MScDB: A mass spectrometry-centric protein sequence database for proteomics

Journal of Proteome Research

Volumn 12, Issue 6, 2013, Pages 2386-2398

  Marx, Harald ^a   Lemeer, Simone ^a   Klaeger, Susan ^a   Rattei, Thomas ^b   Kuster, Bernhard ^a,c  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF VIENNA   (Austria)

^c Munich Center for Integrated Protein Science   (Germany)

Author keywords

mass spectrometry; peptide centric clustering; protein identification; protein inference; protein sequence database; proteomics

Indexed keywords

PEPTIDE; PROTEOME;

ARTICLE; CONTROLLED STUDY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; SEQUENCE DATABASE;

EID: 84879395677     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400215r     Document Type: Article

References (53)

1. Steen, H.; Mann, M. The ABC's (and XYZ's) of peptide sequencing Nat. Rev. Mol. Cell Biol. 2004, 5 (9) 699-711
2. 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) 1985-1988
3. Magrane, M.; UniProt Consortium. UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011, 2011, bar009.
4. Sayers, E. W.; Barrett, T.; Benson, D. A.; Bolton, E.; Bryant, S. H.; Canese, K.; Chetvernin, V.; Church, D. M.; Dicuccio, M.; Federhen, S.; Feolo, M.; Fingerman, I. M.; Geer, L. Y.; Helmberg, W.; Kapustin, Y.; Krasnov, S.; Landsman, D.; Lipman, D. J.; Lu, Z.; Madden, T. L.; Madej, T.; Maglott, D. R.; Marchler-Bauer, A.; Miller, V.; Karsch-Mizrachi, I.; Ostell, J.; Panchenko, A.; Phan, L.; Pruitt, K. D.; Schuler, G. D.; Sequeira, E.; Sherry, S. T.; Shumway, M.; Sirotkin, K.; Slotta, D.; Souvorov, A.; Starchenko, G.; Tatusova, T. A.; Wagner, L.; Wang, Y.; Wilbur, W. J.; Yaschenko, E.; Ye, J. Database resources of the National Center for Biotechnology Information Nucleic Acids Res. 2012, 40 (Database issue) D13-D25
5. Pruitt, K. D.; Tatusova, T.; Maglott, D. R. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res. 2005, 33 (Database issue) D501-D504
6. Karsch-Mizrachi, I.; Nakamura, Y.; Cochrane, G.; International, N. S. D. C. The International Nucleotide Sequence Database Collaboration Nucleic Acids Res. 2012, 40 (Database issue) D33-D37
7. Leinonen, R.; Akhtar, R.; Birney, E.; Bower, L.; Cerdeno-Tárraga, A.; Cheng, Y.; Cleland, I.; Faruque, N.; Goodgame, N.; Gibson, R.; Hoad, G.; Jang, M.; Pakseresht, N.; Plaister, S.; Radhakrishnan, R.; Reddy, K.; Sobhany, S.; Ten Hoopen, P.; Vaughan, R.; Zalunin, V.; Cochrane, G. The European Nucleotide Archive Nucleic Acids Res. 2011, 39 (Database issue) D28-D31
8. Tateno, Y.; Imanishi, T.; Miyazaki, S.; Fukami-Kobayashi, K.; Saitou, N.; Sugawara, H.; Gojobori, T. DNA Data Bank of Japan (DDBJ) for genome scale research in life science Nucleic Acids Res. 2002, 30 (1) 27-30
9. Benson, D. A.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Wheeler, D. L. GenBank: update Nucleic Acids Res. 2004, 32 (Database issue) D23-D26
