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Volumn 14, Issue 23-24, 2014, Pages 2731-2741

ProteoAnnotator - Open source proteogenomics annotation software supporting PSI standards

Author keywords

MzIdentML; Open source; ProteoAnnotator; Proteogenomics; Proteomics Standards Initiative

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CEREBROSPINAL FLUID; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; MARKUP LANGUAGE; NONHUMAN; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN STRUCTURE; PROTEOMICS; PROTEOMICS STANDARD INITIATIVE; TOXOPLASMA GONDII; GENOMICS; METABOLISM; PROCEDURES;

EID: 84913534612     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400265     Document Type: Article
Times cited : (37)

References (27)
  • 1
    • 84859898660 scopus 로고    scopus 로고
    • A beginner's guide to eukaryotic genome annotation
    • Yandell, M., Ence, D., A beginner's guide to eukaryotic genome annotation. Nat. Rev. Genet. 2012, 13, 329-342.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 329-342
    • Yandell, M.1    Ence, D.2
  • 2
    • 56549101959 scopus 로고    scopus 로고
    • Alternative isoform regulation in human tissue transcriptomes
    • Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I. et al., Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456, 470-476.
    • (2008) Nature , vol.456 , pp. 470-476
    • Wang, E.T.1    Sandberg, R.2    Luo, S.3    Khrebtukova, I.4
  • 3
    • 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
  • 5
    • 11144320641 scopus 로고    scopus 로고
    • Open source system for analyzing, validating, and storing protein identification data
    • Craig, R., Cortens, J. P., Beavis, R. C., 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
  • 6
    • 50149117169 scopus 로고    scopus 로고
    • Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases
    • Kim, S., Gupta, N., Pevzner, P. A., Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J. Proteome Res. 2008, 7, 3354-3363.
    • (2008) J. Proteome Res. , vol.7 , pp. 3354-3363
    • Kim, S.1    Gupta, N.2    Pevzner, P.A.3
  • 7
    • 33750127867 scopus 로고    scopus 로고
    • GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra
    • Shadforth, I., Xu, W., Crowther, D., Bessant, C., GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra. J. Proteome Res. 2006, 5, 2849-2852.
    • (2006) J. Proteome Res. , vol.5 , pp. 2849-2852
    • Shadforth, I.1    Xu, W.2    Crowther, D.3    Bessant, C.4
  • 9
    • 84891792626 scopus 로고    scopus 로고
    • Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing
    • Pang, C. N. I., Tay, A. P., Aya, C., Twine, N. A. et al., Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing. J. Proteome Res. 2013, 13, 84-98.
    • (2013) J. Proteome Res. , vol.13 , pp. 84-98
    • Pang, C.N.I.1    Tay, A.P.2    Aya, C.3    Twine, N.A.4
  • 10
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks, J., Nekrutenko, A., Taylor, J., The Galaxy, T., Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010, 11, R86.
    • (2010) Genome Biol. , vol.11 , pp. R86
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3    The Galaxy, T.4
  • 11
    • 84870751362 scopus 로고    scopus 로고
    • iPiG: integrating peptide spectrum matches into genome browser visualizations
    • Kuhring, M., Renard, B. Y., iPiG: integrating peptide spectrum matches into genome browser visualizations. PLoS One 2012, 7, e50246.
    • (2012) PLoS One , vol.7 , pp. e50246
    • Kuhring, M.1    Renard, B.Y.2
  • 12
    • 77953155288 scopus 로고    scopus 로고
    • Template proteogenomics: sequencing whole proteins using an imperfect database
    • Castellana, N. E., Pham, V., Arnott, D., Lill, J. R., Bafna, V., Template proteogenomics: sequencing whole proteins using an imperfect database. Mol. Cell. Proteomics 2010, 9, 1260-1270.
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 1260-1270
    • Castellana, N.E.1    Pham, V.2    Arnott, D.3    Lill, J.R.4    Bafna, V.5
  • 13
