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Volumn 36, Issue 6, 2009, Pages 668-675

The progress of protein quality Control methods in shotgun proteomics

Author keywords

MS MS; Protein assembly; Protein identification; Protein probability; Shotgun proteomics

Indexed keywords


EID: 70349194545     PISSN: 10003282     EISSN: None     Source Type: Journal    
DOI: 10.3724/SP.J.1206.2008.00404     Document Type: Review
Times cited : (8)

References (41)
  • 1
    • 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
  • 2
    • 29244457242 scopus 로고    scopus 로고
    • Human liver proteome project: Plan, progress, and perspectives
    • He F. Human liver proteome project: plan, progress, and perspectives. Mol Cell Proteomics, 2005, 4 (12): 1841 -1848
    • (2005) Mol Cell Proteomics , vol.4 , Issue.12 , pp. 1841-1848
    • He, F.1
  • 3
    • 4444335470 scopus 로고    scopus 로고
    • The ABC's (and XYZ's) of peptide sequencing
    • Steen H, Mann M. The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol, 2004, 5 (9): 699-711
    • (2004) Nat Rev Mol Cell Biol , vol.5 , Issue.9 , pp. 699-711
    • Steen, H.1    Mann, M.2
  • 5
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii A I, Vitek O, Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods, 2007, 4 (10): 787-797
    • (2007) Nat Methods , vol.4 , Issue.10 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 6
    • 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, et al. 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
  • 7
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a proteins database
    • Eng J K, McCormack A L, Yates III J R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a proteins database. J Am Soc Mass Spectrom, 1994, 5 (11): 976-989
    • (1994) J Am Soc Mass Spectrom , vol.5 , Issue.11 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates III, J.R.3
  • 8
    • 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): 1466-1467
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 9
    • 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, et al. 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
  • 10
    • 0043064042 scopus 로고    scopus 로고
    • A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases
    • Sadygov R G, Yates III J R. A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal Chem, 2003, 75 (15): 3792-3798
    • (2003) Anal Chem , vol.75 , Issue.15 , pp. 3792-3798
    • Sadygov, R.G.1    Yates III, J.R.2
  • 11
    • 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, et al. 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
  • 12
    • 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
  • 13
    • 52649158232 scopus 로고    scopus 로고
    • Generalized method for probability-based peptide and protein identification from tandem mass spectrometry data and sequence database searching
    • Ramos-Fernandez A, Paradela A, Navajas R, et al. Generalized method for probability-based peptide and protein identification from tandem mass spectrometry data and sequence database searching. Mol Cell Proteomics, 2008, 7 (9): 1748-1754
    • (2008) Mol Cell Proteomics , vol.7 , Issue.9 , pp. 1748-1754
    • Ramos-Fernandez, A.1    Paradela, A.2    Navajas, R.3
  • 14
    • 27644555055 scopus 로고    scopus 로고
    • Interpretation of shotgun proteomic data: The protein inference problem
    • Nesvizhskii A I, Aebersold R. Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Prot, 2005, 4 (10): 1419-1440
    • (2005) Mol Cell Prot , vol.4 , Issue.10 , pp. 1419-1440
    • Nesvizhskii, A.I.1    Aebersold, R.2
  • 15
    • 7044241344 scopus 로고    scopus 로고
    • DBParser: Web-based software for shotgun proteomic data analyses
    • Yang X, Dondeti V, Dezube R, et al. DBParser: web-based software for shotgun proteomic data analyses. J Proteome Res, 2004, 3 (5): 1002-1008
    • (2004) J Proteome Res , vol.3 , Issue.5 , pp. 1002-1008
    • Yang, X.1    Dondeti, V.2    Dezube, R.3
  • 16
    • 48249106811 scopus 로고    scopus 로고
    • P18-T Mass Sieve: A new tool for mass spectrometry-based proteomics
    • Slotta D J, McFarland M, Makusky A, et al. P18-T Mass Sieve: a new tool for mass spectrometry-based proteomics. J Biom Tech, 2007, 18 (1): 7
    • (2007) J Biom Tech , vol.18 , Issue.1 , pp. 7
    • Slotta, D.J.1    McFarland, M.2    Makusky, A.3
  • 17
    • 20144365752 scopus 로고    scopus 로고
    • Experimental peptide identification repository (EPIR): An integrated peptide-centric platform for validation and mining of tandem mass spectrometry data
