; Yorita, K.; Yoshihara, K.; Young, C.; Young, C. J. S.; Yu, J.; Yu, J.; Yuen, S. P. Y.; Yusuff, I.; Zabinski, B.; Zacharis, G.; Zaidan, R.; Zaitsev, A. M.; Zakharchuk, N.; Zalieckas, J.; Zambito, S.; Zanzi, D.; Zeitnitz, C.; Zemaityte, G.; Zeng, J. C.; Zeng, Q.; Zenin, O.; Ženiš, T.; Zerwas, D.; Zhang, D.; Zhang, D.; Zhang, F.; Zhang, G.; Zhang, H.; Zhang, J.; Zhang, L.; Zhang, L.; Zhang, M.; Zhang, P.; Zhang, R.; Zhang, R.; Zhang, X.; Zhang, Y.; Zhang, Z.; Zhao, X.; Zhao, Y.; Zhao, Z.; Zhemchugov, A.; Zhou, B.; Zhou, C.; Zhou, L.; Zhou, M.; Zhou, M.; Zhou, N.; Zhou, Y.; Zhu, C. G.; Zhu, H.; Zhu, J.; Zhu, Y.; Zhuang, X.; Zhukov, K.; Zhulanov, V.; Zibell, A.; Zieminska, D.; Zimine, N. I.; Zimmermann, S.; Zinonos, Z.; Zinser, M.; Ziolkowski, M.; Živković, L.; Zobernig, G.; Zoccoli, A.; Zorbas, T. G.; Zou, R.; Zur Nedden, M.; Zwalinski, L.; Atlas Collaboration

2018-03-01

A search for electroweak production of supersymmetric particles in scenarios with compressed mass spectra in final states with two low-momentum leptons and missing transverse momentum is presented. This search uses proton-proton collision data recorded by the ATLAS detector at the Large Hadron Collider in 2015-2016, corresponding to 36.1 fb-1 of integrated luminosity at √{s }=13 TeV . Events with same-flavor pairs of electrons or muons with opposite electric charge are selected. The data are found to be consistent with the Standard Model prediction. Results are interpreted using simplified models of R -parity-conserving supersymmetry in which there is a small mass difference between the masses of the produced supersymmetric particles and the lightest neutralino. Exclusion limits at 95% confidence level are set on next-to-lightest neutralino masses of up to 145 GeV for Higgsino production and 175 GeV for wino production, and slepton masses of up to 190 GeV for pair production of sleptons. In the compressed mass regime, the exclusion limits extend down to mass splittings of 2.5 GeV for Higgsino production, 2 GeV for wino production, and 1 GeV for slepton production. The results are also interpreted in the context of a radiatively-driven natural supersymmetry model with nonuniversal Higgs boson masses.

Effects of Whey Protein Alone or as Part of a Multi-ingredient Formulation on Strength, Fat-Free Mass, or Lean Body Mass in Resistance-Trained Individuals: A Meta-analysis.

Science.gov (United States)

Naclerio, Fernando; Larumbe-Zabala, Eneko

2016-01-01

Even though the positive effects of whey protein-containing supplements for optimizing the anabolic responses and adaptations process in resistance-trained individuals have been supported by several investigations, their use continues to be controversial. Additionally, the administration of different multi-ingredient formulations where whey proteins are combined with carbohydrates, other protein sources, creatine, and amino acids or derivatives, has been extensively proposed as an effective strategy to maximize strength and muscle mass gains in athletes. We aimed to systematically summarize and quantify whether whey protein-containing supplements, administered alone or as a part of a multi-ingredient, could improve the effects of resistance training on fat-free mass or lean body mass, and strength in resistance-trained individuals when compared with other iso-energetic supplements containing carbohydrates or other sources of proteins. A structured literature search was conducted on PubMed, Science Direct, Web of Science, Cochrane Libraries, US National Institutes of Health clinicaltrials.gov, SPORTDiscus, and Google Scholar databases. Main inclusion criteria comprised randomized controlled trial study design, adults (aged 18 years and over), resistance-trained individuals, interventions (a resistance training program for a period of 6 weeks or longer, combined with whey protein supplementation administered alone or as a part of a multi-ingredient), and a calorie equivalent contrast supplement from carbohydrates or other non-whey protein sources. Continuous data on fat-free mass and lean body mass, and maximal strength were pooled using a random-effects model. Data from nine randomized controlled trials were included, involving 11 treatments and 192 participants. Overall, with respect to the ingestion of contrast supplements, whey protein supplementation, administered alone or as part of a multi-ingredient, in combination with resistance training, was associated

A computational platform for MALDI-TOF mass spectrometry data: application to serum and plasma samples.

Science.gov (United States)

Mantini, Dante; Petrucci, Francesca; Pieragostino, Damiana; Del Boccio, Piero; Sacchetta, Paolo; Candiano, Giovanni; Ghiggeri, Gian Marco; Lugaresi, Alessandra; Federici, Giorgio; Di Ilio, Carmine; Urbani, Andrea

2010-01-03

Mass spectrometry (MS) is becoming the gold standard for biomarker discovery. Several MS-based bioinformatics methods have been proposed for this application, but the divergence of the findings by different research groups on the same MS data suggests that the definition of a reliable method has not been achieved yet. In this work, we propose an integrated software platform, MASCAP, intended for comparative biomarker detection from MALDI-TOF MS data. MASCAP integrates denoising and feature extraction algorithms, which have already shown to provide consistent peaks across mass spectra; furthermore, it relies on statistical analysis and graphical tools to compare the results between groups. The effectiveness in mass spectrum processing is demonstrated using MALDI-TOF data, as well as SELDI-TOF data. The usefulness in detecting potential protein biomarkers is shown comparing MALDI-TOF mass spectra collected from serum and plasma samples belonging to the same clinical population. The analysis approach implemented in MASCAP may simplify biomarker detection, by assisting the recognition of proteomic expression signatures of the disease. A MATLAB implementation of the software and the data used for its validation are available at http://www.unich.it/proteomica/bioinf. (c) 2009 Elsevier B.V. All rights reserved.

Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry for the Investigation of Proteins and Peptides

Science.gov (United States)

Burnum, Kristin E.; Frappier, Sara L.; Caprioli, Richard M.

2008-07-01

Mass spectrometry (MS) is an excellent technology for molecular imaging because of its high data dimensionality. MS can monitor thousands of individual molecular data channels measured as mass-to-charge (m/z). We describe the use of matrix-assisted laser desorption/ionization (MALDI) MS for the image analysis of proteins, peptides, lipids, drugs, and metabolites in tissues. We discuss the basic instrumentation and sample preparation methods needed to produce high-resolution images and high image reproducibility. Matrix-addition protocols are briefly discussed along with normal operating procedures, and selected biological and medical applications of MALDI imaging MS are described. We give examples of both two- and three-dimensional imaging, including normal mouse embryo implantation, sperm maturation in mouse epididymis, protein distributions in brain sections, protein alterations as a result of drug administration, and protein changes in brain due to neurodegeneration and tumor formation. Advantages of this technology and future challenges for its improvement are discussed.

Targeted mass spectrometry analysis of neutrophil-derived proteins released during sepsis progression

DEFF Research Database (Denmark)

Malmström, E; Davidova, A; Mörgelin, M

2014-01-01

systemic stimulation an immediate increase of neutrophil-borne proteins can be observed into the circulation of sepsis patients. We applied a combination of mass spectrometry (MS) based approaches, LC-MS/MS and selected reaction monitoring (SRM), to characterise and quantify the neutrophil proteome......Early diagnosis of severe infectious diseases is essential for timely implementation of lifesaving therapies. In a search for novel biomarkers in sepsis diagnosis we focused on polymorphonuclear neutrophils (PMNs). Notably, PMNs have their protein cargo readily stored in granules and following...

The BDNYC database of low-mass stars, brown dwarfs, and planetary mass companions

Science.gov (United States)

Cruz, Kelle; Rodriguez, David; Filippazzo, Joseph; Gonzales, Eileen; Faherty, Jacqueline K.; Rice, Emily; BDNYC

2018-01-01

We present a web-interface to a database of low-mass stars, brown dwarfs, and planetary mass companions. Users can send SELECT SQL queries to the database, perform searches by coordinates or name, check the database inventory on specified objects, and even plot spectra interactively. The initial version of this database contains information for 198 objects and version 2 will contain over 1000 objects. The database currently includes photometric data from 2MASS, WISE, and Spitzer and version 2 will include a significant portion of the publicly available optical and NIR spectra for brown dwarfs. The database is maintained and curated by the BDNYC research group and we welcome contributions from other researchers via GitHub.

In-Depth Characterization of Protein Disulfide Bonds by Online Liquid Chromatography-Electrochemistry-Mass Spectrometry

Science.gov (United States)

Switzar, Linda; Nicolardi, Simone; Rutten, Julie W.; Oberstein, Saskia A. J. Lesnik; Aartsma-Rus, Annemieke; van der Burgt, Yuri E. M.

2016-01-01

Disulfide bonds are an important class of protein post-translational modifications, yet this structurally crucial modification type is commonly overlooked in mass spectrometry (MS)-based proteomics approaches. Recently, the benefits of online electrochemistry-assisted reduction of protein S-S bonds prior to MS analysis were exemplified by successful characterization of disulfide bonds in peptides and small proteins. In the current study, we have combined liquid chromatography (LC) with electrochemistry (EC) and mass analysis by Fourier transform ion cyclotron resonance (FTICR) MS in an online LC-EC-MS platform to characterize protein disulfide bonds in a bottom-up proteomics workflow. A key advantage of a LC-based strategy is the use of the retention time in identifying both intra- and interpeptide disulfide bonds. This is demonstrated by performing two sequential analyses of a certain protein digest, once without and once with electrochemical reduction. In this way, the "parent" disulfide-linked peptide detected in the first run has a retention time-based correlation with the EC-reduced peptides detected in the second run, thus simplifying disulfide bond mapping. Using this platform, both inter- and intra-disulfide-linked peptides were characterized in two different proteins, ß-lactoglobulin and ribonuclease B. In order to prevent disulfide reshuffling during the digestion process, proteins were digested at a relatively low pH, using (a combination of) the high specificity proteases trypsin and Glu-C. With this approach, disulfide bonds in ß-lactoglobulin and ribonuclease B were comprehensively identified and localized, showing that online LC-EC-MS is a useful tool for the characterization of protein disulfide bonds.

The effect of instanton-induced interaction on P-wave meson spectra ...

Indian Academy of Sciences (India)

possible to reproduce the observed spectra as the tensor and spin-orbit terms of. OGEP are attractive, and hence naturally triplet states masses will be lower than the corresponding singlet states. Hence, to reproduce the full P-wave spectra it is essential to include the hyperfine interaction term of III to have a consistent. 76.

ROSAT Energy Spectra of Low-Mass X-Ray Binaries

Science.gov (United States)

Schulz, N. S.

