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Volumn 15, Issue 1, 2016, Pages 305-317

PRIDE inspector toolsuite: Moving toward a universal visualization tool for proteomics data standard formats and quality assessment of proteomexchange datasets

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; DATA PROCESSING; INFORMATION PROCESSING; MARKUP LANGUAGE; PEPTIDE LIBRARY; PRIDE INSPECTOR TOOLSUITE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEOMEXCHANGE; PROTEOMICS; PROTEOMICS IDENTIFICATION DATABASE; QUALITY CONTROL; TANDEM MASS SPECTROMETRY; WORKFLOW; BIOLOGY; INTERNET; METABOLISM; PROCEDURES; REPRODUCIBILITY; SOFTWARE;

EID: 84955495782     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O115.050229     Document Type: Article
Times cited : (149)

References (54)
  • 2
    • 84920070787 scopus 로고    scopus 로고
    • Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
    • Perez-Riverol, Y., Alpi, E., Wang, R., Hermjakob, H., and Vizcaíno, J. A. (2015) Making proteomics data accessible and reusable: Current state of proteomics databases and repositories. Proteomics 15, 930-949
    • (2015) Proteomics , vol.15 , pp. 930-949
    • Perez-Riverol, Y.1    Alpi, E.2    Wang, R.3    Hermjakob, H.4    Vizcaíno, J.A.5
  • 6
    • 84891786993 scopus 로고    scopus 로고
    • State of the human proteome in 2013 as viewed through PeptideAtlas: Comparing the kidney, urine, and plasma proteomes for the biology- and diseasedriven Human Proteome Project
    • Farrah, T., Deutsch, E. W., Omenn, G. S., Sun, Z., Watts, J. D., Yamamoto, T., Shteynberg, D., Harris, M. M., and Moritz, R. L. (2014) State of the human proteome in 2013 as viewed through PeptideAtlas: Comparing the kidney, urine, and plasma proteomes for the biology- and diseasedriven Human Proteome Project. J. Proteome Res. 13, 60-75
    • (2014) J. Proteome Res. , vol.13 , pp. 60-75
    • Farrah, T.1    Deutsch, E.W.2    Omenn, G.S.3    Sun, Z.4    Watts, J.D.5    Yamamoto, T.6    Shteynberg, D.7    Harris, M.M.8    Moritz, R.L.9
  • 11
    • 84870721324 scopus 로고    scopus 로고
    • File formats commonly used in mass spectrometry proteomics
    • Deutsch, E. W. (2012) File formats commonly used in mass spectrometry proteomics. Mol. Cell. Proteomics 11, 1612-1621
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1612-1621
    • Deutsch, E.W.1
  • 12
    • 84920070787 scopus 로고    scopus 로고
    • Making proteomics data accessible and reusable: Current state of proteomics databases and repositories
    • Perez-Riverol, Y., Alpi, E., Wang, R., Hermjakob, H., and Vizcaíno, J. A. (2015) Making proteomics data accessible and reusable: Current state of proteomics databases and repositories. Proteomics 15, 930-950
    • (2015) Proteomics , vol.15 , pp. 930-950
    • Perez-Riverol, Y.1    Alpi, E.2    Wang, R.3    Hermjakob, H.4    Vizcaíno, J.A.5
  • 13
    • 84926513336 scopus 로고    scopus 로고
    • Open source libraries and frameworks for biological data visualisation: A guide for developers
    • Wang, R., Perez-Riverol, Y., Hermjakob, H., and Vizcaíno, J. A. (2015) Open source libraries and frameworks for biological data visualisation: A guide for developers. Proteomics 15, 1356-1374
    • (2015) Proteomics , vol.15 , pp. 1356-1374
    • Wang, R.1    Perez-Riverol, Y.2    Hermjakob, H.3    Vizcaíno, J.A.4
  • 14
    • 84890425321 scopus 로고    scopus 로고
    • Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective
