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Journal articles on the topic 'Peptide mass fingerprinting'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Thiede, Bernd, Wolfgang Höhenwarter, Alexander Krah, Jens Mattow, Monika Schmid, Frank Schmidt, and Peter R. Jungblut. "Peptide mass fingerprinting." Methods 35, no. 3 (March 2005): 237–47. http://dx.doi.org/10.1016/j.ymeth.2004.08.015.

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2

He, Z., C. Yang, and W. Yu. "Peak bagging for peptide mass fingerprinting." Bioinformatics 24, no. 10 (April 7, 2008): 1293–99. http://dx.doi.org/10.1093/bioinformatics/btn123.

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3

Damodaran, Senthilkumar, Troy D. Wood, Priyadharsini Nagarajan, and Richard A. Rabin. "Evaluating Peptide Mass Fingerprinting-based Protein Identification." Genomics, Proteomics & Bioinformatics 5, no. 3-4 (2007): 152–57. http://dx.doi.org/10.1016/s1672-0229(08)60002-9.

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4

Alty, Lisa T., and Frederick J. LaRiviere. "Peptide Mass Fingerprinting of Egg White Proteins." Journal of Chemical Education 93, no. 4 (February 9, 2016): 772–77. http://dx.doi.org/10.1021/acs.jchemed.5b00625.

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5

van Ginkel, Jetty, Mike Filius, Malwina Szczepaniak, Pawel Tulinski, Anne S. Meyer, and Chirlmin Joo. "Single-molecule peptide fingerprinting." Proceedings of the National Academy of Sciences 115, no. 13 (March 12, 2018): 3338–43. http://dx.doi.org/10.1073/pnas.1707207115.

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Proteomic analyses provide essential information on molecular pathways of cellular systems and the state of a living organism. Mass spectrometry is currently the first choice for proteomic analysis. However, the requirement for a large amount of sample renders a small-scale proteomics study challenging. Here, we demonstrate a proof of concept of single-molecule FRET-based protein fingerprinting. We harnessed the AAA+ protease ClpXP to scan peptides. By using donor fluorophore-labeled ClpP, we sequentially read out FRET signals from acceptor-labeled amino acids of peptides. The repurposed ClpXP exhibits unidirectional processing with high processivity and has the potential to detect low-abundance proteins. Our technique is a promising approach for sequencing protein substrates using a small amount of sample.

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6

Gay, Steven, Pierre-Alain Binz, Denis F. Hochstrasser, and Ron D. Appel. "Modeling peptide mass fingerprinting data using the atomic composition of peptides." Electrophoresis 20, no. 18 (December 1, 1999): 3527–34. http://dx.doi.org/10.1002/(sici)1522-2683(19991201)20:18<3527::aid-elps3527>3.0.co;2-9.

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7

Bogdan, IstvÁn A., Daniel Coca, and Rob J. Beynon. "Peptide Mass Fingerprinting Using Field-Programmable Gate Arrays." IEEE Transactions on Biomedical Circuits and Systems 3, no. 3 (June 2009): 142–49. http://dx.doi.org/10.1109/tbcas.2008.2010945.

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8

Henzel, William J., Colin Watanabe, and John T. Stults. "Protein identification: The origins of peptide mass fingerprinting." Journal of the American Society for Mass Spectrometry 14, no. 9 (September 2003): 931–42. http://dx.doi.org/10.1016/s1044-0305(03)00214-9.

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9

Pappin, D. J. C., P. Hojrup, and A. J. Bleasby. "Rapid identification of proteins by peptide-mass fingerprinting." Current Biology 3, no. 6 (June 1993): 327–32. http://dx.doi.org/10.1016/0960-9822(93)90195-t.

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10

Chernobrovkin, A. L., O. P. Trifonova, N. A. Petushkova, E. A. Ponomarenko, and A. V. Lisitsa. "Selection of the peptide mass tolerance value for protein identification with peptide mass fingerprinting." Russian Journal of Bioorganic Chemistry 37, no. 1 (January 2011): 119–22. http://dx.doi.org/10.1134/s1068162011010055.

