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Volumn 8, Issue , 2007, Pages

msmsEval: Tandem mass spectral quality assignment for high-throughput proteomics

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; COMPUTING RESOURCE; DATABASE SEARCHES; DATABASE SEARCHING; DISCRIMINANT FUNCTIONS; GAUSSIAN MIXTURE MODEL; PROTEIN IDENTIFICATION; TANDEM MASS SPECTRA;

EID: 33847654762     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-51     Document Type: Article
Times cited : (35)

References (29)
  • 1
    • 0037435030 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics
    • 10.1038/nature01511 12634793
    • Aebersold R Mann M Mass spectrometry-based proteomics Nature 2003 198-207 10.1038/nature01511 12634793
    • (2003) Nature , pp. 198-207
    • Aebersold, R.1    Mann, M.2
  • 2
    • 0035582244 scopus 로고    scopus 로고
    • An automated multidimensional protein identification technology for shotgun proteomics
    • 10.1021/ac010617e 11774908
    • Wolters DA Washburn MP Yates JR 3rd An automated multidimensional protein identification technology for shotgun proteomics Anal Chem 2001 73 23 5683-5690 10.1021/ac010617e 11774908
    • (2001) Anal Chem , vol.73 , Issue.23 , pp. 5683-5690
    • Wolters, D.A.1    Washburn, M.P.2    Yates III, J.R.3
  • 3
    • 0038333588 scopus 로고    scopus 로고
    • Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
    • 10.1038/nbt810 12665801
    • Gevaert K Goethals M Martens L Van Damme J Staes A Thomas GR Vandekerckhove J Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides Nat Biotechnol 2003 21 5 566-569 10.1038/nbt810 12665801
    • (2003) Nat Biotechnol , vol.21 , Issue.5 , pp. 566-569
    • Gevaert, K.1    Goethals, M.2    Martens, L.3    Van Damme, J.4    Staes, A.5    Thomas, G.R.6    Vandekerckhove, J.7
  • 4
    • 0000857494 scopus 로고
    • An Approach to Correlate Tandem Mass Spectra Data of Peptides with Amino Acid Sequences in a Protein Database
    • 10.1016/1044-0305(94)80016-2
    • Eng JK McCormack AL Yates JR An Approach to Correlate Tandem Mass Spectra Data of Peptides with Amino Acid Sequences in a Protein Database J Am Soc Mass Spectrom 1994 5 11 976 10.1016/1044-0305(94)80016-2
    • (1994) J Am Soc Mass Spectrom , vol.5 , Issue.11 , pp. 976
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 5
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: Matching proteins with tandem mass spectra
    • 10.1093/bioinformatics/bth092 14976030
    • Craig R Beavis RC TANDEM: Matching proteins with tandem mass spectra Bioinformatics 2004 20 9 1466-1467 10.1093/bioinformatics/bth092 14976030
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 6
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • 10.1002/ (SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 10612281
    • Perkins DN Pappin DJ Creasy DM Cottrell JS Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 1999 20 18 3551-3567 10.1002/ (SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 10612281
    • (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
  • 7
    • 19544393405 scopus 로고    scopus 로고
    • Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined
    • 10.1093/bioinformatics/bti362 15746284
    • Falkner J Andrews P Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined Bioinformatics 2005 21 10 2177-2184 10.1093/ bioinformatics/bti362 15746284
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2177-2184
    • Falkner, J.1    Andrews, P.2
  • 8
    • 0030725323 scopus 로고    scopus 로고
