메뉴 건너뛰기




Volumn 129, Issue , 2015, Pages 93-97

An extensive library of surrogate peptides for all human proteins

Author keywords

Data integration; Multiple reaction monitoring (MRM); Peptide selection; Scientific workflow; SRM; Targeted proteomics

Indexed keywords

PEPTIDE; PROTEIN; PROTEOME;

EID: 84945461669     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2015.07.025     Document Type: Article
Times cited : (8)

References (39)
  • 1
    • 84871983086 scopus 로고    scopus 로고
    • Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry
    • Gillette M.A., Carr S.A. Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat. Methods 2013, 10:28-34.
    • (2013) Nat. Methods , vol.10 , pp. 28-34
    • Gillette, M.A.1    Carr, S.A.2
  • 3
    • 84898598317 scopus 로고    scopus 로고
    • Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility
    • Percy A.J., Chambers A.G., Yang J., Hardie D., Borchers C.H. Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility. Biochim. Biophys. Acta 2014, 1844:917-926. (pii: S1570-9639(13)00239-2).
    • (2014) Biochim. Biophys. Acta , vol.1844 , pp. 917-926
    • Percy, A.J.1    Chambers, A.G.2    Yang, J.3    Hardie, D.4    Borchers, C.H.5
  • 4
    • 84899997891 scopus 로고    scopus 로고
    • PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments
    • Mohammed Y., Domański D., Jackson A.M., Smith D.S., Deelder A.M., Palmblad M., et al. PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments. J. Proteome 2014, 106:151-161.
    • (2014) J. Proteome , vol.106 , pp. 151-161
    • Mohammed, Y.1    Domański, D.2    Jackson, A.M.3    Smith, D.S.4    Deelder, A.M.5    Palmblad, M.6
  • 5
    • 79960976768 scopus 로고    scopus 로고
    • UniProt Knowledgebase: a hub of integrated protein data
    • bar009
    • Magrane M., Consortium U. UniProt Knowledgebase: a hub of integrated protein data. Database 2011, 2011:bar009.
    • (2011) Database , vol.2011
    • Magrane, M.1    Consortium, U.2
  • 6
    • 0032876978 scopus 로고    scopus 로고
    • DbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation
    • Sherry S.T., Ward M., Sirotkin K. dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res. 1999, 9:677-679.
    • (1999) Genome Res. , vol.9 , pp. 677-679
    • Sherry, S.T.1    Ward, M.2    Sirotkin, K.3
  • 7
    • 0032619552 scopus 로고    scopus 로고
    • Protein identification and analysis tools in the ExPASy server
    • Humana Press, Totowa, NJ, A.J. Link (Ed.)
    • Wilkins M.R., Gasteiger E., Bairocj A., Sanchez J.C., Williams K.L., Appel R.D., et al. Protein identification and analysis tools in the ExPASy server. Methods Mol Biol 1999, 531-552. Humana Press, Totowa, NJ. A.J. Link (Ed.).
    • (1999) Methods Mol Biol , pp. 531-552
    • Wilkins, M.R.1    Gasteiger, E.2    Bairocj, A.3    Sanchez, J.C.4    Williams, K.L.5    Appel, R.D.6
  • 8
    • 43049127826 scopus 로고    scopus 로고
    • PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
    • Deutsch E.W., Lam H., Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 2008, 9:429-434.
    • (2008) EMBO Rep. , vol.9 , pp. 429-434
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 9
    • 84874762979 scopus 로고    scopus 로고
    • The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013
    • Vizcaino J.A., Cote R.G., Csordas A., Dianes J.A., Fabregat A., Foster J.M., et al. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2013, 41(Database issue):D1063-D1069.
    • (2013) Nucleic Acids Res. , vol.41 , Issue.DATABASE ISSUE , pp. D1063-D1069
    • Vizcaino, J.A.1    Cote, R.G.2    Csordas, A.3    Dianes, J.A.4    Fabregat, A.5    Foster, J.M.6
  • 10
    • 11144320641 scopus 로고    scopus 로고
    • An open source system for analyzing, validating and storing protein identification data
    • Craig R., Cortens J.P., Beavis R.C. An open source system for analyzing, validating and storing protein identification data. J. Proteome Res. 2004, 3:1234-1242.
