메뉴 건너뛰기




Volumn 129, Issue , 2015, Pages 56-62

ProCon - PROteomics CONversion tool

Author keywords

Conversion tool; MzIdentML; PRIDE; ProCon; ProteomeXchange; Proteomics

Indexed keywords

ARTICLE; CLINICAL DATA REPOSITORY; COMPUTER LANGUAGE; COMPUTER PROGRAM; DATA BASE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SCIENTIST; SEARCH ENGINE; ALGORITHM; CHEMISTRY; CLASSIFICATION; CONTROLLED VOCABULARY; DATABASE MANAGEMENT SYSTEM; INFORMATION RETRIEVAL; NATURAL LANGUAGE PROCESSING; PROCEDURES; PROTEIN DATABASE; SOFTWARE DESIGN;

EID: 84945497412     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2015.06.015     Document Type: Article
Times cited : (12)

References (58)
  • 1
    • 84870721324 scopus 로고    scopus 로고
    • File formats commonly used in mass spectrometry proteomics
    • Deutsch E.W. File formats commonly used in mass spectrometry proteomics. Mol. Cell. Proteomics 2012, 11:1612-1621.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1612-1621
    • Deutsch, E.W.1
  • 2
    • 84945476337 scopus 로고
    • A tutorial for software development in quantitative proteomics using PSI standard formats
    • Gonzalez-Galarza F.F., Qi D., Fan J., Bessant C., Jones A.R. A tutorial for software development in quantitative proteomics using PSI standard formats. Biochim. Biophys. Acta 1844, 2014:88-97.
    • (1844) Biochim. Biophys. Acta , vol.2014 , pp. 88-97
    • Gonzalez-Galarza, F.F.1    Qi, D.2    Fan, J.3    Bessant, C.4    Jones, A.R.5
  • 3
    • 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., Vizcaíno J.A. Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics 2015, 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
  • 4
    • 70350217754 scopus 로고    scopus 로고
    • Proteomics data repositories
    • Riffle M., Eng J.K. Proteomics data repositories. Proteomics 2009, 9:4653-4663.
    • (2009) Proteomics , vol.9 , pp. 4653-4663
    • Riffle, M.1    Eng, J.K.2
  • 6
    • 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
  • 8
    • 84890425013 scopus 로고    scopus 로고
    • Data standardization and sharing-the work of the HUPO-PSI
    • Orchard S. Data standardization and sharing-the work of the HUPO-PSI. Biochim. Biophys. Acta 2014, 1844(1 Pt A):82-87.
    • (2014) Biochim. Biophys. Acta , vol.1844 , Issue.1 , pp. 82-87
    • Orchard, S.1
  • 9
    • 84938874328 scopus 로고    scopus 로고
    • Development of data representation standards by the human proteome organization proteomics standards initiative
    • Deutsch E.W., Albar J.P., Binz P.A., Eisenacher M., Jones A.R., Mayer G., et al. Development of data representation standards by the human proteome organization proteomics standards initiative. J. Am. Med. Inform. Assoc. 2015, 22:495-506.
    • (2015) J. Am. Med. Inform. Assoc. , vol.22 , pp. 495-506
    • Deutsch, E.W.1    Albar, J.P.2    Binz, P.A.3    Eisenacher, M.4    Jones, A.R.5    Mayer, G.6
  • 12
    • 84887033019 scopus 로고    scopus 로고
    • Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML
    • Ghali F., Krishna R., Lukasse P., Martinez-Bartolome S., Reisinger F., Hermjakob H., et al. Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML. Mol. Cell. Proteomics 2013, 12:3026-3035.
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 3026-3035
    • Ghali, F.1    Krishna, R.2    Lukasse, P.3    Martinez-Bartolome, S.4    Reisinger, F.5    Hermjakob, H.6
  • 17
    • 84870680444 scopus 로고    scopus 로고
    • The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium
    • Coté R.G., Griss J., Dianes J.A., Wang R., Wright J.C., van den Toorn H.W., et al. The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol. Cell. Proteomics 2012, 11:1682-1689.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1682-1689
    • Coté, R.G.1    Griss, J.2    Dianes, J.A.3    Wang, R.4    Wright, J.C.5    van den Toorn, H.W.6
  • 18
    • 77950644384 scopus 로고    scopus 로고