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11

Colquhoun, David R., Kellogg J. Schwab, Robert N. Cole, and Rolf U. Halden. "Detection of Norovirus Capsid Protein in Authentic Standards and in Stool Extracts by Matrix-Assisted Laser Desorption Ionization and Nanospray Mass Spectrometry." Applied and Environmental Microbiology 72, no. 4 (April 2006): 2749–55. http://dx.doi.org/10.1128/aem.72.4.2749-2755.2006.

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ABSTRACT Mass spectrometry (MS) represents a rapid technique for the identification of microbial monocultures, and its adaptation to the detection of pathogens in real-world samples is a public health and homeland security priority. Norovirus, a leading cause of gastroenteritis in the world, is difficult to monitor because it cannot be cultured outside the human body. The detection of norovirus capsid protein was explored using three common MS-based methods: scanning of intact proteins, peptide mass fingerprinting, and peptide sequencing. Detection of intact target protein was limited by poor selectivity and sensitivity. Detection of up to 16 target peptides by peptide mass fingerprinting allowed for the reproducible and confident (P < 0.05) detection of the 56-kDa norovirus capsid protein in the range of 0.1 × 10−12 to 50 × 10−12 mol in authentic standards of recombinant norovirus virus-like particles (VLPs). To explore assay performance in complex matrixes, a non-gel-based, rapid method (2 to 3 h) for virus extraction from human stool was evaluated (72% ± 12% recovery), and additional analyses were performed on norovirus-free stool extracts fortified with VLPs. Whereas peptide mass fingerprinting was rendered impractical by sample interferences, peptide sequencing using nanospray tandem MS facilitated unambiguous identification of ≥250 fmol of capsid protein in stool extracts. This is the first report on MS-based detection of norovirus, accomplished by using structurally identical, noninfective VLPs at clinically relevant concentrations. It represents an important milestone in the development of assays for surveillance of this category B bioterrorism agent.

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12

Jain, Rachana, and Michael Wagner. "Kolmogorov−Smirnov Scores and Intrinsic Mass Tolerances for Peptide Mass Fingerprinting." Journal of Proteome Research 9, no. 2 (February 5, 2010): 737–42. http://dx.doi.org/10.1021/pr9005525.

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13

Dodds, Eric D., Hyun Joo An, Paul J. Hagerman, and Carlito B. Lebrilla. "Enhanced Peptide Mass Fingerprinting through High Mass Accuracy: Exclusion of Non-Peptide Signals Based on Residual Mass." Journal of Proteome Research 5, no. 5 (May 2006): 1195–203. http://dx.doi.org/10.1021/pr050486o.

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14

He, Zengyou, Chao Yang, Can Yang, Robert Z. Qi, Jason Po-Ming Tam, and Weichuan Yu. "Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification." Journal of Computational Biology 17, no. 3 (March 2010): 221–35. http://dx.doi.org/10.1089/cmb.2009.0160.

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15

James, Peter, Manfredo Quadroni, Ernesto Carafoli, and Gaston Gonnet. "Protein identification in DNA databases by peptide mass fingerprinting." Protein Science 3, no. 8 (August 1994): 1347–50. http://dx.doi.org/10.1002/pro.5560030822.

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16

Levander, Fredrik, Thorsteinn Rögnvaldsson, Jim Samuelsson, and Peter James. "Automated methods for improved protein identification by peptide mass fingerprinting." PROTEOMICS 4, no. 9 (September 2004): 2594–601. http://dx.doi.org/10.1002/pmic.200300804.

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17

Gay, Steven, Pierre-Alain Binz, Denis F. Hochstrasser, and Ron D. Appel. "Peptide mass fingerprinting peak intensity prediction: Extracting knowledge from spectra." PROTEOMICS 2, no. 10 (October 2002): 1374–91. http://dx.doi.org/10.1002/1615-9861(200210)2:10<1374::aid-prot1374>3.0.co;2-d.

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18

Wilkins, Bryan J., Kelly A. Daggett, and T. Ashton Cropp. "Peptide mass fingerprinting using isotopically encoded photo-crosslinking amino acids." Molecular BioSystems 4, no. 9 (2008): 934. http://dx.doi.org/10.1039/b801512k.