    • (2004) J. Proteome Res. , vol.3 , pp. 1234-1242
    • Craig, R.1    Cortens, J.P.2    Beavis, R.C.3
  • 11
    • 79952112715 scopus 로고    scopus 로고
    • Mass spectrometric protein identification using the global proteome machine
    • Fenyo D., Eriksson J., Beavis R. Mass spectrometric protein identification using the global proteome machine. Methods Mol. Biol. 2010, 673:189-202.
    • (2010) Methods Mol. Biol. , vol.673 , pp. 189-202
    • Fenyo, D.1    Eriksson, J.2    Beavis, R.3
  • 13
    • 10244255212 scopus 로고    scopus 로고
    • Taverna: a tool for the composition and enactment of bioinformatics workflows
    • Oinn T., Addis M., Ferris J., Marvin D., Senger M., Greenwood M., et al. Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004, 20:3045-3054.
    • (2004) Bioinformatics , vol.20 , pp. 3045-3054
    • Oinn, T.1    Addis, M.2    Ferris, J.3    Marvin, D.4    Senger, M.5    Greenwood, M.6
  • 15
    • 59849093889 scopus 로고    scopus 로고
    • Prediction of high-responding peptides for targeted protein assays by mass spectrometry
    • Fusaro V.A., Mani D.R., Mesirov J.P., Carr S.A. Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat. Biotechnol. 2009, 27:190-198.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 190-198
    • Fusaro, V.A.1    Mani, D.R.2    Mesirov, J.P.3    Carr, S.A.4
  • 16
    • 33846133955 scopus 로고    scopus 로고
    • Computational prediction of proteotypic peptides for quantitative proteomics
    • Mallick P., Schirle M., Chen S.S., Flory M.R., Lee H., Martin D., et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 2007, 12:125-131.
    • (2007) Nat. Biotechnol. , vol.12 , pp. 125-131
    • Mallick, P.1    Schirle, M.2    Chen, S.S.3    Flory, M.R.4    Lee, H.5    Martin, D.6
  • 17
    • 38349172005 scopus 로고    scopus 로고
    • Prediction of peptides observable by mass spectrometry applied at the experimental set level
    • Sanders W.S., Bridges S.M., McCarthy F.M., Nanduri B., Burgess S.C. Prediction of peptides observable by mass spectrometry applied at the experimental set level. BMC Bioinforma. 2007, 1:S23.
    • (2007) BMC Bioinforma. , vol.1 , pp. S23
    • Sanders, W.S.1    Bridges, S.M.2    McCarthy, F.M.3    Nanduri, B.4    Burgess, S.C.5
  • 18
    • 84860848068 scopus 로고    scopus 로고
    • Mass spectrometry-based targeted quantitative proteomics: achieving sensitive and reproducible detection of proteins
    • Boja E.S., Rodriguez H. Mass spectrometry-based targeted quantitative proteomics: achieving sensitive and reproducible detection of proteins. Proteomics 2012, 12:1093-1110.
    • (2012) Proteomics , vol.12 , pp. 1093-1110
    • Boja, E.S.1    Rodriguez, H.2
  • 19
    • 84945447831 scopus 로고    scopus 로고
    • PeptideAtlas http://www.peptideatlas.org.
  • 21
    • 79952703214 scopus 로고    scopus 로고
    • ATAQS: a computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry
    • Brusniak M.-Y.K., Kwok S.-T., Christiansen M., Campbell D., Reiter L., Picotti P., et al. ATAQS: a computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. BMC Bioinforma. 2011, 12.
    • (2011) BMC Bioinforma. , vol.12
    • Brusniak, M.-Y.K.1    Kwok, S.-T.2    Christiansen, M.3    Campbell, D.4    Reiter, L.5    Picotti, P.6
  • 22
    • 84866303718 scopus 로고    scopus 로고
    • MRMaid 2.0: mining PRIDE for evidence-based SRM transitions
    • Fan J., Mohareb F., Bond N.J., Lilley K.S., Bessant C. MRMaid 2.0: mining PRIDE for evidence-based SRM transitions. OMICS 2012, 16:483-488.
    • (2012) OMICS , vol.16 , pp. 483-488
    • Fan, J.1    Mohareb, F.2    Bond, N.J.3    Lilley, K.S.4    Bessant, C.5
  • 23
    • 67649562538 scopus 로고    scopus 로고
    • Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring
    • Walsh G.M., Lin S., Evans D.M., Khosrovi-Eghbal A., Beavis R.C., Kast J. Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring. J. Proteome 2009, 72:838-852.
    • (2009) J. Proteome , vol.72 , pp. 838-852
