GPMDB Data Sources

Revision as of 17:17, 13 January 2016

GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.

Current Public Data Sources

The following public data repositories are checked daily for new suitable raw data for reanalysis:

1. ProteomeXchange/PRIDE;
2. MASSIVE;
3. PeptideAtlas/PASSEL;
4. ProteomicsDB;
5. The Chorus Project; and
6. iProX.

Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.

Previous Data Sources

GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.

Review process

Simply because data is made available does not mean that it will be included in GPMDB. The data must pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.

Data from publications

The following is a list of publications that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of January 13, 2016.

1. Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci U S A (2002) 99(17): 11049-54; PMID:12177431; doi: 10.1073/pnas.172170199. GPMDB files: 498.
2. Liu T, Qian WJ, Strittmatter EF, Camp DG 2nd, Anderson GA, Thrall BD, Smith RD, High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology. Anal Chem (2004) 76(18): 5345-53; PMID:15362891; doi: 10.1021/ac049485q. GPMDB files: 6.
3. Sauer G, Körner R, Hanisch A, Ries A, Nigg EA, Silljé HH, Proteome analysis of the human mitotic spindle. Mol Cell Proteomics (2005) 4(1): 35-43; PMID:15561729; doi: 10.1074/mcp.M400158-MCP200. GPMDB files: 1.
4. Klein C, Garcia-Rizo C, Bisle B, Scheffer B, Zischka H, Pfeiffer F, Siedler F, Oesterhelt D, The membrane proteome of Halobacterium salinarum. Proteomics (2005) 5(1): 180-97; PMID:15619294; doi: 10.1002/pmic.200400943. GPMDB files: 37.
5. Searle BC, Dasari S, Wilmarth PA, Turner M, Reddy AP, David LL, Nagalla SR, Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm. J Proteome Res (2005) 4(2): 546-54; PMID:15822933; doi: 10.1021/pr049781j. GPMDB files: 4.
6. Elias JE, Haas W, Faherty BK, Gygi SP, Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods (2005) 2(9): 667-75; PMID:16118637; doi: 10.1038/nmeth785. GPMDB files: 30.
7. Lee YJ, Rice RH, Lee YM, Proteome analysis of human hair shaft: from protein identification to posttranslational modification. Mol Cell Proteomics (2006) 5(5): 789-800; PMID:16446289; doi: 10.1074/mcp.M500278-MCP200. GPMDB files: 75.
8. Gatlin CL, Pieper R, Huang ST, Mongodin E, Gebregeorgis E, Parmar PP, Clark DJ, Alami H, Papazisi L, Fleischmann RD, Gill SR, Peterson SN, Proteomic profiling of cell envelope-associated proteins from Staphylococcus aureus. Proteomics (2006) 6(5): 1530-49; PMID:16470658; doi: 10.1002/pmic.200500253. GPMDB files: 1603.
9. Keshamouni VG, Michailidis G, Grasso CS, Anthwal S, Strahler JR, Walker A, Arenberg DA, Reddy RC, Akulapalli S, Thannickal VJ, Standiford TJ, Andrews PC, Omenn GS, Differential protein expression profiling by iTRAQ-2DLC-MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype. J Proteome Res (2006) 5(5): 1143-54; PMID:16674103; doi: 10.1021/pr050455t. GPMDB files: 3.
10. Bisle B, Schmidt A, Scheibe B, Klein C, Tebbe A, Kellermann J, Siedler F, Pfeiffer F, Lottspeich F, Oesterhelt D, Quantitative profiling of the membrane proteome in a halophilic archaeon. Mol Cell Proteomics (2006) 5(9): 1543-58; PMID:16804162; doi: 10.1074/mcp.M600106-MCP200. GPMDB files: 32.