1999-01-01

The 0.1-2.4 keV bandpass of the ROSAT Position Sensitive Proportional Counter (PSPC) offers an opportunity to study the very soft X-ray continuum of bright low-mass X-ray binaries (LMXBs). In 46 pointed observations, 23 LMXBs were observed with count rates between 0.4 and 165.4 counts s-1. The survey identified a total of 29 different luminosity levels, which are compared with observations and identified spectral states from other missions. The atoll source 4U 1705-44 was observed near Eddington luminosities in an unusually high intensity state. Spectral analysis provided a measure of the interstellar column density for all 49 observations. The sensitivity of spectral fits depends strongly on column density. Fits to highly absorbed spectra are merely insensitive toward any particular spectral model. Sources with column densities well below 1022 cm-2 are best fitted by power laws, while the blackbody model gives clearly worse fits to the data. Most single-component fits from sources with low column densities, however, are not acceptable at all. The inclusion of a blackbody component in eight sources can improve the fits significantly. The obtained emission radii of less than 5 km suggest emission from the neutron star surface. In 10 sources acceptable fits can only be achieved by including soft-line components. With a spectral resolution of the PSPC of 320-450 eV, between 0.6 and 1.2 keV unresolved broad-line features were detected around 0.65, 0.85, and 1.0 keV. The line fluxes range within 10-11 and 10-12 ergs cm-2 s-1, with equivalent widths between 24 and 210 eV. In LMC X-2, 2S 0918-549, and 4U 1254-690, line emission is indicated for the first time. The soft emission observed in 4U 0614+091 compares with recent ASCA results, with a new feature indicated at 1.31 keV. The deduced line fluxes in 4U 1820-30 and Cyg X-2 showed variability of a factor of 2 within timescales of 1-2 days. Average fluxes of line components in 4U 1820-30 varied by the same factor over a

Dietary protein content alters energy expenditure and composition of the mass gain in grizzly bears (Ursus arctos horribilis).

Science.gov (United States)

Felicetti, Laura A; Robbins, Charles T; Shipley, Lisa A

2003-01-01

Many fruits contain high levels of available energy but very low levels of protein and other nutrients. The discrepancy between available energy and protein creates a physiological paradox for many animals consuming high-fruit diets, as they will be protein deficient if they eat to meet their minimum energy requirement. We fed young grizzly bears both high-energy pelleted and fruit diets containing from 1.6% to 15.4% protein to examine the role of diet-induced thermogenesis and fat synthesis in dealing with high-energy-low-protein diets. Digestible energy intake at mass maintenance increased 2.1 times, and composition of the gain changed from primarily lean mass to entirely fat when the protein content of the diet decreased from 15.4% to 1.6%. Daily fat gain was up to three times higher in bears fed low-protein diets ad lib., compared with bears consuming the higher-protein diet and gaining mass at the same rate. Thus, bears eating fruit can either consume other foods to increase dietary protein content and reduce energy expenditure, intake, and potentially foraging time or overeat high-fruit diets and use diet-induced thermogenesis and fat synthesis to deal with their skewed energy-to-protein ratio. These are not discrete options but a continuum that creates numerous solutions for balancing energy expenditure, intake, foraging time, fat accumulation, and ultimately fitness, depending on food availability, foraging efficiency, bear size, and body condition.

The role of mTOR signaling in the regulation of protein synthesis and muscle mass during immobilization in mice

Science.gov (United States)

You, Jae-Sung; Anderson, Garrett B.; Dooley, Matthew S.; Hornberger, Troy A.

2015-01-01

ABSTRACT The maintenance of skeletal muscle mass contributes substantially to health and to issues associated with the quality of life. It has been well recognized that skeletal muscle mass is regulated by mechanically induced changes in protein synthesis, and that signaling by mTOR is necessary for an increase in protein synthesis and the hypertrophy that occurs in response to increased mechanical loading. However, the role of mTOR signaling in the regulation of protein synthesis and muscle mass during decreased mechanical loading remains largely undefined. In order to define the role of mTOR signaling, we employed a mouse model of hindlimb immobilization along with pharmacological, mechanical and genetic means to modulate mTOR signaling. The results first showed that immobilization induced a decrease in the global rates of protein synthesis and muscle mass. Interestingly, immobilization also induced an increase in mTOR signaling, eIF4F complex formation and cap-dependent translation. Blocking mTOR signaling during immobilization with rapamycin not only impaired the increase in eIF4F complex formation, but also augmented the decreases in global protein synthesis and muscle mass. On the other hand, stimulating immobilized muscles with isometric contractions enhanced mTOR signaling and rescued the immobilization-induced decrease in global protein synthesis through a rapamycin-sensitive mechanism that was independent of ribosome biogenesis. Unexpectedly, the effects of isometric contractions were also independent of eIF4F complex formation. Similar to isometric contractions, overexpression of Rheb in immobilized muscles enhanced mTOR signaling, cap-dependent translation and global protein synthesis, and prevented the reduction in fiber size. Therefore, we conclude that the activation of mTOR signaling is both necessary and sufficient to alleviate the decreases in protein synthesis and muscle mass that occur during immobilization. Furthermore, these results indicate

Multiple-ion-beam time-of-flight mass spectrometer

International Nuclear Information System (INIS)

Rohrbacher, Andreas; Continetti, Robert E.

2001-01-01

An innovative approach to increase the throughput of mass spectrometric analyses using a multiple-ion-beam mass spectrometer is described. Two sample spots were applied onto a laser desorption/ionization target and each spot was simultaneously irradiated by a beam of quadrupled Nd:YLF laser radiation (261.75 nm) to produce ions by laser-desorption ionization. Acceleration of the ions in an electric field created parallel ion beams that were focused by two parallel einzel lens systems. After a flight path of 2.34 m, the ions were detected with a microchannel plate-phosphor screen assembly coupled with a charge coupled device camera that showed two resolved ion beams. Time-of-flight mass spectra were also obtained with this detector. Experiments were performed using both metal atom cations (Ti + and Cr + ) produced by laser desorption/ionization and the molecular ions of two different proteins (myoglobin and lysozyme), created by matrix assisted laser desorption/ionization using an excess of nicotinic acid as matrix

Boundaries of mass resolution in native mass spectrometry.