    • Post-translational modification of proteins and the discovery of new medicine
    • 10.1016/S0958-1669(97)80126-7 9425663
    • Parekh RB Rohlff C Post-translational modification of proteins and the discovery of new medicine Curr Opin Biotechnol 1997 8 6 718-723 10.1016/ S0958-1669(97)80126-7 9425663
    • (1997) Curr Opin Biotechnol , vol.8 , Issue.6 , pp. 718-723
    • Parekh, R.B.1    Rohlff, C.2
  • 9
    • 24744455665 scopus 로고    scopus 로고
    • Automatic Quality Assessment of Peptide Tandem Mass Spectra
    • 10.1093/bioinformatics/bth947 15262780
    • Bern M Goldberg D McDonald WH Yates JR Automatic Quality Assessment of Peptide Tandem Mass Spectra Bioinformatics 2004 20 (Suppl. 1) i49-i54 10.1093/bioinformatics/bth947 15262780
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Bern, M.1    Goldberg, D.2    McDonald, W.H.3    Yates, J.R.4
  • 10
    • 33645653958 scopus 로고    scopus 로고
    • Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering
    • 10.1002/pmic.200500309 16518876
    • Flikka K Martens L Vandekerckhove J Gevaert K Eidhammer I Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering Proteomics 2006 6 2086-2094 10.1002/ pmic.200500309 16518876
    • (2006) Proteomics , vol.6 , pp. 2086-2094
    • Flikka, K.1    Martens, L.2    Vandekerckhove, J.3    Gevaert, K.4    Eidhammer, I.5
  • 11
    • 0034484286 scopus 로고    scopus 로고
    • Method for screening peptide fragment ion mass spectra prior to database searching
    • 10.1016/S1044-0305(00)00097-0 10790846
    • 5Moore RE Young MK Lee TD Method for screening peptide fragment ion mass spectra prior to database searching J Am Soc Mass Spectrom 2000 11 5 422-426 10.1016/S1044-0305(00)00097-0 10790846
    • (2000) J Am Soc Mass Spectrom , vol.11 , Issue.5 , pp. 422-426
    • Moore, R.E.1    Young, M.K.2    Lee, T.D.3
  • 14
    • 17444423714 scopus 로고    scopus 로고
    • Assessing data quality of peptide mass spectra obtained by quadrupole ion trap mass spectrometry
    • 10.1021/pr049844y 15822904
    • Xu M Geer LY Bryant SH Roth JS Kowalak JA Maynard DM Markey SP Assessing data quality of peptide mass spectra obtained by quadrupole ion trap mass spectrometry J Proteome Res 2005 4 2 300-305 10.1021/pr049844y 15822904
    • (2005) J Proteome Res , vol.4 , Issue.2 , pp. 300-305
    • Xu, M.1    Geer, L.Y.2    Bryant, S.H.3    Roth, J.S.4    Kowalak, J.A.5    Maynard, D.M.6    Markey, S.P.7
  • 15
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • 10.1021/ac025747h 12403597
    • Keller A Nesvizhskii AI 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 10.1021/ac025747h 12403597
    • (2002) Anal Chem , vol.74 , Issue.20 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 16
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • 10.1021/ac0341261 14632076
    • Nesvizhskii AI Keller A Kolker E Aebersold R A statistical model for identifying proteins by tandem mass spectrometry Anal Chem 2003 75 17 4646-4658 10.1021/ac0341261 14632076
    • (2003) Anal Chem , vol.75 , Issue.17 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 17
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra
    • 10.1021/ac050102d 16013882
    • Tanner S Shu HJ Frank A Wang LC Zandi E Mumby M Pevzner PA Bafna V InsPecT: Identification of posttranslationally modified peptides from tandem mass spectra Anal Chem 2005 77 14 4626-4639 10.1021/ac050102d 16013882
    • (2005) Anal Chem , vol.77 , Issue.14 , pp. 4626-4639
    • Tanner, S.1    Shu, H.J.2    Frank, A.3    Wang, L.C.4    Zandi, E.5    Mumby, M.6    Pevzner, P.A.7    Bafna, V.8