    • Walsh, G.M.1    Lin, S.2    Evans, D.M.3    Khosrovi-Eghbal, A.4    Beavis, R.C.5    Kast, J.6
  • 24
    • 84873724658 scopus 로고    scopus 로고
    • A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis
    • Picotti P., Clément-Ziza M., Lam H., Campbell D.S., Schmidt A., Deutsch E.W., et al. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature 2013, 494:266-270.
    • (2013) Nature , vol.494 , pp. 266-270
    • Picotti, P.1    Clément-Ziza, M.2    Lam, H.3    Campbell, D.S.4    Schmidt, A.5    Deutsch, E.W.6
  • 25
    • 84903695804 scopus 로고    scopus 로고
    • Institute_for_Systems_Biology SRMAtlas http://www.mrmatlas.org.
    • SRMAtlas
  • 26
    • 43049090085 scopus 로고    scopus 로고
    • Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring
    • Lange V., Malmström J.A., Didion J., King N.L., Johansson B.P., Schäfer J., et al. Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol. Cell. Proteomics Apr 13 2008, 7:1489-1500.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 1489-1500
    • Lange, V.1    Malmström, J.A.2    Didion, J.3    King, N.L.4    Johansson, B.P.5    Schäfer, J.6
  • 28
    • 77951965920 scopus 로고    scopus 로고
    • Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
    • MacLean B., Tomazela D.M., Shulman N., Chambers M., Finney G.L., Frewen B., et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 2010, 26:966-968.
    • (2010) Bioinformatics , vol.26 , pp. 966-968
    • MacLean, B.1    Tomazela, D.M.2    Shulman, N.3    Chambers, M.4    Finney, G.L.5    Frewen, B.6
  • 29
    • 84945456774 scopus 로고    scopus 로고
    • (update v0.7)
    • Skyline_SRM/MRM_Builder Skyline targeted proteomics environment (update v0.7). https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default.
    • Skyline targeted proteomics environment
  • 30
    • 70349972789 scopus 로고    scopus 로고
    • MaRiMba: a software application for spectral library-based MRM transition list assembly
    • Sherwood C., Eastham A., Peterson A., Eng J.K., Shteynberg D., Mendoza L., et al. MaRiMba: a software application for spectral library-based MRM transition list assembly. J. Proteome Res. 2009, 8:4396-4405.
    • (2009) J. Proteome Res. , vol.8 , pp. 4396-4405
    • Sherwood, C.1    Eastham, A.2    Peterson, A.3    Eng, J.K.4    Shteynberg, D.5    Mendoza, L.6
  • 31
    • 77949695871 scopus 로고    scopus 로고
    • Free computational resources for designing selected reaction monitoring transitions
    • Cham Mead J.A., Bianco L., Bessant C. Free computational resources for designing selected reaction monitoring transitions. Proteomics 2010, 10:1106-1126.
    • (2010) Proteomics , vol.10 , pp. 1106-1126
    • Cham Mead, J.A.1    Bianco, L.2    Bessant, C.3
  • 34
    • 0030305457 scopus 로고    scopus 로고
    • R: a language for data analysis and graphics
    • Ihaka R., Gentleman R. R: a language for data analysis and graphics. J. Comput. Graph. Stat. 1996, 5:299-314.
    • (1996) J. Comput. Graph. Stat. , vol.5 , pp. 299-314
    • Ihaka, R.1    Gentleman, R.2
  • 35
    • 79952201691 scopus 로고    scopus 로고
    • PRIDE and "Database on Demand" as valuable tools for computational proteomics
    • Vizcaíno J.A., Reisinger F., Côté R., Martens L. PRIDE and "Database on Demand" as valuable tools for computational proteomics. Methods Mol. Biol. 2011, 696:93-105.
    • (2011) Methods Mol. Biol. , vol.696 , pp. 93-105
    • Vizcaíno, J.A.1    Reisinger, F.2    Côté, R.3    Martens, L.4
  • 36
    • 84858314394 scopus 로고    scopus 로고
    • BioMart: driving a paradigm change in biological data management
    • Kasprzyk A. BioMart: driving a paradigm change in biological data management. Database 2011, 2011:bar049.
    • (2011) Database , vol.2011
    • Kasprzyk, A.1
  • 38
    • 84943239123 scopus 로고    scopus 로고
    • UniProtKB UniProtKB http://www.uniprot.org/help/uniprotkb.
    • UniProtKB


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.