Science.gov (United States)

Lössl, Philip; Snijder, Joost; Heck, Albert J R

2014-06-01

Over the last two decades, native mass spectrometry (MS) has emerged as a valuable tool to study intact proteins and noncovalent protein complexes. Studied experimental systems range from small-molecule (drug)-protein interactions, to nanomachineries such as the proteasome and ribosome, to even virus assembly. In native MS, ions attain high m/z values, requiring special mass analyzers for their detection. Depending on the particular mass analyzer used, instrumental mass resolution does often decrease at higher m/z but can still be above a couple of thousand at m/z 5000. However, the mass resolving power obtained on charge states of protein complexes in this m/z region is experimentally found to remain well below the inherent instrument resolution of the mass analyzers employed. Here, we inquire into reasons for this discrepancy and ask how native MS would benefit from higher instrumental mass resolution. To answer this question, we discuss advantages and shortcomings of mass analyzers used to study intact biomolecules and biomolecular complexes in their native state, and we review which other factors determine mass resolving power in native MS analyses. Recent examples from the literature are given to illustrate the current status and limitations.

Post-Translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins

Energy Technology Data Exchange (ETDEWEB)

Gaucher, S.P.; Redding, A.M.; Mukhopadhyay, A.; Keasling, J.D.; Singh, A.K.

2008-03-01

Recent developments in shotgun proteomics have enabled high-throughput studies of a variety of microorganisms at a proteome level and provide experimental validation for predicted open reading frames in the corresponding genome. More importantly, advances in mass spectrometric data analysis now allow mining of large proteomics data sets for the presence of post-translational modifications(PTMs). Although PTMs are a critical aspectof cellular activity, such information eludes cell-wide studies conducted at the transcript level. Here, we analyze several mass spectrometric data sets acquired using two-dimensional liquid chromatography tandem mass spectrometry, 2D-LC/MS/MS, for the sulfate reducing bacterium, Desulfovibrio vulgaris Hildenborough. Our searches of the raw spectra led us to discover several post-translationally modified peptides in D. vulgaris. Of these, several peptides containing a lysine with a +42 Da modification were found reproducibly across all data sets. Both acetylation and trimethylation have the same nominal +42 Da mass, and are therefore candidates for this modification. Several spectra were identified having markers for trimethylation, while one is consistent with an acetylation. Surprisingly, these modified peptides predominantly mapped to proteins involved in sulfate respiration. Other highly expressed proteins in D. vulgaris, such as enzymes involved in electron transport and other central metabolic processes, did not contain this modification. Decoy database searches were used to control for random spectrum/sequence matches. Additional validation for these modifications was provided by alternate workflows, for example, two-dimensional gel electrophoresis followed by mass spectrometry analysis of the dissimilatory sulfite reductase gamma-subunit(DsrC) protein. MS data for DsrC in this alternate workflow also contained the +42 Da modification at the same loci. Furthermore, the DsrC homologue in another sulfate reducing bacterium

MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics.

Science.gov (United States)

The, Matthew; Käll, Lukas

2016-03-04

Shotgun proteomics experiments generate large amounts of fragment spectra as primary data, normally with high redundancy between and within experiments. Here, we have devised a clustering technique to identify fragment spectra stemming from the same species of peptide. This is a powerful alternative method to traditional search engines for analyzing spectra, specifically useful for larger scale mass spectrometry studies. As an aid in this process, we propose a distance calculation relying on the rarity of experimental fragment peaks, following the intuition that peaks shared by only a few spectra offer more evidence than peaks shared by a large number of spectra. We used this distance calculation and a complete-linkage scheme to cluster data from a recent large-scale mass spectrometry-based study. The clusterings produced by our method have up to 40% more identified peptides for their consensus spectra compared to those produced by the previous state-of-the-art method. We see that our method would advance the construction of spectral libraries as well as serve as a tool for mining large sets of fragment spectra. The source code and Ubuntu binary packages are available at https://github.com/statisticalbiotechnology/maracluster (under an Apache 2.0 license).

Design spectra development considering short time histories

International Nuclear Information System (INIS)

Weiner, E.O.

1983-01-01

Two separate programs, MODQKE and MDOF, were written to provide a capability of obtaining equipment spectra from design spectra. MODQKE generates or modifies acceleration histories to conform with design spectra pertaining to, say, a foundation. MDOF is a simple linear modal superposition program that solves for equipment support histories using the design spectra conforming histories as input. Equipment spectra, then, are obtained from the support histories using MODQKE. MODQKE was written to modify or provide new histories with special attention paid to short seismic records. A technique from the open literature was borrowed to generate an initial history that approximates a given response spectrum. Further refinement is done with smoothing cycles in which several correction signals are added to the history in a way that produces a least squares fit between actual and prescribed spectra. Provision is made for history shaping, a baseline correction, and final scaling. MODQKE performance has been demonstrated with seven examples having zero to ten percent damping ratios, and 2.5 seconds to 20 seconds durations and a variety of target spectra. The examples show the program is inexpensive to use. MDOF is a simple modal superposition program. It has no eigensolver, and the user supplies mode shapes, frequencies, and participation factors as input. Floor spectra can be generated from design spectra by using a history from MODQKE that conforms to the design spectrum as input to MDOF. Floor motions from MDOF can be fed back to MODQKE without modification to obtain the floor spectra. A simple example is given to show how equipment mass effects can be incorporated into the MDOF solution. Any transient solution capability can be used to replace MDOF. For example, a direct transient approach may be desirable if both the equipment and floor structures are to be included in the model with different damping fractions. (orig./HP)

Improved protein hydrogen/deuterium exchange mass spectrometry platform with fully automated data processing.