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19

Tiengo, Alessandra, Nicola Barbarini, Sonia Troiani, Luisa Rusconi, and Paolo Magni. "A Perl procedure for protein identification by Peptide Mass Fingerprinting." BMC Bioinformatics 10, Suppl 12 (2009): S11. http://dx.doi.org/10.1186/1471-2105-10-s12-s11.

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20

Padliya, Neerav D., and Troy D. Wood. "Improved peptide mass fingerprinting matches via optimized sample preparation in MALDI mass spectrometry." Analytica Chimica Acta 627, no. 1 (October 2008): 162–68. http://dx.doi.org/10.1016/j.aca.2008.05.059.

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21

Bhaskaran, Nimesh, Hiroyuki Iwahana, Jonas Bergquist, Ulf Hellman, and Serhiy Souchelnytskyi. "Novel post-translational modifications of Smad2 identified by mass spectrometry." Open Life Sciences 3, no. 4 (December 1, 2008): 359–70. http://dx.doi.org/10.2478/s11535-008-0045-2.

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AbstractSmad2 is a crucial component of transforming growth factor-β (TGFβ) signaling, and is involved in the regulation of cell proliferation, death and differentiation. Phosphorylation, ubiquitylation and acetylation of Smad2 have been found to regulate its activity. We used mass spectrometry to search for novel post-translational modifications (PTMs) of Smad2. Peptide mass fingerprinting (PMF) indicated that Smad2 can be acetylated, methylated, citrullinated, phosphorylated and palmitoylated. Sequencing of selected peptides validated methylation at Gly122 and hydroxylation at Trp18 of Smad2. We also observed a novel, so far unidentified modification at Tyr128 and Tyr151. Our observations open for further exploration of biological importance of the detected PTMs.

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22

Weinkopff, Tiffany, James A. Atwood, George A. Punkosdy, Delynn Moss, D. Brent Weatherly, Ron Orlando, and Patrick Lammie. "Identification of Antigenic Brugia Adult Worm Proteins by Peptide Mass Fingerprinting." Journal of Parasitology 95, no. 6 (December 2009): 1429–35. http://dx.doi.org/10.1645/ge-2083.1.

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23

Wise, Michael J., Timothy G. Littlejohn, and Ian Humphery-Smith. "Peptide-mass fingerprinting and the ideal covering set for protein characterisation." Electrophoresis 18, no. 8 (1997): 1399–409. http://dx.doi.org/10.1002/elps.1150180815.

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24

Song, Zhao, Luonan Chen, and Dong Xu. "Confidence assessment for protein identification by using peptide-mass fingerprinting data." PROTEOMICS 9, no. 11 (June 2009): 3090–99. http://dx.doi.org/10.1002/pmic.200701159.

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25

Zhang, Liwen, Ericka E. Eugeni, Mark R. Parthun, and Michael A. Freitas. "Identification of novel histone post-translational modifications by peptide mass fingerprinting." Chromosoma 112, no. 2 (August 1, 2003): 77–86. http://dx.doi.org/10.1007/s00412-003-0244-6.

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26

Shenar, Nawar, Jean Martinez, and Christine Enjalbal. "Laser desorption/ionization mass spectrometry on porous silica and alumina for peptide mass fingerprinting." Journal of the American Society for Mass Spectrometry 19, no. 5 (May 2008): 632–44. http://dx.doi.org/10.1016/j.jasms.2008.02.006.

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27

Denger, Karin, and Alasdair M. Cook. "Racemase activity effected by two dehydrogenases in sulfolactate degradation by Chromohalobacter salexigens: purification of (S)-sulfolactate dehydrogenase." Microbiology 156, no. 3 (March 1, 2010): 967–74. http://dx.doi.org/10.1099/mic.0.034736-0.