    • JmzML, an open-source Java API for mzML, the PSI standard for MS data
    • Coté R.G., Reisinger F., Martens L. jmzML, an open-source Java API for mzML, the PSI standard for MS data. Proteomics 2010, 10:1332-1335.
    • (2010) Proteomics , vol.10 , pp. 1332-1335
    • Coté, R.G.1    Reisinger, F.2    Martens, L.3
  • 19
    • 80655129284 scopus 로고    scopus 로고
    • JTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions
    • Helsens K., Brusniak M.Y., Deutsch E., Moritz R.L., Martens L. jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions. J. Proteome Res. 2011, 10:5260-5263.
    • (2011) J. Proteome Res. , vol.10 , pp. 5260-5263
    • Helsens, K.1    Brusniak, M.Y.2    Deutsch, E.3    Moritz, R.L.4    Martens, L.5
  • 20
    • 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., Vizcaíno J.A., et al. jmzIdentML API: a Java interface to the mzIdentML standard for peptide and protein identification data. Proteomics 2012, 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    Vizcaíno, J.A.6
  • 21
    • 84895751176 scopus 로고    scopus 로고
    • The jmzQuantML programming interface and validator for the mzQuantML data standard
    • Qi D., Krishna R., Jones A.R. The jmzQuantML programming interface and validator for the mzQuantML data standard. Proteomics 2014, 14:685-688.
    • (2014) Proteomics , vol.14 , pp. 685-688
    • Qi, D.1    Krishna, R.2    Jones, A.R.3
  • 22
    • 84860331423 scopus 로고    scopus 로고
    • JmzReader: a Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats
    • Griss J., Reisinger F., Hermjakob H., Vizcaíno J.A. jmzReader: a Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats. Proteomics 2012, 12:795-798.
    • (2012) Proteomics , vol.12 , pp. 795-798
    • Griss, J.1    Reisinger, F.2    Hermjakob, H.3    Vizcaíno, J.A.4
  • 24
    • 84859229683 scopus 로고    scopus 로고
    • PymzML-Python module for high-throughput bioinformatics on mass spectrometry data
    • Bald T., Barth J., Niehues A., Specht M., Hippler M., Fufezan C. pymzML-Python module for high-throughput bioinformatics on mass spectrometry data. Bioinformatics 2012, 28:1052-1053.
    • (2012) Bioinformatics , vol.28 , pp. 1052-1053
    • Bald, T.1    Barth, J.2    Niehues, A.3    Specht, M.4    Hippler, M.5    Fufezan, C.6
  • 25
    • 54949129419 scopus 로고    scopus 로고
    • ProteoWizard: open source software for rapid proteomics tools development
    • Kessner D., Chambers M., Burke R., Agus D., Mallick P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 2008, 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
  • 26
    • 84891796097 scopus 로고    scopus 로고
    • ProteomeXchange provides globally coordinated proteomics data submission and dissemination
    • Vizcaíno J.A., Deutsch E.W., Wang R., Csordas A., Reisinger F., Ríos D., et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat. Biotechnol. 2014, 32:223-226.
    • (2014) Nat. Biotechnol. , vol.32 , pp. 223-226
    • Vizcaíno, J.A.1    Deutsch, E.W.2    Wang, R.3    Csordas, A.4    Reisinger, F.5    Ríos, D.6
  • 30
    • 66949153240 scopus 로고    scopus 로고
    • Getting a grip on proteomics data - Proteomics Data Collection (ProDaC)
    • Eisenacher M., Martens L., Hardt T., Kohl M., Barsnes H., Helsens K., et al. Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics 2009, 9:3928-3933.
    • (2009) Proteomics , vol.9 , pp. 3928-3933
    • Eisenacher, M.1    Martens, L.2    Hardt, T.3    Kohl, M.4    Barsnes, H.5    Helsens, K.6
  • 31
    • 84865126690 scopus 로고    scopus 로고
    • Scientific workflow systems: Pipeline Pilot and KNIME
    • Warr W.A. Scientific workflow systems: Pipeline Pilot and KNIME. J. Comput. Aided Mol. Des. 2012, 26:801-804.
    • (2012) J. Comput. Aided Mol. Des. , vol.26 , pp. 801-804
    • Warr, W.A.1
  • 32
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database
