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Volumn 14, Issue 9, 2014, Pages 1001-1005

Shedding light on black boxes in protein identification

Author keywords

Bioinformatics; Open Source; Protein Identification; Publication Guidelines; Tutorial

Indexed keywords

PEPTIDE; PROTEIN;

EID: 84898619035     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201300488     Document Type: Article
Times cited : (20)

References (39)
  • 1
    • 77956304093 scopus 로고    scopus 로고
    • Mass spectrometry in high-throughput proteomics: ready for the big time
    • Nilsson, T., Mann, M., Aebersold, R., Yates, J. R., 3rd et al., Mass spectrometry in high-throughput proteomics: ready for the big time. Nat. Methods 2010, 7, 681-685.
    • (2010) Nat. Methods , vol.7 , pp. 681-685
    • Nilsson, T.1    Mann, M.2    Aebersold, R.3    Yates 3rd, J.R.4
  • 3
    • 34248598796 scopus 로고    scopus 로고
    • Trends in sample preparation for classical and second generation proteomics
    • Canas, B., Pineiro, C., Calvo, E., Lopez-Ferrer, D., Gallardo, J. M., Trends in sample preparation for classical and second generation proteomics. J. Chromatogr. A 2007, 1153, 235-258.
    • (2007) J. Chromatogr. A , vol.1153 , pp. 235-258
    • Canas, B.1    Pineiro, C.2    Calvo, E.3    Lopez-Ferrer, D.4    Gallardo, J.M.5
  • 4
    • 34748910605 scopus 로고    scopus 로고
    • Sample preparation by in-gel digestion for mass spectrometry-based proteomics
    • Granvogl, B., Ploscher, M., Eichacker, L. A., Sample preparation by in-gel digestion for mass spectrometry-based proteomics. Anal. Bioanal. Chem. 2007, 389, 991-1002.
    • (2007) Anal. Bioanal. Chem. , vol.389 , pp. 991-1002
    • Granvogl, B.1    Ploscher, M.2    Eichacker, L.A.3
  • 5
    • 84855877960 scopus 로고    scopus 로고
    • Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics
    • Burkhart, J. M., Schumbrutzki, C., Wortelkamp, S., Sickmann, A., Zahedi, R. P., Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics. J. Proteomics 2012, 75, 1454-62.
    • (2012) J. Proteomics , vol.75 , pp. 1454-1462
    • Burkhart, J.M.1    Schumbrutzki, C.2    Wortelkamp, S.3    Sickmann, A.4    Zahedi, R.P.5
  • 6
    • 34548400394 scopus 로고    scopus 로고
    • A la carte proteomics with an emphasis on gel-free techniques
    • Gevaert, K., Van Damme, P., Ghesquiere, B., Impens, F. et al., A la carte proteomics with an emphasis on gel-free techniques. Proteomics 2007, 7, 2698-2718.
    • (2007) Proteomics , vol.7 , pp. 2698-2718
    • Gevaert, K.1    Van Damme, P.2    Ghesquiere, B.3    Impens, F.4
  • 7
    • 0024438708 scopus 로고
    • Electrospray ionization for mass spectrometry of large biomolecules
    • Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., Whitehouse, C. M., Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246, 64-71.
    • (1989) Science , vol.246 , pp. 64-71
    • Fenn, J.B.1    Mann, M.2    Meng, C.K.3    Wong, S.F.4    Whitehouse, C.M.5
  • 8
    • 84875463071 scopus 로고
    • Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers
    • Hillenkamp, F., Karas, M., Beavis, R. C., Chait, B. T., Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal. Chem. 1991, 63, 1193A-1203A.
    • (1991) Anal. Chem. , vol.63
    • Hillenkamp, F.1    Karas, M.2    Beavis, R.C.3    Chait, B.T.4
  • 9
    • 79952303580 scopus 로고    scopus 로고
    • A global analysis of peptide fragmentation variability
    • Barsnes, H., Eidhammer, I., Martens, L., A global analysis of peptide fragmentation variability. Proteomics 2011, 11, 1181-1188.
    • (2011) Proteomics , vol.11 , pp. 1181-1188
    • Barsnes, H.1    Eidhammer, I.2    Martens, L.3
  • 10
    • 0041408938 scopus 로고    scopus 로고
    • Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis
    • Makarov, A., Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal. Chem. 2000, 72, 1156-1162.
    • (2000) Anal. Chem. , vol.72 , pp. 1156-1162
    • Makarov, A.1
  • 11
    • 77957221582 scopus 로고    scopus 로고
    • A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
    • Nesvizhskii, A. I., A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J. Proteomics 2010, 73, 2092-2123.
    • (2010) J. Proteomics , vol.73 , pp. 2092-2123