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Chromohalobacter salexigens DSM 3043, whose genome has been sequenced, is known to degrade (R,S)-sulfolactate as a sole carbon and energy source for growth. Utilization of the compound(s) was shown to be quantitative, and an eight-gene cluster (Csal_1764–Csal_1771) was hypothesized to encode the enzymes in the degradative pathway. It comprised a transcriptional regulator (SuyR), a Tripartite Tricarboxylate Transporter-family uptake system for sulfolactate (SlcHFG), two sulfolactate dehydrogenases of opposite sulfonate stereochemistry, namely novel SlcC and ComC [(R)-sulfolactate dehydrogenase] [EC1.1.1.272] and desulfonative sulfolactate sulfo-lyase (SuyAB) [EC4.4.1.24]. Inducible reduction of 3-sulfopyruvate, inducible SuyAB activity and induction of an unknown protein were detected. Separation of the soluble proteins from induced cells on an anion-exchange column yielded four relevant fractions. Two different fractions reduced sulfopyruvate with NAD(P)H, a third yielded SuyAB activity, and the fourth contained the unknown protein. The latter was identified by peptide-mass fingerprinting as SlcH, the candidate periplasmic binding protein of the transport system. Separated SuyB was also identified by peptide-mass fingerprinting. ComC was partially purified and identified by peptide-mass fingerprinting. The (R)-sulfolactate that ComC produced from sulfopyruvate was a substrate for SuyAB, which showed that SuyAB is (R)-sulfolactate sulfo-lyase. SlcC was purified to homogeneity. This enzyme also formed sulfolactate from sulfopyruvate, but the latter enantiomer was not a substrate for SuyAB. SlcC was obviously (S)-sulfolactate dehydrogenase.

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28

Karring, Henrik, Ida B. Thøgersen, Gordon K. Klintworth, Torben Møller-Pedersen, and Jan J. Enghild. "A Dataset of Human Cornea Proteins Identified by Peptide Mass Fingerprinting and Tandem Mass Spectrometry." Molecular & Cellular Proteomics 4, no. 9 (May 23, 2005): 1406–8. http://dx.doi.org/10.1074/mcp.d500003-mcp200.

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29

Parker, Kenneth C. "Scoring methods in MALDI peptide mass fingerprinting: ChemScore, and the ChemApplex program." Journal of the American Society for Mass Spectrometry 13, no. 1 (January 2002): 22–39. http://dx.doi.org/10.1016/s1044-0305(01)00320-8.

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30

Kjellander, Marcus, Erika Billinger, Harisha Ramachandraiah, Mats Boman, Sara Bergström Lind, and Gunnar Johansson. "A flow-through nanoporous alumina trypsin bioreactor for mass spectrometry peptide fingerprinting." Journal of Proteomics 172 (February 2018): 165–72. http://dx.doi.org/10.1016/j.jprot.2017.09.008.

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31

Yang, Dongmei, Kevin Ramkissoon, Eric Hamlett, and Morgan C. Giddings. "High-Accuracy Peptide Mass Fingerprinting Using Peak Intensity Data with Machine Learning." Journal of Proteome Research 7, no. 1 (January 2008): 62–69. http://dx.doi.org/10.1021/pr070088g.

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32

Hynes, Gillian, Chris W. Sutton, Sally U, and Keith R. Wiluson. "Peptide mass fingerprinting of chaperonin‐containing TCP‐1 (CCT) and copurifying proteins." FASEB Journal 10, no. 1 (January 1996): 137–47. http://dx.doi.org/10.1096/fasebj.10.1.8566534.

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33

Hekmat, Omid, Young-Wan Kim, Spencer J. Williams, Shouming He, and Stephen G. Withers. "Active-site Peptide “Fingerprinting” of Glycosidases in Complex Mixtures by Mass Spectrometry." Journal of Biological Chemistry 280, no. 42 (August 5, 2005): 35126–35. http://dx.doi.org/10.1074/jbc.m508434200.

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34

Magnin, Jérôme, Alexandre Masselot, Christoph Menzel, and Jacques Colinge. "OLAV-PMF: A Novel Scoring Scheme for High-Throughput Peptide Mass Fingerprinting." Journal of Proteome Research 3, no. 1 (February 2004): 55–60. http://dx.doi.org/10.1021/pr034055m.