10. Flicek, P.; Amode, M. R.; Barrell, D.; Beal, K.; Brent, S.; Chen, Y.; Clapham, P.; Coates, G.; Fairley, S.; Fitzgerald, S.; Gordon, L.; Hendrix, M.; Hourlier, T.; Johnson, N.; Kähäri, A.; Keefe, D.; Keenan, S.; Kinsella, R.; Kokocinski, F.; Kulesha, E.; Larsson, P.; Longden, I.; McLaren, W.; Overduin, B.; Pritchard, B.; Riat, H. S.; Rios, D.; Ritchie, G. R. S.; Ruffier, M.; Schuster, M.; Sobral, D.; Spudich, G.; Tang, Y. A.; Trevanion, S.; Vandrovcova, J.; Vilella, A. J.; White, S.; Wilder, S. P.; Zadissa, A.; Zamora, J.; Aken, B. L.; Birney, E.; Cunningham, F.; Dunham, I.; Durbin, R.; Fernández-Suarez, X. M.; Herrero, J.; Hubbard, T. J. P.; Parker, A.; Proctor, G.; Vogel, J.; Searle, S. M. J. Ensembl 2011 Nucleic Acids Res. 2011, 39 (Database issue) D800-D806
11. Yamasaki, C.; Murakami, K.; Takeda, J.-i.; Sato, Y.; Noda, A.; Sakate, R.; Habara, T.; Nakaoka, H.; Todokoro, F.; Matsuya, A.; Imanishi, T.; Gojobori, T. H-InvDB in 2009: extended database and data mining resources for human genes and transcripts Nucleic Acids Res. 2010, 38 (Database issue) D626-D632
12. Wilming, L. G.; Gilbert, J. G. R.; Howe, K.; Trevanion, S.; Hubbard, T.; Harrow, J. L. The vertebrate genome annotation (Vega) database Nucleic Acids Res. 2008, 36 (Database issue) D753-D760
13. Lamesch, P.; Berardini, T. Z.; Li, D.; Swarbreck, D.; Wilks, C.; Sasidharan, R.; Muller, R.; Dreher, K.; Alexander, D. L.; Garcia-Hernandez, M.; Karthikeyan, A. S.; Lee, C. H.; Nelson, W. D.; Ploetz, L.; Singh, S.; Wensel, A.; Huala, E. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools Nucleic Acids Res. 2012, 40 (Database issue) D1202-D1210
14. Pruitt, K. D.; Harrow, J.; Harte, R. A.; Wallin, C.; Diekhans, M.; Maglott, D. R.; Searle, S.; Farrell, C. M.; Loveland, J. E.; Ruef, B. J.; Hart, E.; Suner, M.-M.; Landrum, M. J.; Aken, B.; Ayling, S.; Baertsch, R.; Fernandez-Banet, J.; Cherry, J. L.; Curwen, V.; Dicuccio, M.; Kellis, M.; Lee, J.; Lin, M. F.; Schuster, M.; Shkeda, A.; Amid, C.; Brown, G.; Dukhanina, O.; Frankish, A.; Hart, J.; Maidak, B. L.; Mudge, J.; Murphy, M. R.; Murphy, T.; Rajan, J.; Rajput, B.; Riddick, L. D.; Snow, C.; Steward, C.; Webb, D.; Weber, J. A.; Wilming, L.; Wu, W.; Birney, E.; Haussler, D.; Hubbard, T.; Ostell, J.; Durbin, R.; Lipman, D. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes Genome Res. 2009, 19 (7) 1316-1323
15. Suzek, B. E.; Huang, H.; McGarvey, P.; Mazumder, R.; Wu, C. H. UniRef: comprehensive and non-redundant UniProt reference clusters Bioinformatics 2007, 23 (10) 1282-1288
16. Li, W.; Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics 2006, 22 (13) 1658-1659
17. Enright, A. J.; Ouzounis, C. A. GeneRAGE: a robust algorithm for sequence clustering and domain detection Bioinformatics 2000, 16 (5) 451-457
18. Mika, S.; Rost, B. UniqueProt: Creating representative protein sequence sets Nucleic Acids Res. 2003, 31 (13) 3789-3791
19. Paccanaro, A.; Casbon, J. A.; Saqi, M. A. S. Spectral clustering of protein sequences Nucleic Acids Res. 2006, 34 (5) 1571-1580
20. Pipenbacher, P.; Schliep, A.; Schneckener, S.; Schönhuth, A.; Schomburg, D.; Schrader, R. ProClust: improved clustering of protein sequences with an extended graph-based approach Bioinformatics 2002, 18 (Suppl 2) S182-S191