    • Nesvizhskii, A.I.1
  • 12
    • 84876692278 scopus 로고    scopus 로고
    • Crowdsourcing in proteomics: public resources lead to better experiments
    • Barsnes, H., Martens, L., Crowdsourcing in proteomics: public resources lead to better experiments. Amino Acids 2013, 44, 1129-1137.
    • (2013) Amino Acids , vol.44 , pp. 1129-1137
    • Barsnes, H.1    Martens, L.2
  • 13
    • 84870596405 scopus 로고    scopus 로고
    • Current methods for global proteome identification
    • Vaudel, M., Sickmann, A., Martens, L., Current methods for global proteome identification. Expert Rev. Proteomics 2012, 9, 519-532.
    • (2012) Expert Rev. Proteomics , vol.9 , pp. 519-532
    • Vaudel, M.1    Sickmann, A.2    Martens, L.3
  • 14
    • 34547176285 scopus 로고    scopus 로고
    • Proteomics data validation: why all must provide data
    • Martens, L., Hermjakob, H., Proteomics data validation: why all must provide data. Mol. Biosyst. 2007, 3, 518-522.
    • (2007) Mol. Biosyst. , vol.3 , pp. 518-522
    • Martens, L.1    Hermjakob, H.2
  • 15
    • 84890548691 scopus 로고    scopus 로고
    • Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics
    • Vaudel, M., Sickmann, A., Martens, L., Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics. Biochim. Biophys. Acta 2014, 1844, 12-20.
    • (2014) Biochim. Biophys. Acta , vol.1844 , pp. 12-20
    • Vaudel, M.1    Sickmann, A.2    Martens, L.3
  • 16
    • 76149098839 scopus 로고    scopus 로고
    • Unbiased statistical analysis for multi-stage proteomic search strategies
    • Everett, L. J., Bierl, C., Master, S. R., Unbiased statistical analysis for multi-stage proteomic search strategies. J. Proteome Res. 2010, 9, 700-707.
    • (2010) J. Proteome Res. , vol.9 , pp. 700-707
    • Everett, L.J.1    Bierl, C.2    Master, S.R.3
  • 17
    • 79953170260 scopus 로고    scopus 로고
    • Interpretation of data underlying the link between colony collapse disorder (CCD) and an invertebrate iridescent virus
    • Foster, L. J., Interpretation of data underlying the link between colony collapse disorder (CCD) and an invertebrate iridescent virus. Mol. Cell Proteomics 2011, 10, M110.006387.
    • (2011) Mol. Cell Proteomics , vol.10
    • Foster, L.J.1
  • 18
    • 84883355771 scopus 로고    scopus 로고
    • Matters of significance
    • Editors
    • Editors, Matters of significance. Nat. Methods 2013, 10, 805.
    • (2013) Nat. Methods , vol.10 , pp. 805
  • 19
    • 84893351260 scopus 로고    scopus 로고
    • PROTEINCHALLENGE: crowd sourcing in proteomics analysis and software development
    • Martin, S. F., Falkenberg, H., Dyrlund, T. F., Khoudoli, G. A. et al., PROTEINCHALLENGE: crowd sourcing in proteomics analysis and software development. J. Proteomics 2013, 88, 41-46.
    • (2013) J. Proteomics , vol.88 , pp. 41-46
    • Martin, S.F.1    Falkenberg, H.2    Dyrlund, T.F.3    Khoudoli, G.A.4
  • 20
    • 84885582360 scopus 로고    scopus 로고
    • In need of an upgrade
    • Editors
    • Editors, In need of an upgrade. Nat. Biotechnol. 2013, 31, 857.
    • (2013) Nat. Biotechnol. , vol.31 , pp. 857
  • 21
    • 84863012827 scopus 로고    scopus 로고
    • Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles)
    • Kinsinger, C. R., Apffel, J., Baker, M., Bian, X. et al., Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). J. Proteome Res. 2012, 11, 1412-1419.
    • (2012) J. Proteome Res. , vol.11 , pp. 1412-1419
    • Kinsinger, C.R.1    Apffel, J.2    Baker, M.3    Bian, X.4
  • 22
    • 79952294100 scopus 로고    scopus 로고
    • Quality control in proteomics
    • Martens, L., Vizcaino, J. A., Banks, R., Quality control in proteomics. Proteomics 2011, 11, 1015-1016.
    • (2011) Proteomics , vol.11 , pp. 1015-1016
    • Martens, L.1    Vizcaino, J.A.2    Banks, R.3
  • 23
    • 84868325438 scopus 로고    scopus 로고
    • SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments
    • Pichler, P., Mazanek, M., Dusberger, F., Weilnbock, L. et al., SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on Orbitrap instruments. J. Proteome Res. 2012, 11, 5540-5547.
    • (2012) J. Proteome Res. , vol.11 , pp. 5540-5547
    • Pichler, P.1    Mazanek, M.2    Dusberger, F.3    Weilnbock, L.4