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35

Li, Youyuan, Pei Hao, Siliang Zhang, and Yixue Li. "Feature-matching Pattern-based Support Vector Machines for Robust Peptide Mass Fingerprinting." Molecular & Cellular Proteomics 10, no. 12 (July 20, 2011): M110.005785. http://dx.doi.org/10.1074/mcp.m110.005785.

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36

Sutton, Chris W., Kay S. Pemberton, John S. Cottrell, Joseph M. Corbett, Colin H. Wheeler, Michael J. Dunn, and Darryl J. Pappin. "Identification of myocardial proteins from two-dimensional gels by peptide mass fingerprinting." Electrophoresis 16, no. 1 (1995): 308–16. http://dx.doi.org/10.1002/elps.1150160151.

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37

Qiao, Liang, Fangzheng Su, Hongyan Bi, Hubert H. Girault, and Baohong Liu. "Ga2O3 photocatalyzed on-line tagging of cysteine to facilitate peptide mass fingerprinting." PROTEOMICS 11, no. 17 (July 21, 2011): 3501–9. http://dx.doi.org/10.1002/pmic.201100208.

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38

Molloy, Mark P., Nikhil D. Phadke, Janine R. Maddock, and Philip C. Andrews. "Two-dimensional electrophoresis and peptide mass fingerprinting of bacterial outer membrane proteins." ELECTROPHORESIS 22, no. 9 (May 2001): 1686–96. http://dx.doi.org/10.1002/1522-2683(200105)22:9<1686::aid-elps1686>3.0.co;2-l.

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39

Samuelsson, J., D. Dalevi, F. Levander, and T. Rognvaldsson. "Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting." Bioinformatics 20, no. 18 (August 5, 2004): 3628–35. http://dx.doi.org/10.1093/bioinformatics/bth460.

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40

d'Acierno, Antonio. "IsAProteinDB: An Indexed Database of Trypsinized Proteins for Fast Peptide Mass Fingerprinting." IEEE/ACM Transactions on Computational Biology and Bioinformatics 14, no. 5 (September 1, 2017): 1195–201. http://dx.doi.org/10.1109/tcbb.2016.2564964.

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41

Li, Youyuan, and Yingping Zhuang. "fmpRPMF: A Web Implementation for Protein Identification by Robust Peptide Mass Fingerprinting." IEEE/ACM Transactions on Computational Biology and Bioinformatics 15, no. 5 (September 1, 2018): 1728–31. http://dx.doi.org/10.1109/tcbb.2017.2762682.

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42

Planatscher, Hannes, Frederik Weiß, David Eisen, B. H. J. van den Berg, Andreas Zell, Thomas Joos, and Oliver Poetz. "Identification of short terminal motifs enriched by antibodies using peptide mass fingerprinting." Bioinformatics 30, no. 9 (January 9, 2014): 1205–13. http://dx.doi.org/10.1093/bioinformatics/btu009.

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43

Liang, Zhewei, Gilles Lajoie, and Kaizhong Zhang. "NBPMF." International Journal of Cognitive Informatics and Natural Intelligence 11, no. 4 (October 2017): 41–65. http://dx.doi.org/10.4018/ijcini.2017100103.

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Mass spectrometry (MS) is an analytical technique for determining the composition of a sample. In bottom-up techniques, peptide mass fingerprinting (PMF) is widely used to identify proteins from MS dataset. In this article, the authors developed a novel network-based inference software termed NBPMF. By analyzing peptide-protein bipartite network, they designed new peptide protein matching score functions. They present two methods: the static one, ProbS, is based on an independent probability framework; and the dynamic one, HeatS, depicts input data as dependent peptides. The authors also use linear regression to adjust the matching score according to the masses of proteins. In addition, they consider the order of retention time to further correct the score function. In post processing, a peak can only be assigned to one peptide in order to reduce random matches. Finally, the authors try to filter out false positive proteins. The experiments on simulated and real data demonstrate that their NBPMF approaches lead to significantly improved performance compared to several state-of-the-art methods.