Science.gov (United States)

Zhang, Zhongqi; Zhang, Aming; Xiao, Gang

2012-06-05

Protein hydrogen/deuterium exchange (HDX) followed by protease digestion and mass spectrometric (MS) analysis is accepted as a standard method for studying protein conformation and conformational dynamics. In this article, an improved HDX MS platform with fully automated data processing is described. The platform significantly reduces systematic and random errors in the measurement by introducing two types of corrections in HDX data analysis. First, a mixture of short peptides with fast HDX rates is introduced as internal standards to adjust the variations in the extent of back exchange from run to run. Second, a designed unique peptide (PPPI) with slow intrinsic HDX rate is employed as another internal standard to reflect the possible differences in protein intrinsic HDX rates when protein conformations at different solution conditions are compared. HDX data processing is achieved with a comprehensive HDX model to simulate the deuterium labeling and back exchange process. The HDX model is implemented into the in-house developed software MassAnalyzer and enables fully unattended analysis of the entire protein HDX MS data set starting from ion detection and peptide identification to final processed HDX output, typically within 1 day. The final output of the automated data processing is a set (or the average) of the most possible protection factors for each backbone amide hydrogen. The utility of the HDX MS platform is demonstrated by exploring the conformational transition of a monoclonal antibody by increasing concentrations of guanidine.

A 5-year cohort study of the effects of high protein intake on lean mass and BMC in elderly postmenopausal women.

Science.gov (United States)

Meng, Xingqiong; Zhu, Kun; Devine, Amanda; Kerr, Deborah A; Binns, Colin W; Prince, Richard L

2009-11-01

Long-term effects of high dietary protein intake on muscle and bone structure in the elderly are not clear. The aim of this study was to investigate the relationship between baseline protein intake and lean mass and BMC 5 yr later in a cohort of elderly postmenopausal women. A total of 862 community-dwelling women 75 +/- 3 yr of age provided baseline data including nutrient intake assessed by a food frequency questionnaire. At 5 yr, upper arm muscle area (UAMA) and body composition using DXA were measured. Baseline protein intake was 81 +/- 28 g/d (1.2 +/- 0.4 g/kg/d), contributing 19 +/- 3% of total energy intake. There were positive correlations between baseline protein intake and whole body and appendicular bone-free lean mass and BMC (r = 0.14-0.18, p 87 g/d) had 5.4-6.0% higher whole body and appendicular lean mass and UAMA and 5.3-6.0% higher whole body and appendicular BMC. These effects remained after adjusting for potential confounders. However, the effect on BMC disappeared after further adjustment for lean mass. This study shows that high protein intake is associated with long-term beneficial effects on muscle mass and size and bone mass in elderly women. The protein effect on bone may be partly mediated by its effects on muscle.

Identification of marker proteins for the adulteration of meat products with soybean proteins by multidimensional liquid chromatography-tandem mass spectrometry.

Science.gov (United States)

Leitner, Alexander; Castro-Rubio, Florentina; Marina, Maria Luisa; Lindner, Wolfgang

2006-09-01

Soybean proteins are frequently added to processed meat products for economic reasons and to improve their functional properties. Monitoring of the addition of soybean protein to meat products is of high interest due to the existence of regulations forbidding or limiting the amount of soybean proteins that can be added during the processing of meat products. We have used chromatographic prefractionation on the protein level by perfusion liquid chromatography to isolate peaks of interest from extracts of soybean protein isolate (SPI) and of meat products containing SPI. After enzymatic digestion using trypsin, the collected fractions were analyzed by nanoflow liquid chromatography-tandem mass spectrometry. Several variants and subunits of the major seed proteins, glycinin and beta-conglycinin, were identified in SPI, along with two other proteins. In soybean-protein-containing meat samples, different glycinin A subunits could be identified from the peak discriminating between samples with and without soybean proteins added. Among those, glycinin G4 subunit A4 was consistently found in all samples. Consequently, this protein (subunit) can be used as a target for new analytical techniques in the course of identifying the addition of soybean protein to meat products.

Identification of intact high molecular weight glutenin subunits from the wheat proteome using combined liquid chromatography-electrospray ionization mass spectrometry.

Science.gov (United States)

Lagrain, Bert; Brunnbauer, Markus; Rombouts, Ine; Koehler, Peter

2013-01-01

The present paper describes a method for the identification of intact high molecular weight glutenin subunits (HMW-GS), the quality determining proteins from the wheat storage proteome. The method includes isolation of HMW-GS from wheat flour, further separation of HMW-GS by reversed-phase high-performance liquid chromatography (RP-HPLC), and their subsequent molecular identification with electrospray ionization mass spectrometry using a quadrupole-time-of-flight mass analyzer. For HMW-GS isolation, wheat proteins were reduced and extracted from flour with 50% 1-propanol containing 1% dithiothreitol. HMW-GS were then selectively precipitated from the protein mixture by adjusting the 1-propanol concentration to 60%. The composition of the precipitated proteins was first evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis with Coomassie staining and RP-HPLC with ultraviolet detection. Besides HMW-GS (≥65%), the isolated proteins mainly contained ω5-gliadins. Secondly, the isolated protein fraction was analyzed by liquid chromatography-mass spectrometry. Optimal chromatographic separation of HMW-GS from the other proteins in the isolated fraction was obtained when the mobile phase contained 0.1% trifluoroacetic acid as ion-pairing agent. Individual HMW-GS were then identified by determining their molecular masses from the high-resolution mass spectra and comparing these with theoretical masses calculated from amino acid sequences. Using formic acid instead of trifluoroacetic acid in the mobile phase increased protein peak intensities in the base peak mass chromatogram. This allowed the detection of even traces of other wheat proteins than HMW-GS in the isolated fraction, but the chromatographic separation was inferior with a major overlap between the elution ranges of HMW-GS and ω-gliadins. Overall, the described method allows a rapid assessment of wheat quality through the direct determination of the HMW-GS composition and offers a basis for

Analysis of the lipidated recombinant outer surface protein A from Borrelia burgdorferi by mass spectrometry

NARCIS (Netherlands)

Bouchon, B.; Klein, Michele; Bischoff, Rainer; Van Dorsselaer, A.; Roitsch, C.