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: identification of posttranslationally modified peptides from tandem mass spectra
    • Tanner, S., Shu, H., Frank, A., Wang, L.-C. et al., InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem. 2005, 77, 4626-4639.
    • (2005) Anal. Chem. , vol.77 , pp. 4626-4639
    • Tanner, S.1    Shu, H.2    Frank, A.3    Wang, L.-C.4
  • 14
    • 84891760451 scopus 로고    scopus 로고
    • An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays
    • Castellana, N. E., Shen, Z., He, Y., Walley, J. W. et al., An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. Mol. Cell. Proteomics 2014, 13, 157-167.
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 157-167
    • Castellana, N.E.1    Shen, Z.2    He, Y.3    Walley, J.W.4
  • 15
    • 84859868686 scopus 로고    scopus 로고
    • The mzIdentML data standard for mass spectrometry-based proteomics results
    • Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O. et al., The mzIdentML data standard for mass spectrometry-based proteomics results. Mol. Cell. Proteomics 2012, 11, 1-10.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1-10
    • Jones, A.R.1    Eisenacher, M.2    Mayer, G.3    Kohlbacher, O.4
  • 16
    • 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., Martínez-Bartolomé, S. 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    Martínez-Bartolomé, S.4
  • 17
    • 84891796097 scopus 로고    scopus 로고
    • ProteomeXchange provides globally coordinated proteomics data submission and dissemination
    • Vizcaino, J. A., Deutsch, E. W., Wang, R., Csordas, A. et al., ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat. Biotech. 2014, 32, 223-226.
    • (2014) Nat. Biotech. , vol.32 , pp. 223-226
    • Vizcaino, J.A.1    Deutsch, E.W.2    Wang, R.3    Csordas, A.4
  • 18
    • 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. et al., The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2013, 41, D1063-D1069.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D1063-D1069
    • Vizcaino, J.A.1    Cote, R.G.2    Csordas, A.3    Dianes, J.A.4
  • 19
    • 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., 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    Martens, L.5
  • 20
    • 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
  • 21
    • 84873695876 scopus 로고    scopus 로고
    • Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics
    • Granholm, V., Navarro, J. F., Noble, W. S., Kall, L., Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics. J. Proteomics 2012, 80c, 123-131.
    • (2012) J. Proteomics , vol.80 C , pp. 123-131
    • Granholm, V.1    Navarro, J.F.2    Noble, W.S.3    Kall, L.4
  • 22
    • 84879329259 scopus 로고    scopus 로고
    • The HUPO Proteomics Standards Initiative - mass spectrometry controlled vocabulary
    • bat009.
    • Mayer, G., Montecchi-Palazzi, L., Ovelleiro, D., Jones, A. R. et al., The HUPO Proteomics Standards Initiative - mass spectrometry controlled vocabulary. Database 2013, 2013, bat009.
    • (2013) Database , vol.2013
    • Mayer, G.1    Montecchi-Palazzi, L.2    Ovelleiro, D.3    Jones, A.R.4
  • 24
    • 2942527473 scopus 로고    scopus 로고
    • Gene prediction with a hidden Markov model and a new intron submodel
    • Stanke, M., Waack, S., Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 2003, 19, ii215-ii225.
    • (2003) Bioinformatics , vol.19 , pp. ii215-ii225
    • Stanke, M.1    Waack, S.2
  • 26
    • 84910044581 scopus 로고    scopus 로고
    • In-depth characterization of the cerebrospinal fluid proteome displayed through the CSF Proteome Resource (CSF-PR)
    • M114.038554.
    • Guldbrandsen, A., Vethe, H., Farag, Y., Oveland, E. et al., In-depth characterization of the cerebrospinal fluid proteome displayed through the CSF Proteome Resource (CSF-PR). Mol. Cell. Proteomics 2014, M114.038554.
    • (2014) Mol. Cell. Proteomics
    • Guldbrandsen, A.1    Vethe, H.2    Farag, Y.3    Oveland, E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.