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Volumn 7, Issue 1, 2008, Pages 96-103

The standard protein mix database: A diverse data set to assist in the production of improved peptide and protein identification software tools

Author keywords

Database search software; Proteomics; Reference data set; Standard protein mix; Standard Protein Mix Database

Indexed keywords

PROTEIN;

EID: 38649094868     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr070244j     Document Type: Article
Times cited : (154)

References (26)
  • 2
    • 33645813378 scopus 로고    scopus 로고
    • Mass spectrometry and protein analysis
    • Domon, B.; Aebersold, R. Mass spectrometry and protein analysis. Science 2006, 312 (5771), 212-217.
    • (2006) Science , vol.312 , Issue.5771 , pp. 212-217
    • Domon, B.1    Aebersold, R.2
  • 3
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422 (6928), 198-207.
    • (2003) Nature , vol.422 , Issue.6928 , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 4
    • 0000857494 scopus 로고
    • An approach to correlate tamdem 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 tamdem 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
  • 5
    • 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.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20 (18), 3551-3567.
    • (1999) Electrophoresis , vol.20 , Issue.18 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 6
    • 13444304209 scopus 로고    scopus 로고
    • Computational analysis of shotgun proteomics data
    • MacCoss, M. J. Computational analysis of shotgun proteomics data. Curr. Opin. Chem. Biol. 2005, 9 (1), 88-94.
    • (2005) Curr. Opin. Chem. Biol , vol.9 , Issue.1 , pp. 88-94
    • MacCoss, M.J.1
  • 7
    • 14844336631 scopus 로고    scopus 로고
    • Tandem mass spectrometry database searching
    • Dunn, M, Jorde, L, Little, P, Subramaniam, S, Eds, John Wiley & Sons, Ltd: Hoboken, NJ
    • Eng, J. K.; Martin, D. B.; Aebersold, R. Tandem mass spectrometry database searching. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics; Dunn, M., Jorde, L., Little, P., Subramaniam, S., Eds.; John Wiley & Sons, Ltd: Hoboken, NJ, 2004.
    • (2004) Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
    • Eng, J.K.1    Martin, D.B.2    Aebersold, R.3
  • 8
    • 0034789979 scopus 로고    scopus 로고
    • Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry
    • Han, D. K.; Eng, J.; Zhou, H.; Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 2001, 19 (10), 946-951.
    • (2001) Nat. Biotechnol , vol.19 , Issue.10 , pp. 946-951
    • Han, D.K.1    Eng, J.2    Zhou, H.3    Aebersold, R.4
  • 10
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn, M. P.; Wolters, D.; Yates, J. R., III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19 (3), 242-247.
    • (2001) Nat. Biotechnol , vol.19 , Issue.3 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates III, J.R.3
  • 11
    • 38649132122 scopus 로고    scopus 로고
    • Quantitative profiling of peptide identifications made by MS/MS and database search
    • Keller, A.; Eng, J.; Zhou, H.; Aebersold, R. Quantitative profiling of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74 (20), 946-951.
    • (2002) Anal. Chem , vol.74 , Issue.20 , pp. 946-951
    • Keller, A.1    Eng, J.2    Zhou, H.3    Aebersold, R.4
  • 12
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74 (20), 5383-5392.
    • (2002) Anal. Chem , vol.74 , Issue.20 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 13
    • 33746930864 scopus 로고    scopus 로고
    • Keller, A.; Eng, J.; Zhang, N.; Li, X. J.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005, 1,2005.0017.
    • Keller, A.; Eng, J.; Zhang, N.; Li, X. J.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005, 1,2005.0017.
  • 14
    • 39049175370 scopus 로고    scopus 로고
    • Protein identification by tandem mass spectrometry and sequence database searching
    • Nesvizhskii, A. I. Protein identification by tandem mass spectrometry and sequence database searching. Methods Mol. Biol. 2006, 367, 87-120.