    • Eng J.K., Mccormack A.L., Yates J.R. An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5:976-989.
    • (1994) J. Am. Soc. Mass Spectrom. , vol.5 , pp. 976-989
    • Eng, J.K.1    Mccormack, A.L.2    Yates, J.R.3
  • 33
    • 84872371907 scopus 로고    scopus 로고
    • Comet: an open-source MS/MS sequence database search tool
    • Eng J.K., Jahan T.A., Hoopmann M.R. Comet: an open-source MS/MS sequence database search tool. Proteomics 2013, 13:22-24.
    • (2013) Proteomics , vol.13 , pp. 22-24
    • Eng, J.K.1    Jahan, T.A.2    Hoopmann, M.R.3
  • 35
    • 35948989284 scopus 로고    scopus 로고
    • The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    • Smith B., Ashburner M., Rosse C., Bard J., Bug W., Ceusters W., et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 2007, 25:1251-1255.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 1251-1255
    • Smith, B.1    Ashburner, M.2    Rosse, C.3    Bard, J.4    Bug, W.5    Ceusters, W.6
  • 36
    • 77949753443 scopus 로고    scopus 로고
    • Managing proteomics data: from generation and data warehousing to central data repository
    • Thiele H., Glandorf J., Hufnagel P., Korting G., Bluggel M. Managing proteomics data: from generation and data warehousing to central data repository. J. Proteomics Bioinform. 2008, 01:485-507.
    • (2008) J. Proteomics Bioinform. , vol.1 , pp. 485-507
    • Thiele, H.1    Glandorf, J.2    Hufnagel, P.3    Korting, G.4    Bluggel, M.5
  • 37
    • 77954701890 scopus 로고    scopus 로고
    • Bioinformatics strategies in life sciences: from data processing and data warehousing to biological knowledge extraction
    • Thiele H., Glandorf J., Hufnagel P. Bioinformatics strategies in life sciences: from data processing and data warehousing to biological knowledge extraction. J. Integr. Bioinform. 2010, 7:141.
    • (2010) J. Integr. Bioinform. , vol.7 , pp. 141
    • Thiele, H.1    Glandorf, J.2    Hufnagel, P.3
  • 38
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins D.N., Pappin D.J.C., Creasy D.M., Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
    • (1999) Electrophoresis , vol.20 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.C.2    Creasy, D.M.3    Cottrell, J.S.4
  • 39
    • 3042735333 scopus 로고    scopus 로고
    • High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics
    • Colinge J., Masselot A., Cusin I., Mahe E., Niknejad A., Argoud-Puy G., et al. High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics 2004, 4:1977-1984.
    • (2004) Proteomics , vol.4 , pp. 1977-1984
    • Colinge, J.1    Masselot, A.2    Cusin, I.3    Mahe, E.4    Niknejad, A.5    Argoud-Puy, G.6
  • 41
    • 1542720811 scopus 로고    scopus 로고
    • Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data
    • Chamrad D.C., Korting G., Stuhler K., Meyer H.E., Klose J., Bluggel M. Evaluation of algorithms for protein identification from sequence databases using mass spectrometry data. Proteomics 2004, 4:619-628.
    • (2004) Proteomics , vol.4 , pp. 619-628
    • Chamrad, D.C.1    Korting, G.2    Stuhler, K.3    Meyer, H.E.4    Klose, J.5    Bluggel, M.6
  • 42
    • 0034213595 scopus 로고    scopus 로고
    • Profound: an expert system for protein identification using mass spectrometric peptide mapping information
    • Zhang W.Z., Chait B.T. Profound: an expert system for protein identification using mass spectrometric peptide mapping information. Anal. Chem. 2000, 72:2482-2489.
    • (2000) Anal. Chem. , vol.72 , pp. 2482-2489
    • Zhang, W.Z.1    Chait, B.T.2
  • 43
    • 0033565832 scopus 로고    scopus 로고
    • Role of accurate mass measurement (+/-10ppm) in protein identification strategies employing MS or MS/MS and database searching
    • Clauser K.R., Baker P., Burlingame A.L. Role of accurate mass measurement (+/-10ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 1999, 71:2871-2882.
    • (1999) Anal. Chem. , vol.71 , pp. 2871-2882
