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Volumn 12, Issue 11, 2013, Pages 3026-3035

Tools (viewer, library and validator) that facilitate use of the peptide and protein identification standard format, termed mzidentML

Author keywords

[No Author keywords available]

Indexed keywords

ASPARAGINE; ISOPROTEIN;

EID: 84887033019     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O113.029777     Document Type: Article
Times cited : (36)

References (32)
  • 3
    • 2942568222 scopus 로고    scopus 로고
    • Unimod: Protein modifications for mass spectrometry
    • DOI 10.1002/pmic.200300744
    • Creasy, D. M., and Cottrell, J. S. (2004) Unimod: protein modifications for mass spectrometry. Proteomics 4, 1534-1536. (Pubitemid 38738312)
    • (2004) Proteomics , vol.4 , Issue.6 , pp. 1534-1536
    • Creasy, D.M.1    Cottrell, J.S.2
  • 5
    • 27644555055 scopus 로고    scopus 로고
    • Interpretation of shotgun proteomic data: The protein inference problem
    • DOI 10.1074/mcp.R500012-MCP200
    • Nesvizhskii, A. I., and Aebersold, R. (2005) Interpretation of shotgun proteomic data: The protein inference problem. Mol. Cell. Proteomics 4, 1419-1440. (Pubitemid 41555469)
    • (2005) Molecular and Cellular Proteomics , vol.4 , Issue.10 , pp. 1419-1440
    • Nesvizhskii, A.I.1    Aebersold, R.2
  • 7
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567. (Pubitemid 30007252)
    • (1999) Electrophoresis , vol.20 , Issue.18 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.C.2    Creasy, D.M.3    Cottrell, J.S.4
  • 8
    • 0041358793 scopus 로고    scopus 로고
    • OLAV: Towards high-throughput tandem mass spectrometry data identification
    • DOI 10.1002/pmic.200300485
    • Colinge, J., Masselot, A., Giron, M., Dessingy, T., and Magnin, J. (2003) OLAV: Towards high-throughput tandem mass spectrometry data identification. Proteomics 3, 1454-1463. (Pubitemid 37048071)
    • (2003) Proteomics , vol.3 , Issue.8 , pp. 1454-1463
    • Colinge, J.1    Masselot, A.2    Giron, M.3    Dessingy, T.4    Magnin, J.5
  • 9
    • 77949695293 scopus 로고    scopus 로고
    • Scaffold: A bioinformatic tool for validating ms/msbased proteomic studies
    • Searle, B. C. (2010) Scaffold: A bioinformatic tool for validating MS/MSbased proteomic studies. Proteomics 10, 1265-1269.
    • (2010) Proteomics , vol.10 , pp. 1265-1269
    • Searle, B.C.1
  • 11
    • 33847401893 scopus 로고    scopus 로고
    • MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
    • DOI 10.1021/pr0604054
    • Tabb, D. L., Fernando, C. G., and Chambers, M. C. (2007) MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res. 6, 654-661. (Pubitemid 46340169)
    • (2007) Journal of Proteome Research , vol.6 , Issue.2 , pp. 654-661
    • Tabb, D.L.1    Fernando, C.G.2    Chambers, M.C.3
  • 13
    • 54949129419 scopus 로고    scopus 로고
    • Proteowizard: Open source software for rapid proteomics tools development
    • Kessner, D., Chambers, M., Burke, R., Agus, D., and Mallick, P. (2008) ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24, 2534-2536.
    • (2008) Bioinformatics , vol.24 , pp. 2534-2536
    • Kessner, D.1    Chambers, M.2    Burke, R.3    Agus, D.4    Mallick, P.5
  • 15
    • 84860348402 scopus 로고    scopus 로고
    • Jmzidentml api: A java interface to the mzidentml standard for peptide and protein identification data
    • Reisinger, F., Krishna, R., Ghali, F., Ríos, D., Hermjakob, H., Antonio Vizcaíno, J., and Jones, A. R. (2012) jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data. Proteomics 12, 790-794.
    • (2012) Proteomics , vol.12 , pp. 790-794
    • Reisinger, F.1    Krishna, R.2    Ghali, F.3    Ríos, D.4    Hermjakob, H.5    Antonio Vizcaíno, J.6    Jones, A.R.7
  • 17
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • DOI 10.1093/bioinformatics/bth092
    • Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467. (Pubitemid 38931421)
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 19
    • 63049120021 scopus 로고    scopus 로고
    • Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
    • Jones, A. R., Siepen, J. A., Hubbard, S. J., and Paton, N. W. (2009) Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. Proteomics 9, 1220-1229.
    • (2009) Proteomics , vol.9 , pp. 1220-1229
    • Jones, A.R.1    Siepen, J.A.2    Hubbard, S.J.3    Paton, N.W.4
  • 20
    • 26844559000 scopus 로고    scopus 로고
    • Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    • DOI 10.1074/mcp.M500061-MCP200
    • Ishihama, Y., Oda, Y., Tabata, T., Sato, T., Nagasu, T., Rappsilber, J., and Mann, M. (2005) Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 4, 1265-1272. (Pubitemid 41448714)
    • (2005) Molecular and Cellular Proteomics , vol.4 , Issue.9 , pp. 1265-1272
    • Ishihama, Y.1    Oda, Y.2    Tabata, T.3    Sato, T.4    Nagasu, T.5    Rappsilber, J.6    Mann, M.7
  • 21
    • 68049100378 scopus 로고    scopus 로고
    • Omssa parser: An open-source library to parse and extract data from omssa ms/ms search results
    • Barsnes, H., Huber, S., Sickmann, A., Eidhammer, I., and Martens, L. (2009) OMSSA parser: An open-source library to parse and extract data from OMSSA MS/MS search results. Proteomics 9, 3772-3774.
    • (2009) Proteomics , vol.9 , pp. 3772-3774
    • Barsnes, H.1    Huber, S.2    Sickmann, A.3    Eidhammer, I.4    Martens, L.5
  • 22
    • 77950650434 scopus 로고    scopus 로고
    • Xtandem parser: An open-source library to parse and analyse x!tandem ms/ms search results
    • Muth, T., Vaudel, M., Barsnes, H., Martens, L., and Sickmann, A. (2010) XTandem parser: An open-source library to parse and analyse X!Tandem MS/MS search results. Proteomics 10, 1522-1524.
    • (2010) Proteomics , vol.10 , pp. 1522-1524
    • Muth, T.1    Vaudel, M.2    Barsnes, H.3    Martens, L.4    Sickmann, A.5
  • 23
    • 57449099865 scopus 로고    scopus 로고
    • Maxquant enables high peptide identification rates, individualized P.P.B.-range mass accuracies and proteome-wide protein quantification
    • Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-1372.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 24
    • 0037442649 scopus 로고    scopus 로고
    • A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes
    • DOI 10.1021/ac0258709
    • Fenyo, D., and Beavis, R. C. (2003) A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 75, 768-774. (Pubitemid 36232428)
    • (2003) Analytical Chemistry , vol.75 , Issue.4 , pp. 768-774
    • Fenyo, D.1    Beavis, R.C.2
  • 26
    • 0036393898 scopus 로고    scopus 로고
    • Dtaselect and contrast: Tools for assembling and comparing protein identifications from shotgun proteomics
    • Tabb, D. L., McDonald, W. H., and Yates, J. R. (2002) DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 1, 21-26.
    • (2002) J. Proteome Res. , vol.1 , pp. 21-26
    • Tabb, D.L.1    McDonald, W.H.2    Yates, J.R.3
  • 27
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • DOI 10.1021/ac0341261
    • Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658. (Pubitemid 37082259)
    • (2003) Analytical Chemistry , vol.75 , Issue.17 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 28
    • 34948874252 scopus 로고    scopus 로고
    • Proteomic parsimony through bipartite graph analysis improves accuracy and transparency
    • DOI 10.1021/pr070230d
    • Zhang, B., Chambers, M. C., and Tabb, D. L. (2007) Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J. Proteome Res. 6, 3549-3557. (Pubitemid 47522746)
    • (2007) Journal of Proteome Research , vol.6 , Issue.9 , pp. 3549-3557
    • Zhang, B.1    Chambers, M.C.2    Tabb, D.L.3
  • 29
    • 77955595309 scopus 로고    scopus 로고
    • Masssieve: Panning ms/ms peptide data for proteins
    • Slotta, D. J., McFarland, M. A., and Markey, S. P. (2010) MassSieve: panning MS/MS peptide data for proteins. Proteomics 10, 3035-3039.
    • (2010) Proteomics , vol.10 , pp. 3035-3039
    • Slotta, D.J.1    McFarland, M.A.2    Markey, S.P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.