    • (2006) Methods Mol. Biol , vol.367 , pp. 87-120
    • Nesvizhskii, A.I.1
  • 16
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75 (17), 4646-4658.
    • (2003) Anal. Chem , vol.75 , Issue.17 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 17
    • 0036209134 scopus 로고    scopus 로고
    • Qscore: An algorithm for evaluating SEQUEST database search results
    • Moore, R. E.; Young, M. K.; Lee, T. D. Qscore: an algorithm for evaluating SEQUEST database search results. J. Am. Soc. Mass Spectrom. 2002, 13 (4), 378-386.
    • (2002) J. Am. Soc. Mass Spectrom , vol.13 , Issue.4 , pp. 378-386
    • Moore, R.E.1    Young, M.K.2    Lee, T.D.3
  • 18
    • 24044513966 scopus 로고    scopus 로고
    • Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations
    • Elias, J. E.; Haas, W.; Faherty, B. K.; Gygi, S. P. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2005, 2 (9), 667-675.
    • (2005) Nat. Methods , vol.2 , Issue.9 , pp. 667-675
    • Elias, J.E.1    Haas, W.2    Faherty, B.K.3    Gygi, S.P.4
  • 19
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias, J. E.; Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 2007, 4 (3), 207-214.
    • (2007) Nat. Methods , vol.4 , Issue.3 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 20
    • 26844475051 scopus 로고    scopus 로고
    • Ultra fast trypsin digestion of proteins by high intensity focused ultrasound
    • Lopez-Ferrer, D.; Capelo, J. L.; Vazquez, J. Ultra fast trypsin digestion of proteins by high intensity focused ultrasound. J. Proteome Res. 2005, 4 (5), 1569-1574.
    • (2005) J. Proteome Res , vol.4 , Issue.5 , pp. 1569-1574
    • Lopez-Ferrer, D.1    Capelo, J.L.2    Vazquez, J.3
  • 21
    • 0041834903 scopus 로고    scopus 로고
    • A microcapillary trap cartridge-microcapillary high-performance liquid chromatography electrospray ionization emitter device capable of peptide tandem mass spectrometry at the attomole level on an ion trap mass spectrometer with automated routine operation
    • Yi, E. C.; Lee, H.; Aebersold, R.; Goodlett, D. R. A microcapillary trap cartridge-microcapillary high-performance liquid chromatography electrospray ionization emitter device capable of peptide tandem mass spectrometry at the attomole level on an ion trap mass spectrometer with automated routine operation. Rapid Commun. Mass Spectrom. 2003, 17 (18), 2093-2098.
    • (2003) Rapid Commun. Mass Spectrom , vol.17 , Issue.18 , pp. 2093-2098
    • Yi, E.C.1    Lee, H.2    Aebersold, R.3    Goodlett, D.R.4
  • 23
    • 33746930864 scopus 로고    scopus 로고
    • A uniform proteomics MS/MS analysis platform utilizing open XML file formats
    • Keller, A.; Eng, J.; Zhang, N.; Li, X. J.; Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005, 1, 1-8.
    • (2005) Mol. Syst. Biol , vol.1 , pp. 1-8
    • Keller, A.1    Eng, J.2    Zhang, N.3    Li, X.J.4    Aebersold, R.5
  • 24
    • 1842681979 scopus 로고    scopus 로고
    • Standard mixtures for proteome studies
    • Purvine, S.; Picone, A. F.; Kolker, E. Standard mixtures for proteome studies. OMICS 2004, 8 (1), 79-92.
    • (2004) OMICS , vol.8 , Issue.1 , pp. 79-92
    • Purvine, S.1    Picone, A.F.2    Kolker, E.3
  • 25
    • 0036406762 scopus 로고    scopus 로고
    • Experimental protein mixture for validating tandem mass spectral analysis
    • Keller, A.; Purvine, S.; Nesvizhskii, A. I.; Stolyar, S.; Goodlett, D. R.; Kolker, E. Experimental protein mixture for validating tandem mass spectral analysis. OMICS 2002, 6 (2), 207-212.
    • (2002) OMICS , vol.6 , Issue.2 , pp. 207-212
    • Keller, A.1    Purvine, S.2    Nesvizhskii, A.I.3    Stolyar, S.4    Goodlett, D.R.5    Kolker, E.6
  • 26
    • 34848903890 scopus 로고    scopus 로고
    • The implications of proteolytic background for shotgun proteomics
    • in press
    • Picotti, P.; Aebersold, R.; Domon, B. The implications of proteolytic background for shotgun proteomics. Mol. Cell. Proteomics 2007,in press.
    • (2007) Mol. Cell. Proteomics
    • Picotti, P.1    Aebersold, R.2    Domon, B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.