1997-01-01

The outer surface protein A, OspA, from the spirochete Borrelia burgdorferi is a lipoprotein of 25 kDa. The recombinant OspA (rOspA) expressed in Escherichia coli has been purified and analyzed by electrospray mass spectrometry (ESMS). A heterogenous spectrum gave a measured mass of 28,462 +/- 9 Da

Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

Energy Technology Data Exchange (ETDEWEB)

Haskins, William E.; Leavell, Michael D.; Lane, Pamela; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Wood, Nichole L.; Schoeniger, Joseph S.; Kruppa, Gary Hermann; Sale, Kenneth L.; Young, Malin M.; Novak, Petr

2005-03-01

Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

Examining the Heterogeneous Genome Content of Multipartite Viruses BMV and CCMV by Native Mass Spectrometry

Science.gov (United States)

van de Waterbeemd, Michiel; Snijder, Joost; Tsvetkova, Irina B.; Dragnea, Bogdan G.; Cornelissen, Jeroen J.; Heck, Albert J. R.

2016-06-01

Since the concept was first introduced by Brian Chait and co-workers in 1991, mass spectrometry of proteins and protein complexes under non-denaturing conditions (native MS) has strongly developed, through parallel advances in instrumentation, sample preparation, and data analysis tools. However, the success rate of native MS analysis, particularly in heterogeneous mega-Dalton (MDa) protein complexes, still strongly depends on careful instrument modification. Here, we further explore these boundaries in native mass spectrometry, analyzing two related endogenous multipartite viruses: the Brome Mosaic Virus (BMV) and the Cowpea Chlorotic Mottle Virus (CCMV). Both CCMV and BMV are approximately 4.6 megadalton (MDa) in mass, of which approximately 1 MDA originates from the genomic content of the virion. Both viruses are produced as mixtures of three particles carrying different segments of the genome, varying by approximately 0.1 MDA in mass (~2%). This mixture of particles poses a challenging analytical problem for high-resolution native MS analysis, given the large mass scales involved. We attempt to unravel the particle heterogeneity using both Q-TOF and Orbitrap mass spectrometers extensively modified for analysis of very large assemblies. We show that manipulation of the charging behavior can provide assistance in assigning the correct charge states. Despite their challenging size and heterogeneity, we obtained native mass spectra with resolved series of charge states for both BMV and CCMV, demonstrating that native MS of endogenous multipartite virions is feasible.

Nuclear Neutrino Spectra in Late Stellar Evolution

Science.gov (United States)

Misch, G. Wendell; Sun, Yang; Fuller, George

2018-05-01

Neutrinos are the principle carriers of energy in massive stars, beginning from core carbon burning and continuing through core collapse and after the core bounce. In fact, it may be possible to detect neutrinos from nearby pre-supernova stars. Therefore, it is of great interest to understand the neutrino energy spectra from these stars. Leading up to core collapse, beginning around core silicon burning, nuclei become dominant producers of neutrinos, particularly at high neutrino energy, so a systematic study of nuclear neutrino spectra is desirable. We have done such a study, and we present our sd-shell model calculations of nuclear neutrino energy spectra for nuclei in the mass number range A = 21 - 35. Our study includes neutrinos produced by charged lepton capture, charged lepton emission, and neutral current nuclear deexcitation. Previous authors have tabulated the rates of charged current nuclear weak interactions in astrophysical conditions, but the present work expands on this not only by providing neutrino energy spectra, but also by including the heretofore untabulated neutral current de-excitation neutrino pairs.

Probing protein surface with a solvent mimetic carbene coupled to detection by mass spectrometry.

Science.gov (United States)

Gómez, Gabriela E; Mundo, Mariana R; Craig, Patricio O; Delfino, José M

2012-01-01

Much knowledge into protein folding, ligand binding, and complex formation can be derived from the examination of the nature and size of the accessible surface area (SASA) of the polypeptide chain, a key parameter in protein science not directly measurable in an experimental fashion. To this end, an ideal chemical approach should aim at exerting solvent mimicry and achieving minimal selectivity to probe the protein surface regardless of its chemical nature. The choice of the photoreagent diazirine to fulfill these goals arises from its size comparable to water and from being a convenient source of the extremely reactive methylene carbene (:CH(2)). The ensuing methylation depends primarily on the solvent accessibility of the polypeptide chain, turning it into a valuable signal to address experimentally the measurement of SASA in proteins. The superb sensitivity and high resolution of modern mass spectrometry techniques allows us to derive a quantitative signal proportional to the extent of modification (EM) of the sample. Thus, diazirine labeling coupled to electrospray mass spectrometry (ESI-MS) detection can shed light on conformational features of the native as well as non-native states, not easily addressable by other methods. Enzymatic fragmentation of the polypeptide chain at the level of small peptides allows us to locate the covalent tag along the amino acid sequence, therefore enabling the construction of a map of solvent accessibility. Moreover, by subsequent MS/MS analysis of peptides, we demonstrate here the feasibility of attaining amino acid resolution in defining the target sites. © American Society for Mass Spectrometry, 2011

Affinity capture of biotinylated proteins at acidic conditions to facilitate hydrogen/deuterium exchange mass spectrometry analysis of multimeric protein complexes

DEFF Research Database (Denmark)

Jensen, Pernille Foged; Jørgensen, Thomas J. D.; Koefoed, Klaus

2013-01-01

Characterization of conformational and dynamic changes associated with protein interactions can be done by hydrogen/deuterium exchange mass spectrometry (HDX-MS) by comparing the deuterium uptake in the bound and unbound state of the proteins. Investigation of local hydrogen/deuterium exchange...... in heteromultimeric protein complexes poses a challenge for the method due to the increased complexity of the mixture of peptides originating from all interaction partners in the complex. Previously, interference of peptides from one interaction partner has been removed by immobilizing the intact protein on beads...... complexes without interference of peptides originating from other interaction partners in the complex. The biotin-streptavidin strategy has been successfully implemented in a model system with two recombinant monoclonal antibodies that target nonoverlapping epitopes on the human epidermal growth factor...