    • Kristensen D B, Brond J C, Nielsen P A, et al. Experimental peptide identification repository (EPIR): an integrated peptide-centric platform for validation and mining of tandem mass spectrometry data. Mol Cell Proteomics, 2004, 3 (10): 1023-1038
    • (2004) Mol Cell Proteomics , vol.3 , Issue.10 , pp. 1023-1038
    • Kristensen, D.B.1    Brond, J.C.2    Nielsen, P.A.3
  • 18
    • 3042737683 scopus 로고    scopus 로고
    • Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics
    • Resing K A, Meyer-Arendt K, Mendoza A M, et al. Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal Chem, 2004, 76 (13): 3556-3568
    • (2004) Anal Chem , vol.76 , Issue.13 , pp. 3556-3568
    • Resing, K.A.1    Meyer-Arendt, K.2    Mendoza, A.M.3
  • 19
    • 0036393898 scopus 로고    scopus 로고
    • DTASelect and Contrast: Tools for assembling and comparing protein identifications from shotgun proteomics
    • Tabb D L, McDonald W H, Yates III J R. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res, 2002, 1 (1): 21-26
    • (2002) J Proteome Res , vol.1 , Issue.1 , pp. 21-26
    • Tabb, D.L.1    McDonald, W.H.2    Yates III, J.R.3
  • 20
    • 33749240944 scopus 로고    scopus 로고
    • Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO brain proteome project pilot phase
    • Stephan C, Reidegeld K A, Hamacher M, et al. Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO brain proteome project pilot phase. Proteomics, 2006, 6 (18): 5015-5029
    • (2006) Proteomics , vol.6 , Issue.18 , pp. 5015-5029
    • Stephan, C.1    Reidegeld, K.A.2    Hamacher, M.3
  • 21
    • 33749248174 scopus 로고    scopus 로고
    • HUPO brain proteome project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy
    • Hamacher M, Apweiler R, Arnold G, et al. HUPO brain proteome project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy. Proteomics, 2006, 6 (18): 4890-4898
    • (2006) Proteomics , vol.6 , Issue.18 , pp. 4890-4898
    • Hamacher, M.1    Apweiler, R.2    Arnold, G.3
  • 22
    • 34948874252 scopus 로고    scopus 로고
    • Proteomic parsimony through bipartite graph analysis improves accuracy and transparency
    • Zhang B, Chambers M, Tabb D. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. J Proteome Res, 2007, 6 (9): 3549-3557
    • (2007) J Proteome Res , vol.6 , Issue.9 , pp. 3549-3557
    • Zhang, B.1    Chambers, M.2    Tabb, D.3
  • 23
    • 0036209134 scopus 로고    scopus 로고
    • Qscore: An algorithm for evaluating SEQUEST database search results
    • 2002
    • 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
    • J Am Soc Mass Spectrom , vol.13 , Issue.4 , pp. 378-386
    • Moore, R.E.1    Young, M.K.2    Lee, T.D.3
  • 24
    • 0141585549 scopus 로고    scopus 로고
    • PRISM, a generic large scale proteomic investigation strategy for mammals
    • Kislinger T, Rahman K, Radulovic D, et al. PRISM, a generic large scale proteomic investigation strategy for mammals. Mol Cell Proteomics, 2003, 2 (2): 96-106
    • (2003) Mol Cell Proteomics , vol.2 , Issue.2 , pp. 96-106
    • Kislinger, T.1    Rahman, K.2    Radulovic, D.3
  • 25
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii A I, Keller A, Kolker E, et al. 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
  • 26
    • 1542617945 scopus 로고    scopus 로고
    • Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases
    • Sadygov R G, Liu H, Yates J R. Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases. Anal Chem, 2004, 76 (6): 1664-1671
    • (2004) Anal Chem , vol.76 , Issue.6 , pp. 1664-1671
    • Sadygov, R.G.1    Liu, H.2    Yates, J.R.3
  • 27
    • 34249047337 scopus 로고    scopus 로고
    • Probability model for assessing proteins assembled from peptide sequences inferred from tandem mass spectrometry data
    • Feng J, Naiman D Q, Cooper B. Probability model for assessing proteins assembled from peptide sequences inferred from tandem mass spectrometry data. Anal Chem, 2007, 79 (10): 3901-3911
    • (2007) Anal Chem , vol.79 , Issue.10 , pp. 3901-3911
    • Feng, J.1    Naiman, D.Q.2    Cooper, B.3
  • 28
    • 34147115205 scopus 로고    scopus 로고
    • EBP, a program for protein identification using multiple tandem mass spectrometry datasets
    • Price T S, Lucitt M B, Wu W, et al. EBP, a program for protein identification using multiple tandem mass spectrometry datasets. Mol Cell Proteomics, 2007, 6 (3): 527-536
    • (2007) Mol Cell Proteomics , vol.6 , Issue.3 , pp. 527-536
    • Price, T.S.1    Lucitt, M.B.2    Wu, W.3
  • 29
    • 47349095790 scopus 로고    scopus 로고
    • A mouse plasma peptide atlas as a resource for disease proteomics
