메뉴 건너뛰기




Volumn 15, Issue 11, 2016, Pages 4091-4100

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics

Author keywords

human; search databases; shotgun mass spectrometry

Indexed keywords

AMINO ACID; PEPTIDE; PROTEIN; TRYPSIN; ISOPROTEIN;

EID: 84994618574     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.6b00445     Document Type: Article
Times cited : (22)

References (30)
  • 1
    • 41349096900 scopus 로고    scopus 로고
    • Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics
    • Deutsch, E. W.; Lam, H.; Aebersold, R. Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics Physiol. Genomics 2008, 33 (1) 18-25 10.1152/physiolgenomics.00298.2007
    • (2008) Physiol. Genomics , vol.33 , Issue.1 , pp. 18-25
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 2
    • 80555146717 scopus 로고    scopus 로고
    • A face in the crowd: Recognizing peptides through database search
    • Eng, J. K.; Searle, B. C.; Clauser, K. R.; Tabb, D. L. A face in the crowd: recognizing peptides through database search Mol. Cell. Proteomics 2011, 10 (11) R111.009522 10.1074/mcp.R111.009522
    • (2011) Mol. Cell. Proteomics , vol.10 , Issue.11 , pp. R111009522
    • Eng, J.K.1    Searle, B.C.2    Clauser, K.R.3    Tabb, D.L.4
  • 7
    • 3042818018 scopus 로고    scopus 로고
    • The International Protein Index: An integrated database for proteomics experiments
    • Kersey, P. J.; Duarte, J.; Williams, A.; Karavidopoulou, Y.; Birney, E.; Apweiler, R. The International Protein Index: an integrated database for proteomics experiments Proteomics 2004, 4 (7) 1985-8 10.1002/pmic.200300721
    • (2004) Proteomics , vol.4 , Issue.7 , pp. 1985-1988
    • Kersey, P.J.1    Duarte, J.2    Williams, A.3    Karavidopoulou, Y.4    Birney, E.5    Apweiler, R.6
  • 8
    • 84879395677 scopus 로고    scopus 로고
    • MScDB: A mass spectrometry-centric protein sequence database for proteomics
    • Marx, H.; Lemeer, S.; Klaeger, S.; Rattei, T.; Kuster, B. MScDB: a mass spectrometry-centric protein sequence database for proteomics J. Proteome Res. 2013, 12 (6) 2386-98 10.1021/pr400215r
    • (2013) J. Proteome Res. , vol.12 , Issue.6 , pp. 2386-2398
    • Marx, H.1    Lemeer, S.2    Klaeger, S.3    Rattei, T.4    Kuster, B.5
  • 11
    • 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.; Deutsch, E. W. Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification J. Proteome Res. 2015, 14 (9) 3452-60 10.1021/acs.jproteome.5b00499
    • (2015) J. Proteome Res. , vol.14 , Issue.9 , 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
  • 12
    • 84994589094 scopus 로고    scopus 로고
    • Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications
    • Omenn, G. S.; Lane, L.; Lundberg, E. K.; Beavis, R. C.; Overall, C. M.; Deutsch, E. W. Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications J. Proteome Res. 2016, 10.1021/acs.jproteome.6b00511
    • (2016) J. Proteome Res.
    • Omenn, G.S.1    Lane, L.2    Lundberg, E.K.3    Beavis, R.C.4    Overall, C.M.5    Deutsch, E.W.6
  • 14
    • 80055109819 scopus 로고    scopus 로고
    • Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB ″complete proteome″ sets
    • Griss, J.; Martin, M.; O'Donovan, C.; Apweiler, R.; Hermjakob, H.; Vizcaino, J. A. Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB ″complete proteome″ sets Proteomics 2011, 11 (22) 4434-8 10.1002/pmic.201100363
    • (2011) Proteomics , vol.11 , Issue.22 , pp. 4434-4438
    • Griss, J.1    Martin, M.2    O'Donovan, C.3    Apweiler, R.4    Hermjakob, H.5    Vizcaino, J.A.6
  • 16
    • 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 (6) 1234-42 10.1021/pr049882h
    • (2004) J. Proteome Res. , vol.3 , Issue.6 , pp. 1234-1242
    • Craig, R.1    Cortens, J.P.2    Beavis, R.C.3
  • 17
    • 84897474589 scopus 로고    scopus 로고
    • Detection of viral proteins in human cells lines by xeno-proteomics: Elimination of the last valid excuse for not testing every cellular proteome dataset for viral proteins
    • Chernobrovkin, A. L.; Zubarev, R. A. Detection of viral proteins in human cells lines by xeno-proteomics: elimination of the last valid excuse for not testing every cellular proteome dataset for viral proteins PLoS One 2014, 9 (3) e91433 10.1371/journal.pone.0091433
    • (2014) PLoS One , vol.9 , Issue.3 , pp. e91433
    • Chernobrovkin, A.L.1    Zubarev, R.A.2
  • 22
    • 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 (1) 22-4 10.1002/pmic.201200439
    • (2013) Proteomics , vol.13 , Issue.1 , pp. 22-24
    • Eng, J.K.1    Jahan, T.A.2    Hoopmann, M.R.3
  • 23
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • Craig, R.; Beavis, R. C. TANDEM: matching proteins with tandem mass spectra Bioinformatics 2004, 20 (9) 1466-7 10.1093/bioinformatics/bth092
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 24
    • 33750979860 scopus 로고    scopus 로고
    • General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
    • MacLean, B.; Eng, J. K.; Beavis, R. C.; McIntosh, M. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine Bioinformatics 2006, 22 (22) 2830-2 10.1093/bioinformatics/btl379
    • (2006) Bioinformatics , vol.22 , Issue.22 , pp. 2830-2832
    • Maclean, B.1    Eng, J.K.2    Beavis, R.C.3    McIntosh, M.4
  • 25
  • 26
    • 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, 2005.0017 10.1038/msb4100024
    • (2005) Mol. Syst. Biol. , vol.1 , pp. 20050017
    • Keller, A.1    Eng, J.2    Zhang, N.3    Li, X.J.4    Aebersold, R.5
  • 28
    • 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, 5383-5392 10.1021/ac025747h
    • (2002) Anal. Chem. , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 29
    • 80053387432 scopus 로고    scopus 로고
    • IProphet: Multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
    • Shteynberg, D.; Deutsch, E. W.; Lam, H.; Eng, J. K.; Sun, Z.; Tasman, N.; Mendoza, L.; Moritz, R. L.; Aebersold, R.; Nesvizhskii, A. I. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates Mol. Cell. Proteomics 2011, 10 (12) M111.007690 10.1074/mcp.M111.007690
    • (2011) Mol. Cell. Proteomics , vol.10 , Issue.12 , pp. M111007690
    • Shteynberg, D.1    Deutsch, E.W.2    Lam, H.3    Eng, J.K.4    Sun, Z.5    Tasman, N.6    Mendoza, L.7    Moritz, R.L.8    Aebersold, R.9    Nesvizhskii, A.I.10
  • 30
    • 84908540871 scopus 로고    scopus 로고
    • Proteogenomics: Concepts, applications and computational strategies
    • Nesvizhskii, A. I. Proteogenomics: concepts, applications and computational strategies Nat. Methods 2014, 11 (11) 1114-25 10.1038/nmeth.3144
    • (2014) Nat. Methods , vol.11 , Issue.11 , pp. 1114-1125
    • Nesvizhskii, A.I.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.