Uncertainty analysis in Titan ionospheric simulated ion mass spectra: unveiling a set of issues for models accuracy improvement

Science.gov (United States)

Hébrard, Eric; Carrasco, Nathalie; Dobrijevic, Michel; Pernot, Pascal

Ion Neutral Mass Spectrometer (INMS) aboard Cassini revealed a rich coupled ion-neutral chemistry in the ionosphere, producing heavy hydrocarbons and nitriles ions. The modeling of such a complex environment is challenging, as it requires a detailed and accurate description of the different relevant processes such as photodissociation cross sections and neutral-neutral reaction rates on one hand, and ionisation cross sections, ion-molecule and recombination reaction rates on the other hand. Underpinning models calculations, each of these processes is parameterized by kinetic constants which, when known, have been studied experimentally and/or theoretically over a range of temperatures and pressures that are most often not representative of Titan's atmosphere. The sizeable experimental and theoretical uncertainties reported in the literature merge therefore with the uncertainties resulting subsequently from the unavoidable estimations or extrapolations to Titan's atmosphere conditions. Such large overall uncertainties have to be accounted for in all resulting inferences most of all to evaluate the quality of the model definition. We have undertaken a systematic study of the uncertainty sources in the simulation of ion mass spectra as recorded by Cassini/INMS in Titan ionosphere during the T5 flyby at 1200 km. Our simulated spectra seem much less affected by the uncertainties on ion-molecule reactions than on neutral-neutral reactions. Photochemical models of Titan's atmosphere are indeed so poorly predictive at high altitudes, in the sense that their computed predictions display such large uncertainties, that we found them to give rise to bimodal and hypersensitive abundance distributions for some major compounds like acetylene C2 H2 and ethylene C2 H4 . We will show to what extent global uncertainty and sensitivity analysis enabled us to identify the causes of this bimodality and to pinpoint the key processes that mostly contribute to limit the accuracy of the

Quality evaluation of tandem mass spectral libraries.

Science.gov (United States)

Oberacher, Herbert; Weinmann, Wolfgang; Dresen, Sebastian

2011-06-01

Tandem mass spectral libraries are gaining more and more importance for the identification of unknowns in different fields of research, including metabolomics, forensics, toxicology, and environmental analysis. Particularly, the recent invention of reliable, robust, and transferable libraries has increased the general acceptance of these tools. Herein, we report on results obtained from thorough evaluation of the match reliabilities of two tandem mass spectral libraries: the MSforID library established by the Oberacher group in Innsbruck and the Weinmann library established by the Weinmann group in Freiburg. Three different experiments were performed: (1) Spectra of the libraries were searched against their corresponding library after excluding either this single compound-specific spectrum or all compound-specific spectra prior to searching; (2) the libraries were searched against each other using either library as reference set or sample set; (3) spectra acquired on different mass spectrometric instruments were matched to both libraries. Almost 13,000 tandem mass spectra were included in this study. The MSforID search algorithm was used for spectral matching. Statistical evaluation of the library search results revealed that principally both libraries enable the sensitive and specific identification of compounds. Due to higher mass accuracy of the QqTOF compared with the QTrap instrument, matches to the MSforID library were more reliable when comparing spectra with both libraries. Furthermore, only the MSforID library was shown to be efficiently transferable to different kinds of tandem mass spectrometers, including "tandem-in-time" instruments; this is due to the coverage of a large range of different collision energy settings-including the very low range-which is an outstanding characteristics of the MSforID library.

A NEXAFS and mass spectrometry study of cysteine, cystine and insulin irradiated with intermediate energy (0.8 keV) electrons

Energy Technology Data Exchange (ETDEWEB)

Simões, G., E-mail: simoes.grazieli@gmail.com [Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, 21941-909 Rio de Janeiro (Brazil); Rodrigues, F.N. [Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, 21941-909 Rio de Janeiro (Brazil); Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Maracanã, 20270-021 Rio de Janeiro (Brazil); Bernini, R.B. [Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, 21941-909 Rio de Janeiro (Brazil); Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Duque de Caxias, 25050-100 Rio de Janeiro (Brazil); Castro, C.S.C. [Instituto Nacional de Metrologia, Qualidade e Tecnologia – Inmetro, 25250-020 Rio de Janeiro (Brazil); Souza, G.G.B. de, E-mail: gerson@iq.ufrj.br [Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, 21941-909 Rio de Janeiro (Brazil)

2014-03-01

Highlights: • Structural modifications in sulfur containing biomolecules were investigated. • Significant modifications were observed in insulin irradiated NEXAFS spectra. • Degradation of insulin can be observed even at low temperature. • Alterations in insulin spectrum were characterized according to the state of sulfur. - Abstract: We have performed a NEXAFS (S 1s) and mass spectrometry study of solid samples of cysteine, cystine and insulin irradiated with 0.8 keV electrons. The measured mass spectra point out to processes of desulfurization, deamination, decarbonylation and decarboxylation in the irradiated biomolecules. Electron beam irradiation was also conducted at low temperatures in order to evaluate the possible contribution from thermal degradation processes. The NEXAFS spectra of irradiated cysteine and cystine did not show substantial changes when compared to the same spectra obtained using non-irradiated samples. The sulfur K-edge photoabsorption spectrum of irradiated insulin, however, showed clear modifications when compared to the spectrum of the non-irradiated protein, even when the irradiation was conducted at low temperature. Using an empirical combination of the photoabsorption spectra of cysteine and cystine (which are associated respectively with reduced and oxidized forms of sulfur) we have been able to reproduce the absorption spectrum of irradiated insulin.