21. Enright, A. J.; Van Dongen, S.; Ouzounis, C. A. An efficient algorithm for large-scale detection of protein families Nucleic Acids Res. 2002, 30 (7) 1575-1584
22. Li, W.; Jaroszewski, L.; Godzik, A. Clustering of highly homologous sequences to reduce the size of large protein databases Bioinformatics 2001, 17 (3) 282-283
23. Holm, L.; Sander, C. Removing near-neighbour redundancy from large protein sequence collections Bioinformatics 1998, 14 (5) 423-429
24. Altschul, S. F.; Madden, T. L.; Schäffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 1997, 25 (17) 3389-3402
25. Nesvizhskii, A. I.; Aebersold, R. Interpretation of shotgun proteomic data: the protein inference problem Mol. Cell. Proteomics 2005, 4 (10) 1419-1440
26. 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
27. 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
28. Serang, O.; MacCoss, M. J.; Noble, W. S. Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data J. Proteome Res. 2010, 9 (10) 5346-5357
29. Li, Y. F.; Arnold, R. J.; Li, Y.; Radivojac, P.; Sheng, Q.; Tang, H. A bayesian approach to protein inference problem in shotgun proteomics J. Comput. Biol. 2009, 16 (8) 1183-1193
30. Ma, Z.-Q.; Dasari, S.; Chambers, M. C.; Litton, M. D.; Sobecki, S. M.; Zimmerman, L. J.; Halvey, P. J.; Schilling, B.; Drake, P. M.; Gibson, B. W.; Tabb, D. L. IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering J. Proteome Res. 2009, 8 (8) 3872-3881
31. Grobei, M. A.; Qeli, E.; Brunner, E.; Rehrauer, H.; Zhang, R.; Roschitzki, B.; Basler, K.; Ahrens, C. H.; Grossniklaus, U. Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function Genome Res. 2009, 19 (10) 1786-1800
32. Qeli, E.; Ahrens, C. H. PeptideClassifier for protein inference and targeted quantitative proteomics Nat. Biotechnol. 2010, 28 (7) 647-650
33. Li, J.; Zimmerman, L. J.; Park, B.-H.; Tabb, D. L.; Liebler, D. C.; Zhang, B. Network-assisted protein identification and data interpretation in shotgun proteomics Mol. Syst. Biol. 2009, 5, 303
34. Zhang, B.; Chambers, M. C.; Tabb, D. L. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency J. Proteome Res. 2007, 6 (9) 3549-3557
35. Mallick, P.; Schirle, M.; Chen, S. S.; Flory, M. R.; Lee, H.; Martin, D.; Ranish, J.; Raught, B.; Schmitt, R.; Werner, T.; Kuster, B.; Aebersold, R. Computational prediction of proteotypic peptides for quantitative proteomics Nat. Biotechnol. 2007, 25 (1) 125-131
36. Tang, H.; Arnold, R. J.; Alves, P.; Xun, Z.; Clemmer, D. E.; Novotny, M. V.; Reilly, J. P.; Radivojac, P. A computational approach toward label-free protein quantification using predicted peptide detectability Bioinformatics 2006, 22 (14) e481-e488
37. Alves, P.; Arnold, R. J.; Novotny, M. V.; Radivojac, P.; Reilly, J. P.; Tang, H. Advancement in protein inference from shotgun proteomics using peptide detectability Pac. Symp. Biocomput. 2007, 409-420
38. Meyer-Arendt, K.; Old, W. M.; Houel, S.; Renganathan, K.; Eichelberger, B.; Resing, K. A.; Ahn, N. G. IsoformResolver: A peptide-centric algorithm for protein inference J. Proteome Res. 2011, 10 (7) 3060-3075