    • Perez-Riverol, Y., Wang, R., Hermjakob, H., Müller, M., Vesada, V., and Vizcaíno, J. A. (2014) Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective. Biochim. Biophys. Acta 1844, 63-76
    • (2014) Biochim. Biophys. Acta , vol.1844 , pp. 63-76
    • Perez-Riverol, Y.1    Wang, R.2    Hermjakob, H.3    Müller, M.4    Vesada, V.5    Vizcaíno, J.A.6
  • 15
    • 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
  • 17
    • 79952198684 scopus 로고    scopus 로고
    • OpenMS and TOPP: Open source software for LC-MS data analysis
    • Bertsch, A., Gröpl, C., Reinert, K., and Kohlbacher, O. (2011) OpenMS and TOPP: Open source software for LC-MS data analysis. Meth. Mol. Biol. 696, 353-367
    • (2011) Meth. Mol. Biol. , vol.696 , pp. 353-367
    • Bertsch, A.1    Gröpl, C.2    Reinert, K.3    Kohlbacher, O.4
  • 18
    • 84899735221 scopus 로고    scopus 로고
    • MS-viewer: A web-based spectral viewer for proteomics results
    • Baker, P. R., and Chalkley, R. J. (2014) MS-viewer: A web-based spectral viewer for proteomics results. Mol. Cell. Proteomics 13, 1392-1396
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 1392-1396
    • Baker, P.R.1    Chalkley, R.J.2
  • 22
    • 33749853607 scopus 로고    scopus 로고
    • A probability-based approach for high-throughput protein phosphorylation analysis and site localization
    • Beausoleil, S. A., Villén, J., Gerber, S. A., Rush, J., and Gygi, S. P. (2006) A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nature Biotechnol. 24, 1285-1292
    • (2006) Nature Biotechnol. , vol.24 , pp. 1285-1292
    • Beausoleil, S.A.1    Villén, J.2    Gerber, S.A.3    Rush, J.4    Gygi, S.P.5
  • 23
    • 84905397897 scopus 로고    scopus 로고
    • MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra
    • Dorfer, V., Pichler, P., Stranzl, T., Stadlmann, J., Taus, T., Winkler, S., and Mechtler, K. (2014) MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra. J. Proteome Res. 13, 3679-3684
    • (2014) J. Proteome Res. , vol.13 , pp. 3679-3684
    • Dorfer, V.1    Pichler, P.2    Stranzl, T.3    Stadlmann, J.4    Taus, T.5    Winkler, S.6    Mechtler, K.7
  • 26
    • 2942568222 scopus 로고    scopus 로고
    • Unimod: Protein modifications for mass spectrometry
    • Creasy, D. M., and Cottrell, J. S. (2004) Unimod: Protein modifications for mass spectrometry. Proteomics 4, 1534-1536
    • (2004) Proteomics , vol.4 , pp. 1534-1536
    • Creasy, D.M.1    Cottrell, J.S.2
  • 28
    • 84923247212 scopus 로고    scopus 로고
    • MS-GF+ makes progress towards a universal database search tool for proteomics
    • Kim, S., and Pevzner, P. A. (2014) MS-GF+ makes progress towards a universal database search tool for proteomics. Nature Commun. 5, 5277
    • (2014) Nature Commun. , vol.5 , pp. 5277
    • Kim, S.1    Pevzner, P.A.2
  • 29
  • 30
    • 33847401893 scopus 로고    scopus 로고
    • MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
    • 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
    • (2007) J. Proteome Res. , vol.6 , pp. 654-661
    • Tabb, D.L.1    Fernando, C.G.2    Chambers, M.C.3
  • 32
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • Craig, R., and Beavis, R. C. (2004) TANDEM: Matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 34
    • 80052435590 scopus 로고    scopus 로고
    • Faster SEQUEST searching for peptide identification from tandem mass spectra
    • Diament, B. J., and Noble, W. S. (2011) Faster SEQUEST searching for peptide identification from tandem mass spectra. J. Proteome Res. 10, 3871-3879
    • (2011) J. Proteome Res. , vol.10 , pp. 3871-3879