Multi photon ionization mass spectrometry of carbamate pesticides, herbicides and fungicides

International Nuclear Information System (INIS)

Grun, Carsten; Koenig, Marcelle; Grotemeyer, Juergen

2001-01-01

Pesticides and herbicides are useful for a wide range of applications today. The determination of these substances either in the pure form or in complex matrices is of high analytical interest. Especially since these substances can by found in every day products. The combination of multi photon ionization (MUPI) and time of flight laser mass spectrometry may be a powerful tool for achieving fast well interpretable mass spectra for analytical purposes. In this paper we will discuss the mass spectra of several pesticides and herbicides accessed by MUPI-time-of-flight mass spectrometry. The influence of the laser pulse duration on the mass spectra are discussed

Electrospray Ionization Mass Spectrometry: A Technique to Access the Information beyond the Molecular Weight of the Analyte

Science.gov (United States)

Banerjee, Shibdas; Mazumdar, Shyamalava

2012-01-01

The Electrospray Ionization (ESI) is a soft ionization technique extensively used for production of gas phase ions (without fragmentation) of thermally labile large supramolecules. In the present review we have described the development of Electrospray Ionization mass spectrometry (ESI-MS) during the last 25 years in the study of various properties of different types of biological molecules. There have been extensive studies on the mechanism of formation of charged gaseous species by the ESI. Several groups have investigated the origin and implications of the multiple charge states of proteins observed in the ESI-mass spectra of the proteins. The charged analytes produced by ESI can be fragmented by activating them in the gas-phase, and thus tandem mass spectrometry has been developed, which provides very important insights on the structural properties of the molecule. The review will highlight recent developments and emerging directions in this fascinating area of research. PMID:22611397

Electrospray ionization mass spectrometry: a technique to access the information beyond the molecular weight of the analyte.

Science.gov (United States)

Banerjee, Shibdas; Mazumdar, Shyamalava

2012-01-01

The Electrospray Ionization (ESI) is a soft ionization technique extensively used for production of gas phase ions (without fragmentation) of thermally labile large supramolecules. In the present review we have described the development of Electrospray Ionization mass spectrometry (ESI-MS) during the last 25 years in the study of various properties of different types of biological molecules. There have been extensive studies on the mechanism of formation of charged gaseous species by the ESI. Several groups have investigated the origin and implications of the multiple charge states of proteins observed in the ESI-mass spectra of the proteins. The charged analytes produced by ESI can be fragmented by activating them in the gas-phase, and thus tandem mass spectrometry has been developed, which provides very important insights on the structural properties of the molecule. The review will highlight recent developments and emerging directions in this fascinating area of research.

Transverse and Longitudinal Doppler Effects of the Sunbeam Spectra and Earth-Self Rotation and Orbital Velocities, the Mass of the Sun and Others

OpenAIRE

Nam, Sang Boo

2009-01-01

The transverse and longitudinal Doppler effects of the sunbeam spectra are shown to result in the earth parameters such as the earth-self rotation and revolution velocities, the earth orbit semi-major axis, the earth orbital angular momentum, the earth axial tilt, the earth orbit eccentricity, the local latitude and the mass of the sun. The sunbeam global positioning scheme is realized, including the earth orbital position. PACS numbers: 91.10.Fc, 95.10.Km, 91.10.Da, 91.10.Jf.

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows.

Science.gov (United States)

Verheggen, Kenneth; Raeder, Helge; Berven, Frode S; Martens, Lennart; Barsnes, Harald; Vaudel, Marc

2017-09-13

Sequence database search engines are bioinformatics algorithms that identify peptides from tandem mass spectra using a reference protein sequence database. Two decades of development, notably driven by advances in mass spectrometry, have provided scientists with more than 30 published search engines, each with its own properties. In this review, we present the common paradigm behind the different implementations, and its limitations for modern mass spectrometry datasets. We also detail how the search engines attempt to alleviate these limitations, and provide an overview of the different software frameworks available to the researcher. Finally, we highlight alternative approaches for the identification of proteomic mass spectrometry datasets, either as a replacement for, or as a complement to, sequence database search engines. © 2017 Wiley Periodicals, Inc.

A simple algorithm improves mass accuracy to 50-100 ppm for delayed extraction linear MALDI-TOF mass spectrometry

Energy Technology Data Exchange (ETDEWEB)

Hack, Christopher A.; Benner, W. Henry

2001-10-31

A simple mathematical technique for improving mass calibration accuracy of linear delayed extraction matrix assisted laser desorption ionization time-of-flight mass spectrometry (DE MALDI-TOF MS) spectra is presented. The method involves fitting a parabola to a plot of Dm vs. mass data where Dm is the difference between the theoretical mass of calibrants and the mass obtained from a linear relationship between the square root of m/z and ion time of flight. The quadratic equation that describes the parabola is then used to correct the mass of unknowns by subtracting the deviation predicted by the quadratic equation from measured data. By subtracting the value of the parabola at each mass from the calibrated data, the accuracy of mass data points can be improved by factors of 10 or more. This method produces highly similar results whether or not initial ion velocity is accounted for in the calibration equation; consequently, there is no need to depend on that uncertain parameter when using the quadratic correction. This method can be used to correct the internally calibrated masses of protein digest peaks. The effect of nitrocellulose as a matrix additive is also briefly discussed, and it is shown that using nitrocellulose as an additive to a CHCA matrix does not significantly change initial ion velocity but does change the average position of ions relative to the sample electrode at the instant the extraction voltage is applied.

Description of width and spectra of two relativistic fermions bound states

International Nuclear Information System (INIS)