39. Zhou, A.; Zhang, F.; Chen, J. Y. PEPPI: a peptidomic database of human protein isoforms for proteomics experiments BMC Bioinform. 2010, 11 (Suppl 6) S7
40. Schandorff, S.; Olsen, J. V.; Bunkenborg, J.; Blagoev, B.; Zhang, Y.; Andersen, J. S.; Mann, M. A mass spectrometry-friendly database for cSNP identification Nat. Methods 2007, 4 (6) 465-466
41. de Souza, G. A.; Arntzen, M. Ø.; Fortuin, S.; Schürch, A. C.; MaÌŠlen, H.; McEvoy, C. R. E.; van Soolingen, D.; Thiede, B.; Warren, R. M.; Wiker, H. G. Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database Mol. Cell. Proteomics 2011, 10 (1) M110.002527
42. Griss, J.; Martín, M.; O'Donovan, C.; Apweiler, R.; Hermjakob, H.; Vizcaíno, 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) 4434-4438
43. Bantscheff, M.; Eberhard, D.; Abraham, Y.; Bastuck, S.; Boesche, M.; Hobson, S.; Mathieson, T.; Perrin, J.; Raida, M.; Rau, C.; Reader, V.; Sweetman, G.; Bauer, A.; Bouwmeester, T.; Hopf, C.; Kruse, U.; Neubauer, G.; Ramsden, N.; Rick, J.; Kuster, B.; Drewes, G. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors Nat. Biotechnol. 2007, 25 (9) 1035-1044
44. Wiśniewski, J. R.; Zougman, A.; Nagaraj, N.; Mann, M. Universal sample preparation method for proteome analysis Nat. Methods 2009, 6 (5) 359-362
45. Rappsilber, J.; Ishihama, Y.; Mann, M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics Anal. Chem. 2003, 75 (3) 663-670
46. Wei, Y.; Tong, J.; Taylor, P.; Strumpf, D.; Ignatchenko, V.; Pham, N.-A.; Yanagawa, N.; Liu, G.; Jurisica, I.; Shepherd, F. A.; Tsao, M.-S.; Kislinger, T.; Moran, M. F. Primary tumor xenografts of human lung adeno and squamous cell carcinoma express distinct proteomic signatures J. Proteome Res. 2011, 10 (1) 161-174
47. Datta, S.; Datta, S. Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes BMC Bioinform. 2006, 7, 397
48. R Development Core Team R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2008.
49. Smoot, M. E.; Ono, K.; Ruscheinski, J.; Wang, P.-L.; Ideker, T. Cytoscape 2.8: new features for data integration and network visualization Bioinformatics 2011, 27 (3) 431-432
50. Edwards, N.; Lippert, R.; Edwards, N. Generating peptide candidates from amino-acid sequence databases for protein identification via mass spectrometry. In Algorithms in Bioinformatics: Second International Workshop, WABI 2002, Rome, Italy, September 17-21, 2002, Proceedings; Guigo, R.; Gusfield, D., Eds.; Springer-Verlag: New York, 2002; pp 68-81.
51. Wilmes, P.; Bond, P. L. Metaproteomics: studying functional gene expression in microbial ecosystems Trends Microbiol. 2006, 14 (2) 92-97
52. Verberkmoes, N. C.; Russell, A. L.; Shah, M.; Godzik, A.; Rosenquist, M.; Halfvarson, J.; Lefsrud, M. G.; Apajalahti, J.; Tysk, C.; Hettich, R. L.; Jansson, J. K. Shotgun metaproteomics of the human distal gut microbiota ISME J. 2009, 3 (2) 179-189
53. Mallick, P.; Kuster, B. Proteomics: a pragmatic perspective Nat. Biotechnol. 2010, 28 (7) 695-709 Cellular Systems (GRK 1563)