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44

Mathesius, Ulrike, Nijat Imin, Hancai Chen, Michael A. Djordjevic, Jeremy J. Weinman, Siria H. A. Natera, Angela C. Morris, et al. "Evaluation of proteome reference maps for cross-species identification of proteins by peptide mass fingerprinting." PROTEOMICS 2, no. 9 (September 2002): 1288–303. http://dx.doi.org/10.1002/1615-9861(200209)2:9<1288::aid-prot1288>3.0.co;2-h.

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45

Chuang, Adina S., and Timothy E. Mattes. "Identification of Polypeptides Expressed in Response to Vinyl Chloride, Ethene, and Epoxyethane in Nocardioides sp. Strain JS614 by Using Peptide Mass Fingerprinting." Applied and Environmental Microbiology 73, no. 13 (May 4, 2007): 4368–72. http://dx.doi.org/10.1128/aem.00086-07.

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ABSTRACT Enzymes expressed in response to vinyl chloride, ethene, and epoxyethane by Nocardioides sp. strain JS614 were identified by using a peptide mass fingerprinting (PMF) approach. PMF provided insight concerning vinyl chloride biodegradation in strain JS614 and extends the use of matrix-assisted laser desorption-ionization time of flight mass spectrometry as a tool to enhance characterization of biodegradation pathways.

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46

Hammack, B. N., G. P. Owens, M. P. Burgoon, and D. H. Gilden. "Improved resolution of human cerebrospinal fluid proteins on two-dimensional gels." Multiple Sclerosis Journal 9, no. 5 (October 2003): 472–75. http://dx.doi.org/10.1191/1352458503ms954oa.

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Proteomics combines two-dimensional gel electro phoresis and peptide mass fingerprinting and can potentially identify a protein(s) unique to disease. Such proteins can be used either for diagnosis or may be relevant to the pathogenesis of disease. Because patients with multiple sclerosis (MS) have increased amounts of immunoglobulin (Ig) G in their cerebrospinal fluid (C SF) that is directed against an as yet unidentified protein, we are applying proteomics to MS C SF, studies that require optimal separation of proteins in human C SF. We found that recovery of proteins from C SF of MS patients was improved using ultrafiltration, rather than dialysis, for desalting. Resolution of these proteins was enhanced by aceto ne precipitatio n of desalted C SF before electrophoresis and by fractionation of C SF using C ibacron Blue sepharose affinity chromatography. Improved protein recovery and resolution will facilitate excision from gels for analysis by peptide mass fingerprinting.

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47

Horn, David M., Eric C. Peters, Heath Klock, Andrew Meyers, and Ansgar Brock. "Improved protein identification using automated high mass measurement accuracy MALDI FT-ICR MS peptide mass fingerprinting." International Journal of Mass Spectrometry 238, no. 2 (November 2004): 189–96. http://dx.doi.org/10.1016/j.ijms.2004.03.016.

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48

Savary, Brett J., Prasanna Vasu, Alberto Nunez, and Randall G. Cameron. "Identification of Thermolabile Pectin Methylesterases from Sweet Orange Fruit by Peptide Mass Fingerprinting." Journal of Agricultural and Food Chemistry 58, no. 23 (December 8, 2010): 12462–68. http://dx.doi.org/10.1021/jf102558y.

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49

Sloane, Andrew J., Janice L. Duff, Nicole L. Wilson, Parag S. Gandhi, Cameron J. Hill, Femia G. Hopwood, Paul E. Smith, et al. "High Throughput Peptide Mass Fingerprinting and Protein Macroarray Analysis Using Chemical Printing Strategies." Molecular & Cellular Proteomics 1, no. 7 (July 2002): 490–99. http://dx.doi.org/10.1074/mcp.m200020-mcp200.

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50

Gattiker, Alexandre, Willy V. Bienvenut, Amos Bairoch, and Elisabeth Gasteiger. "FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification." PROTEOMICS 2, no. 10 (October 2002): 1435–44. http://dx.doi.org/10.1002/1615-9861(200210)2:10<1435::aid-prot1435>3.0.co;2-9.

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