  • 18
    • 28644447919 scopus 로고    scopus 로고
    • Identification of post-translational modifications by blind search of mass spectra
    • 10.1038/nbt1168 16311586
    • Tsur D Tanner S Zandi E Bafna V Pevzner PA Identification of post-translational modifications by blind search of mass spectra Nat Biotechnol 2005 23 12 1562-1567 10.1038/nbt1168 16311586
    • (2005) Nat Biotechnol , vol.23 , Issue.12 , pp. 1562-1567
    • Tsur, D.1    Tanner, S.2    Zandi, E.3    Bafna, V.4    Pevzner, P.A.5
  • 19
    • 22544465253 scopus 로고    scopus 로고
    • SPIDER: Software for protein identification from sequence tags with de novo sequencing error
    • 10.1142/S0219720005001247 16108090
    • Han Y Ma B Zhang K SPIDER: Software for protein identification from sequence tags with de novo sequencing error. J Bioinform Comput Biol 2005 3 3 697-716 10.1142/S0219720005001247 16108090
    • (2005) J Bioinform Comput Biol , vol.3 , Issue.3 , pp. 697-716
    • Han, Y.1    Ma, B.2    Zhang, K.3
  • 22
    • 0026952628 scopus 로고
    • An investigation of fragmentation mechanisms of doubly protonated tryptic peptides
    • 10.1002/rcm.1290061105 1467549
    • Tang XJ Boyd RK An investigation of fragmentation mechanisms of doubly protonated tryptic peptides Rapid Commun Mass Spectrom 1992 6 11 651-657 10.1002/rcm.1290061105 1467549
    • (1992) Rapid Commun Mass Spectrom , vol.6 , Issue.11 , pp. 651-657
    • Tang, X.J.1    Boyd, R.K.2
  • 23
    • 0035870190 scopus 로고    scopus 로고
    • SALSA: A pattern recognition algorithm to detect electrophile-adducted peptides by automated evaluation of CID spectra in LC-MS-MS analyses
    • 10.1021/ac001172h 11338579
    • Hansen BT Jones JA Mason DE Liebler DC SALSA: A pattern recognition algorithm to detect electrophile-adducted peptides by automated evaluation of CID spectra in LC-MS-MS analyses Anal Chem 2001 73 8 1676-1683 10.1021/ac001172h 11338579
    • (2001) Anal Chem , vol.73 , Issue.8 , pp. 1676-1683
    • Hansen, B.T.1    Jones, J.A.2    Mason, D.E.3    Liebler, D.C.4
  • 24
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the em algorithm
    • Dempster AP Laird NM Rubin DB Maximum likelihood from incomplete data via the em algorithm J Royal Stat Soc 1977 39 1-38
    • (1977) J Royal Stat Soc , vol.39 , pp. 1-38
    • Dempster, A.P.1    Laird, N.M.2    Rubin, D.B.3
  • 26
    • 26844564069 scopus 로고    scopus 로고
    • Human Tissue Profiling with Multidimensional Protein Identification Technology
    • 10.1021/pr0500354 16212430
    • Cagney G Park S Chung C Tong B O'Dushlaine C Shields DC Emili A Human Tissue Profiling with Multidimensional Protein Identification Technology J Proteome Res 2005 4 5 1757-1767 10.1021/pr0500354 16212430
    • (2005) J Proteome Res , vol.4 , Issue.5 , pp. 1757-1767
    • Cagney, G.1    Park, S.2    Chung, C.3    Tong, B.4    O'Dushlaine, C.5    Shields, D.C.6    Emili, A.7
  • 27
    • 13844319908 scopus 로고    scopus 로고
    • PepNovo: De novo peptide sequencing via probabilistic network modeling
    • 10.1021/ac048788h 15858974
    • Frank A Pevzner P PepNovo: De novo peptide sequencing via probabilistic network modeling Anal Chem 2005 77 4 964-973 10.1021/ac048788h 15858974
    • (2005) Anal Chem , vol.77 , Issue.4 , pp. 964-973
    • Frank, A.1    Pevzner, P.2
  • 29
    • 84874660316 scopus 로고    scopus 로고
    • Institute of System Biology S
    • Institute of System Biology S Sashimi project http://sashimi.sourceforge.net


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