    • Diament, B.J.1    Noble, W.S.2
  • 36
    • 84872371907 scopus 로고    scopus 로고
    • Comet: An opensource MS/MS sequence database search tool
    • Eng, J. K., Jahan, T. A., and Hoopmann, M. R. (2013) Comet: An opensource MS/MS sequence database search tool. Proteomics 13, 22-24
    • (2013) Proteomics , vol.13 , pp. 22-24
    • Eng, J.K.1    Jahan, T.A.2    Hoopmann, M.R.3
  • 38
    • 67649400942 scopus 로고    scopus 로고
    • A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
    • Cox, J., Matic, I., Hilger, M., Nagaraj, N., Selbach, M., Olsen, J. V., and Mann, M. (2009) A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nature Protocols 4, 698-705
    • (2009) Nature Protocols , vol.4 , pp. 698-705
    • Cox, J.1    Matic, I.2    Hilger, M.3    Nagaraj, N.4    Selbach, M.5    Olsen, J.V.6    Mann, M.7
  • 40
    • 84860331423 scopus 로고    scopus 로고
    • Jmz- Reader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats
    • Griss, J., Reisinger, F., Hermjakob, H., and Vizcaíno, J. A. (2012) jmz- Reader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats. Proteomics 12, 795-798
    • (2012) Proteomics , vol.12 , pp. 795-798
    • Griss, J.1    Reisinger, F.2    Hermjakob, H.3    Vizcaíno, J.A.4
  • 41
    • 84895071750 scopus 로고    scopus 로고
    • Drift time-specific collision energies enable deep-coverage dataindependent acquisition proteomics
    • Distler, U., Kuharev, J., Navarro, P., Levin, Y., Schild, H., and Tenzer, S. (2014) Drift time-specific collision energies enable deep-coverage dataindependent acquisition proteomics. Nature Meth. 11, 167-170
    • (2014) Nature Meth. , vol.11 , pp. 167-170
    • Distler, U.1    Kuharev, J.2    Navarro, P.3    Levin, Y.4    Schild, H.5    Tenzer, S.6
  • 43
    • 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
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 44
    • 71049162549 scopus 로고    scopus 로고
    • Rapid validation of Mascot search results via stable isotope labeling, pair picking, and deconvolution of fragmentation patterns
    • Volchenboum, S. L., Kristjansdottir, K., Wolfgeher, D., and Kron, S. J. (2009) Rapid validation of Mascot search results via stable isotope labeling, pair picking, and deconvolution of fragmentation patterns. Mol. Cell. Proteomics 8, 2011-2022
    • (2009) Mol. Cell. Proteomics , vol.8 , pp. 2011-2022
    • Volchenboum, S.L.1    Kristjansdottir, K.2    Wolfgeher, D.3    Kron, S.J.4
  • 51
    • 85006189429 scopus 로고    scopus 로고
    • Dissemination of metabolomics results: Role of MetaboLights and COSMOS
    • Salek, R. M., Haug, K., and Steinbeck, C. (2013) Dissemination of metabolomics results: Role of MetaboLights and COSMOS. GigaScience 2, 8
    • (2013) GigaScience , vol.2 , pp. 8
    • Salek, R.M.1    Haug, K.2    Steinbeck, C.3
  • 54
    • 84941057782 scopus 로고    scopus 로고
    • Metrics for the Human Proteome Project 2015: Progress on the human proteome and guidelines for high-confidence protein identification
    • Omenn, G. S., Lane, L., Lundberg, E. K., Beavis, R. C., Nesvizhskii, A. I., and Deutsch, E. W. (2015) Metrics for the Human Proteome Project 2015: Progress on the human proteome and guidelines for high-confidence protein identification. J. Proteome Res. 14, 3452-3460
    • (2015) J. Proteome Res. , vol.14 , pp. 3452-3460
    • Omenn, G.S.1    Lane, L.2    Lundberg, E.K.3    Beavis, R.C.4    Nesvizhskii, A.I.5    Deutsch, E.W.6


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