    • Zhang Q, Menon R, Deutsch E, et al. A mouse plasma peptide atlas as a resource for disease proteomics. Genome Biology, 2008, 9 (6): R93
    • (2008) Genome Biology , vol.9 , Issue.6
    • Zhang, Q.1    Menon, R.2    Deutsch, E.3
  • 31
    • 36048937342 scopus 로고    scopus 로고
    • Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences
    • Padliya N D, Garrett W M, Campbell K B, et al. Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences. Proteomics, 2007, 7 (21): 3932-3942
    • (2007) Proteomics , vol.7 , Issue.21 , pp. 3932-3942
    • Padliya, N.D.1    Garrett, W.M.2    Campbell, K.B.3
  • 32
    • 33747885134 scopus 로고    scopus 로고
    • A computational approach toward label-free protein quantification using predicted peptide detectability
    • Tang H, Arnold R J, Alves P, et al. A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics, 2006, 22 (14): e481-e488
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Tang, H.1    Arnold, R.J.2    Alves, P.3
  • 33
    • 37549023558 scopus 로고    scopus 로고
    • Advancement in protein inference from shotgun proteomics using peptide detectability
    • Alves P, Arnold R J, Novotny M V, et al. Advancement in protein inference from shotgun proteomics using peptide detectability. Pac Symp Biocomput, 2007.409-420
    • (2007) Pac Symp Biocomput , pp. 409-420
    • Alves, P.1    Arnold, R.J.2    Novotny, M.V.3
  • 35
    • 9144236198 scopus 로고    scopus 로고
    • Human protein reference database as a discovery resource for proteomics
    • Peri S, Navarro J D, Kristiansen T Z, et al. Human protein reference database as a discovery resource for proteomics. Nucl Acids Res, 2004, 32 (suppl 1): D497-D501
    • (2004) Nucl Acids Res , vol.32 , Issue.SUPPL 1
    • Peri, S.1    Navarro, J.D.2    Kristiansen, T.Z.3
  • 36
    • 43849087678 scopus 로고    scopus 로고
    • Analysis of the zebrafish proteome during embryonic development
    • Lucitt M B, Price T S, Pizarro A, et al. Analysis of the zebrafish proteome during embryonic development. Mol Cell Proteomics, 2008, 7 (5): 981-994
    • (2008) Mol Cell Proteomics , vol.7 , Issue.5 , pp. 981-994
    • Lucitt, M.B.1    Price, T.S.2    Pizarro, A.3
  • 37
    • 33644864034 scopus 로고    scopus 로고
    • Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study
    • States D J, Omenn G S, Blackwell T W, et al. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol, 2006, 24 (3): 333-338
    • (2006) Nat Biotechnol , vol.24 , Issue.3 , pp. 333-338
    • States, D.J.1    Omenn, G.S.2    Blackwell, T.W.3
  • 38
    • 23944493647 scopus 로고    scopus 로고
    • Data management and preliminary data analysis in the pilot phase of the HUPO plasma proteome project
    • Adamski M, Blackwell T, Menon R, et al. Data management and preliminary data analysis in the pilot phase of the HUPO plasma proteome project. Proteomics, 2005, 5(13): 3246-3261
    • (2005) Proteomics , vol.5 , Issue.13 , pp. 3246-3261
    • Adamski, M.1    Blackwell, T.2    Menon, R.3
  • 39
    • 34249342349 scopus 로고    scopus 로고
    • Verification of single-peptide protein identifications by the application of complementary database search algorithms
    • Rohrbough J G, Breci L, Merchant N, et al. Verification of single-peptide protein identifications by the application of complementary database search algorithms. J Biomol Tech, 2006, 17 (5): 327-332
    • (2006) J Biomol Tech , vol.17 , Issue.5 , pp. 327-332
    • Rohrbough, J.G.1    Breci, L.2    Merchant, N.3
  • 40
    • 21044459357 scopus 로고    scopus 로고
    • A Heuristic method for assigning a false-discovery rate for protein identifications from Mascot database search results
    • Weatherly D B, Astwood III J A, Minning T A, et al. A Heuristic method for assigning a false-discovery rate for protein identifications from Mascot database search results. Mol Cell Proteomics, 2005, 4 (6): 762-772
    • (2005) Mol Cell Proteomics , vol.4 , Issue.6 , pp. 762-772
    • Weatherly, D.B.1    Astwood III, J.A.2    Minning, T.A.3
  • 41
    • 33845577817 scopus 로고    scopus 로고
    • Protein probabilities in shotgun proteomics: Evaluating different estimation methods using a semi-random sampling model
    • Xue X, Wu S, Wang Z, et al. Protein probabilities in shotgun proteomics: evaluating different estimation methods using a semi-random sampling model. Proteomics, 2006, 6 (23): 6134 -6145
    • (2006) Proteomics , vol.6 , Issue.23 , pp. 6134-6145
    • Xue, X.1    Wu, S.2    Wang, Z.3


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