11. Hamacher M, Apweiler R, Arnold G, Becker A, Blüggel M, Carrette O, Colvis C, Dunn MJ, Fröhlich T, Fountoulakis M, van Hall A, Herberg F, Ji J, Kretzschmar H, Lewczuk P, Lubec G, Marcus K, Martens L, Palacios Bustamante N, Park YM, Pennington SR, Robben J, Stühler K, Reidegeld KA, Riederer P, Rossier J, Sanchez JC, Schrader M, Stephan C, Tagle D, Thiele H, Wang J, Wiltfang J, Yoo JS, Zhang C, Klose J, Meyer HE, HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy. Proteomics (2006) 6(18): 4890-8; PMID:16927433; doi: 10.1002/pmic.200600295. GPMDB files: 296.
12. Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP, A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol (2006) 24(10): 1285-92; PMID:16964243; doi: 10.1038/nbt1240. GPMDB files: 31.
13. Whitehead K, Kish A, Pan M, Kaur A, Reiss DJ, King N, Hohmann L, DiRuggiero J, Baliga NS, An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol (2006) 2: 47; PMID:16969339; doi: 10.1038/msb4100091. GPMDB files: 27.
14. Price TS, Lucitt MB, Wu W, Austin DJ, Pizarro A, Yocum AK, Blair IA, FitzGerald GA, Grosser T, EBP, a program for protein identification using multiple tandem mass spectrometry datasets. Mol Cell Proteomics (2007) 6(3): 527-36; PMID:17164401; doi: 10.1074/mcp.T600049-MCP200. GPMDB files: 314.
15. Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V, Improving gene annotation using peptide mass spectrometry. Genome Res (2007) 17(2): 231-9; PMID:17189379; doi: 10.1101/gr.5646507. GPMDB files: 1.
16. Konstantinidis K, Tebbe A, Klein C, Scheffer B, Aivaliotis M, Bisle B, Falb M, Pfeiffer F, Siedler F, Oesterhelt D, Genome-wide proteomics of Natronomonas pharaonis. J Proteome Res (2007) 6(1): 185-93; PMID:17203963; doi: 10.1021/pr060352q. GPMDB files: 176.
17. Villén J, Beausoleil SA, Gerber SA, Gygi SP, Large-scale phosphorylation analysis of mouse liver. Proc Natl Acad Sci U S A (2007) 104(5): 1488-93; PMID:17242355; doi: 10.1073/pnas.0609836104. GPMDB files: 1.
18. Klein C, Aivaliotis M, Olsen JV, Falb M, Besir H, Scheffer B, Bisle B, Tebbe A, Konstantinidis K, Siedler F, Pfeiffer F, Mann M, Oesterhelt D, The low molecular weight proteome of Halobacterium salinarum. J Proteome Res (2007) 6(4): 1510-8; PMID:17326674; doi: 10.1021/pr060634q. GPMDB files: 10.
19. Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC, Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science (2007) 316(5822): 280-5; PMID:17431180; doi: 10.1126/science.1137614. GPMDB files: 2.
20. Lowery DM, Clauser KR, Hjerrild M, Lim D, Alexander J, Kishi K, Ong SE, Gammeltoft S, Carr SA, Yaffe MB, Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate. EMBO J (2007) 26(9): 2262-73; PMID:17446864; doi: 10.1038/sj.emboj.7601683. GPMDB files: 24.
21. Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R, A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol (2007) 25(5): 576-83; PMID:17450130; doi: 10.1038/nbt1300. GPMDB files: 1907.
22. Wu L, Hwang SI, Rezaul K, Lu LJ, Mayya V, Gerstein M, Eng JK, Lundgren DH, Han DK, Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling. Mol Cell Proteomics (2007) 6(8): 1343-53; PMID:17519225; doi: 10.1074/mcp.M700017-MCP200. GPMDB files: 2299.
23. Au CE, Bell AW, Gilchrist A, Hiding J, Nilsson T, Bergeron JJ, Organellar proteomics to create the cell map. Curr Opin Cell Biol (2007) 19(4): 376-85; PMID:17689063; doi: 10.1016/j.ceb.2007.05.004. GPMDB files: 4090.