  • 24
    • 54049090766 scopus 로고    scopus 로고
    • Selected reaction monitoring for quantitative proteomics: a tutorial
    • Lange, V., Picotti, P., Domon, B., Aebersold, R., Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 2008, 4, 222.
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 222
    • Lange, V.1    Picotti, P.2    Domon, B.3    Aebersold, R.4
  • 25
    • 38549097071 scopus 로고    scopus 로고
    • The universal protein resource (UniProt)
    • UniProt Consortium
    • UniProt Consortium, The universal protein resource (UniProt). Nucleic Acids Res. 2008, 36, D190-D195.
    • (2008) Nucleic Acids Res. , vol.36
  • 26
    • 84867345063 scopus 로고    scopus 로고
    • A cross-platform toolkit for mass spectrometry and proteomics
    • Chambers, M. C., Maclean, B., Burke, R., Amodei, D. et al., A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 2012, 30, 918-920.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 918-920
    • Chambers, M.C.1    Maclean, B.2    Burke, R.3    Amodei, D.4
  • 28
    • 0037442649 scopus 로고    scopus 로고
    • A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
    • Fenyo, D., Beavis, R. C., A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 2003, 75, 768-774.
    • (2003) Anal. Chem. , vol.75 , pp. 768-774
    • Fenyo, D.1    Beavis, R.C.2
  • 29
    • 79951750784 scopus 로고    scopus 로고
    • SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches
    • Vaudel, M., Barsnes, H., Berven, F. S., Sickmann, A., Martens, L., SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics 2011, 11, 996-999.
    • (2011) Proteomics , vol.11 , pp. 996-999
    • Vaudel, M.1    Barsnes, H.2    Berven, F.S.3    Sickmann, A.4    Martens, L.5
  • 30
    • 77449146854 scopus 로고    scopus 로고
    • Target-decoy search strategy for mass spectrometry-based proteomics
    • Elias, J. E., Gygi, S. P., Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol. Biol. 2010, 604, 55-71.
    • (2010) Methods Mol. Biol. , vol.604 , pp. 55-71
    • Elias, J.E.1    Gygi, S.P.2
  • 32
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D. et al., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4
  • 34
    • 84876515907 scopus 로고    scopus 로고
    • STRING v9.1: protein-protein interaction networks, with increased coverage and integration
    • Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M. et al., STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013, 41, D808-D815.
    • (2013) Nucleic Acids Res. , vol.41
    • Franceschini, A.1    Szklarczyk, D.2    Frankild, S.3    Kuhn, M.4
  • 35
    • 58149177166 scopus 로고    scopus 로고
    • Reactome knowledgebase of human biological pathways and processes
    • Matthews, L., Gopinath, G., Gillespie, M., Caudy, M. et al., Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 2009, 37, D619-D622.
    • (2009) Nucleic Acids Res. , vol.37
    • Matthews, L.1    Gopinath, G.2    Gillespie, M.3    Caudy, M.4
  • 37
    • 65549111862 scopus 로고    scopus 로고
    • Charting online OMICS resources: a navigational chart for clinical researchers
    • Vizcaino, J. A., Mueller, M., Hermjakob, H., Martens, L., Charting online OMICS resources: a navigational chart for clinical researchers. Proteomics Clin. Appl. 2009, 3, 18-29.
    • (2009) Proteomics Clin. Appl. , vol.3 , pp. 18-29
    • Vizcaino, J.A.1    Mueller, M.2    Hermjakob, H.3    Martens, L.4
  • 38
    • 23944526367 scopus 로고    scopus 로고
    • PRIDE: the proteomics identifications database
    • Martens, L., Hermjakob, H., Jones, P., Adamski, M. et al., PRIDE: the proteomics identifications database. Proteomics 2005, 5, 3537-3545.
    • (2005) Proteomics , vol.5 , pp. 3537-3545
    • Martens, L.1    Hermjakob, H.2    Jones, P.3    Adamski, M.4
  • 39
    • 84863011685 scopus 로고    scopus 로고
    • PRIDE Inspector: a tool to visualize and validate MS proteomics data
    • Wang, R., Fabregat, A., Rios, D., Ovelleiro, D. et al., PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat. Biotechnol. 2012, 30, 135-137.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 135-137
    • Wang, R.1    Fabregat, A.2    Rios, D.3    Ovelleiro, D.4


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