    • Clauser, K.R.1    Baker, P.2    Burlingame, A.L.3
  • 44
    • 0036211823 scopus 로고    scopus 로고
    • RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database
    • Field H.I., Fenyo D., Beavis R.C. RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics 2002, 2:36-47.
    • (2002) Proteomics , vol.2 , pp. 36-47
    • Field, H.I.1    Fenyo, D.2    Beavis, R.C.3
  • 46
    • 0029045645 scopus 로고
    • Calculation of the isoelectric points of native proteins with spreading of pKa values
    • Henriksson G., Englund A.K., Johansson G., Lundahl P. Calculation of the isoelectric points of native proteins with spreading of pKa values. Electrophoresis 1995, 16:1377-1380.
    • (1995) Electrophoresis , vol.16 , pp. 1377-1380
    • Henriksson, G.1    Englund, A.K.2    Johansson, G.3    Lundahl, P.4
  • 47
    • 79961225175 scopus 로고    scopus 로고
    • Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files
    • Colaert N., Barsnes H., Vaudel M., Helsens K., Timmerman E., Sickmann A., et al. Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files. J. Proteome Res. 2011, 10:3840-3843.
    • (2011) J. Proteome Res. , vol.10 , pp. 3840-3843
    • Colaert, N.1    Barsnes, H.2    Vaudel, M.3    Helsens, K.4    Timmerman, E.5    Sickmann, A.6
  • 48
    • 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
  • 49
    • 41549089987 scopus 로고    scopus 로고
    • An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications
    • Reidegeld K.A., Eisenacher M., Kohl M., Chamrad D., Korting G., Bluggel M., et al. An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications. Proteomics 2008, 8:1129-1137.
    • (2008) Proteomics , vol.8 , pp. 1129-1137
    • Reidegeld, K.A.1    Eisenacher, M.2    Kohl, M.3    Chamrad, D.4    Korting, G.5    Bluggel, M.6
  • 50
    • 84945483209 scopus 로고    scopus 로고
    • M2Lite: an Open-source, Light-weight, Pluggable and Fast Proteome Discoverer MSF to mzIdentML Tool
    • Aiyetan P., Zhang B., Chen L., Zhang Z., Zhang H. M2Lite: an Open-source, Light-weight, Pluggable and Fast Proteome Discoverer MSF to mzIdentML Tool. J. Bioinforma. 2014, 1:40-49.
    • (2014) J. Bioinforma. , vol.1 , pp. 40-49
    • Aiyetan, P.1    Zhang, B.2    Chen, L.3    Zhang, Z.4    Zhang, H.5
  • 52
    • 84907951027 scopus 로고    scopus 로고
    • The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience
    • Griss J., Jones A.R., Sachsenberg T., Walzer M., Gatto L., Hartler J., et al. The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Mol. Cell. Proteomics 2014, 13:2765-2775.
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 2765-2775
    • Griss, J.1    Jones, A.R.2    Sachsenberg, T.3    Walzer, M.4    Gatto, L.5    Hartler, J.6
  • 54
    • 74049115774 scopus 로고    scopus 로고
    • Mass spectrometry-based label-free quantitative proteomics
    • Zhu W., Smith J.W., Huang C.M. Mass spectrometry-based label-free quantitative proteomics. J. Biomed. Biotechnol. 2010, 2010:840518.
    • (2010) J. Biomed. Biotechnol. , vol.2010 , pp. 840518
    • Zhu, W.1    Smith, J.W.2    Huang, C.M.3
  • 56
    • 67650382229 scopus 로고    scopus 로고
    • Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles
    • Rodriguez H., Snyder M., Uhlen M., Andrews P., Beavis R., Borchers C., et al. Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J. Proteome Res. 2009, 8:3689-3692.
    • (2009) J. Proteome Res. , vol.8 , pp. 3689-3692
    • Rodriguez, H.1    Snyder, M.2    Uhlen, M.3    Andrews, P.4    Beavis, R.5    Borchers, C.6
  • 57
  • 58
    • 84862918606 scopus 로고    scopus 로고
    • Target discovery from data mining approaches
    • Yang Y., Adelstein S.J., Kassis A.I. Target discovery from data mining approaches. Drug Discov. Today 2012, 17:S16-S23. (Suppl.).
    • (2012) Drug Discov. Today , vol.17 , pp. S16-S23
    • Yang, Y.1    Adelstein, S.J.2    Kassis, A.I.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.