메뉴 건너뛰기




Volumn 14, Issue 20, 2014, Pages 2275-2279

A collection of open source applications for mass spectrometry data mining

Author keywords

Bioinformatics; Data analysis; Data handling; Phosphoproteomics; Search engine

Indexed keywords

ARTICLE; BIOINFORMATICS; CLINICAL DATA REPOSITORY; COMPUTER INTERFACE; COMPUTER LANGUAGE; COMPUTER PROGRAM; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; DATA BASE; DATA MINING; DATA PROCESSING; LIMIT OF QUANTITATION; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SEARCH ENGINE; WORKFLOW; ANIMAL; HUMAN; PROCEDURES; PROTEIN DATABASE;

EID: 84907882523     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400124     Document Type: Article
Times cited : (11)

References (19)
  • 1
    • 61349179532 scopus 로고    scopus 로고
    • Phosphorylation analysis of primary human T lymphocytes using sequential IMAC and titanium oxide enrichment
    • Carrascal, M., Ovelleiro, D., Casas, V., Gay, M., Abian, J., Phosphorylation analysis of primary human T lymphocytes using sequential IMAC and titanium oxide enrichment. J. Proteome Res. 2008, 7, 5167-5176.
    • (2008) J. Proteome Res. , vol.7 , pp. 5167-5176
    • Carrascal, M.1    Ovelleiro, D.2    Casas, V.3    Gay, M.4    Abian, J.5
  • 2
    • 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., Gygi, S. P., A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat. Biotechnol. 2006, 24, 1285-1292.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1285-1292
    • Beausoleil, S.A.1    Villén, J.2    Gerber, S.A.3    Rush, J.4    Gygi, S.P.5
  • 3
    • 68049108471 scopus 로고    scopus 로고
    • LymPHOS: design of a phosphosite database of primary human T cells
    • Ovelleiro, D., Carrascal, M., Casas, V., Abian, J., LymPHOS: design of a phosphosite database of primary human T cells. Proteomics 2009, 9, 3741-3751.
    • (2009) Proteomics , vol.9 , pp. 3741-3751
    • Ovelleiro, D.1    Carrascal, M.2    Casas, V.3    Abian, J.4
  • 4
    • 84907869714 scopus 로고    scopus 로고
    • The GNU General Public License v3.0-GNU project-free software Foundation (FSF) n.d.
    • The GNU General Public License v3.0-GNU project-free software Foundation (FSF) n.d.
  • 6
    • 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., III, 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 III, J.R.3
  • 7
    • 0141989734 scopus 로고    scopus 로고
    • PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry
    • Ma, B., Zhang, K., Hendrie, C., Liang, C. et al., PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2003, 17, 2337-2342.
    • (2003) Rapid Commun. Mass Spectrom. , vol.17 , pp. 2337-2342
    • Ma, B.1    Zhang, K.2    Hendrie, C.3    Liang, C.4
  • 8
    • 0041358793 scopus 로고    scopus 로고
    • OLAV: towards high-throughput tandem mass spectrometry data identification
    • Colinge, J., Masselot, A., Giron, M., Dessingy, T., Magnin, J., OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 2003, 3, 1454-1463.
    • (2003) Proteomics , vol.3 , pp. 1454-1463
    • Colinge, J.1    Masselot, A.2    Giron, M.3    Dessingy, T.4    Magnin, J.5
  • 9
    • 84872387673 scopus 로고    scopus 로고
    • EasyProt-an easy-to-use graphical platform for proteomics data analysis
    • Gluck, F., Hoogland, C., Antinori, P., Robin, X. et al., EasyProt-an easy-to-use graphical platform for proteomics data analysis. J. Proteomics 2013, 79, 146-160.
    • (2013) J. Proteomics , vol.79 , pp. 146-160
    • Gluck, F.1    Hoogland, C.2    Antinori, P.3    Robin, X.4
  • 11
    • 84887052462 scopus 로고    scopus 로고
    • LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach
    • Fermin, D., Walmsley, S. J., Gingras, A.-C., Choi, H., Nesvizhskii, A. I., LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Mol. Cell. Proteomics 2013, 12, 3409-3419.
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 3409-3419
    • Fermin, D.1    Walmsley, S.J.2    Gingras, A.-C.3    Choi, H.4    Nesvizhskii, A.I.5
  • 12
    • 74849138649 scopus 로고    scopus 로고
    • Combining low- and high-energy tandem mass spectra for optimized peptide quantification with isobaric tags
    • Dayon, L., Pasquarello, C., Hoogland, C., Sanchez, J.-C., Scherl, A., Combining low- and high-energy tandem mass spectra for optimized peptide quantification with isobaric tags. J. Proteomics 2010, 73, 769-777.
    • (2010) J. Proteomics , vol.73 , pp. 769-777
    • Dayon, L.1    Pasquarello, C.2    Hoogland, C.3    Sanchez, J.-C.4    Scherl, A.5
  • 13
    • 76749122411 scopus 로고    scopus 로고
    • Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses
    • Rudnick, P. A., Clauser, K. R., Kilpatrick, L. E., Tchekhovskoi, D. V. et al., Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol. Cell. Proteomics 2010, 9, 225-241.
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 225-241
    • Rudnick, P.A.1    Clauser, K.R.2    Kilpatrick, L.E.3    Tchekhovskoi, D.V.4
  • 14
    • 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., Paton, N. W., Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. Proteomics 2009, 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
  • 15
    • 48249129089 scopus 로고    scopus 로고
    • OMSSAGUI: an open-source user interface component to configure and run the OMSSA search engine
    • Tharakan, R., Martens, L., Van Eyk, J. E., Graham, D. R., OMSSAGUI: an open-source user interface component to configure and run the OMSSA search engine. Proteomics 2008, 8, 2376-2378.
    • (2008) Proteomics , vol.8 , pp. 2376-2378
    • Tharakan, R.1    Martens, L.2    Van Eyk, J.E.3    Graham, D.R.4
  • 16
    • 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., Lennart 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    Lennart Martens, L.5
  • 17
    • 2942568222 scopus 로고    scopus 로고
    • Unimod: protein modifications for mass spectrometry
    • Creasy, D. M., Cottrell, J. S., Unimod: protein modifications for mass spectrometry. Proteomics 2004, 4, 1534-1536.
    • (2004) Proteomics , vol.4 , pp. 1534-1536
    • Creasy, D.M.1    Cottrell, J.S.2
  • 18
    • 76149133112 scopus 로고    scopus 로고
    • Characterization of the human plasma phosphoproteome using linear ion trap mass spectrometry and multiple search engines
    • Carrascal, M., Gay, M., Ovelleiro, D., Casas, V. et al., Characterization of the human plasma phosphoproteome using linear ion trap mass spectrometry and multiple search engines. J. Proteome Res. 2009, 9, 876-884.
    • (2009) J. Proteome Res. , vol.9 , pp. 876-884
    • Carrascal, M.1    Gay, M.2    Ovelleiro, D.3    Casas, V.4
  • 19
    • 84907869712 scopus 로고    scopus 로고
    • RFC 4627: the application/json Media Type for JavaScript Object Notation (JSON)
    • Crockford, D., RFC 4627: the application/json Media Type for JavaScript Object Notation (JSON) 2006.
    • (2006)
    • Crockford, D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.