GPMDB Data Sources

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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;
  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Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.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 data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of January 14, 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/ GPMDB files: 4090.
  24. Whiteaker JR, Zhang H, Zhao L, Wang P, Kelly-Spratt KS, Ivey RG, Piening BD, Feng LC, Kasarda E, Gurley KE, Eng JK, Chodosh LA, Kemp CJ, McIntosh MW, Paulovich AG, Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res (2007) 6(10): 3962-75; PMID:17711321; doi: 10.1021/pr070202v. GPMDB files: 84.
  25. 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): 1035-44; PMID:17721511; doi: 10.1038/nbt1328. GPMDB files: 729.
  26. Padliya ND, Garrett WM, Campbell KB, Tabb DL, Cooper B, Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences. Proteomics (2007) 7(21): 3932-42; PMID:17922518; doi: 10.1002/pmic.200700419. GPMDB files: 1.
  27. Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ, Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell (2007) 131(6): 1190-203; PMID:18083107; doi: 10.1016/j.cell.2007.11.025. GPMDB files: 104.
  28. Ansong C, Yoon H, Norbeck AD, Gustin JK, McDermott JE, Mottaz HM, Rue J, Adkins JN, Heffron F, Smith RD, Proteomics analysis of the causative agent of typhoid fever. J Proteome Res (2008) 7(2): 546-57; PMID:18166006; doi: 10.1021/pr070434u. GPMDB files: 313.
  29. Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, MacCoss MJ, Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution muLC-MS data. Anal Chem (2008) 80(4): 961-71; PMID:18189369; doi: 10.1021/ac701649e. GPMDB files: 12.
  30. Stevens SM Jr, Duncan RS, Koulen P, Prokai L, Proteomic analysis of mouse brain microsomes: identification and bioinformatic characterization of endoplasmic reticulum proteins in the mammalian central nervous system. J Proteome Res (2008) 7(3): 1046-54; PMID:18271522; doi: 10.1021/pr7006279. GPMDB files: 4.
  31. Yocum AK, Gratsch TE, Leff N, Strahler JR, Hunter CL, Walker AK, Michailidis G, Omenn GS, O'Shea KS, Andrews PC, Coupled global and targeted proteomics of human embryonic stem cells during induced differentiation. Mol Cell Proteomics (2008) 7(4): 750-67; PMID:18304949; doi: 10.1074/mcp.M700399-MCP200. GPMDB files: 18.
  32. Lemeer S, Pinkse MW, Mohammed S, van Breukelen B, den Hertog J, Slijper M, Heck AJ, Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo. J Proteome Res (2008) 7(4): 1555-64; PMID:18307296; doi: 10.1021/pr700667w. GPMDB files: 148.
  33. Zhai B, Villén J, Beausoleil SA, Mintseris J, Gygi SP, Phosphoproteome analysis of Drosophila melanogaster embryos. J Proteome Res (2008) 7(4): 1675-82; PMID:18327897; doi: 10.1021/pr700696a. GPMDB files: 24.
  34. Denny P, Hagen FK, Hardt M, Liao L, Yan W, Arellanno M, Bassilian S, Bedi GS, Boontheung P, Cociorva D, Delahunty CM, Denny T, Dunsmore J, Faull KF, Gilligan J, Gonzalez-Begne M, Halgand F, Hall SC, Han X, Henson B, Hewel J, Hu S, Jeffrey S, Jiang J, Loo JA, Ogorzalek Loo RR, Malamud D, Melvin JE, Miroshnychenko O, Navazesh M, Niles R, Park SK, Prakobphol A, Ramachandran P, Richert M, Robinson S, Sondej M, Souda P, Sullivan MA, Takashima J, Than S, Wang J, Whitelegge JP, Witkowska HE, Wolinsky L, Xie Y, Xu T, Yu W, Ytterberg J, Wong DT, Yates JR 3rd, Fisher SJ, The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J Proteome Res (2008) 7(5): 1994-2006; PMID:18361515; doi: 10.1021/pr700764j. GPMDB files: 102.
  35. Simó C, Bachi A, Cattaneo A, Guerrier L, Fortis F, Boschetti E, Podtelejnikov A, Righetti PG, Performance of combinatorial peptide libraries in capturing the low-abundance proteome of red blood cells. 1. Behavior of mono- to hexapeptides. Anal Chem (2008) 80(10): 3547-56; PMID:18399644; doi: 10.1021/ac702635v. GPMDB files: 19.
  36. Bachi A, Simó C, Restuccia U, Guerrier L, Fortis F, Boschetti E, Masseroli M, Righetti PG, Performance of combinatorial peptide libraries in capturing the low-abundance proteome of red blood cells. 2. Behavior of resins containing individual amino acids. Anal Chem (2008) 80(10): 3557-65; PMID:18410134; doi: 10.1021/ac8001353. GPMDB files: 2.
  37. Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S, Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science (2008) 320(5878): 938-41; PMID:18436743; doi: 10.1126/science.1157956. GPMDB files: 28.
  38. Ji H, Erfani N, Tauro BJ, Kapp EA, Zhu HJ, Moritz RL, Lim JW, Simpson RJ, Difference gel electrophoresis analysis of Ras-transformed fibroblast cell-derived exosomes. Electrophoresis (2008) 29(12): 2660-71; PMID:18494037; doi: 10.1002/elps.200800015. GPMDB files: 26.
  39. Cao Z, Li C, Higginbotham JN, Franklin JL, Tabb DL, Graves-Deal R, Hill S, Cheek K, Jerome WG, Lapierre LA, Goldenring JR, Ham AJ, Coffey RJ, Use of fluorescence-activated vesicle sorting for isolation of Naked2-associated, basolaterally targeted exocytic vesicles for proteomics analysis. Mol Cell Proteomics (2008) 7(9): 1651-67; PMID:18504258; doi: 10.1074/mcp.M700155-MCP200. GPMDB files: 6.
  40. Lemeer S, Jopling C, Gouw J, Mohammed S, Heck AJ, Slijper M, den Hertog J, Comparative phosphoproteomics of zebrafish Fyn/Yes morpholino knockdown embryos. Mol Cell Proteomics (2008) 7(11): 2176-87; PMID:18550893; doi: 10.1074/mcp.M800081-MCP200. GPMDB files: 31.
  41. Sodek KL, Evangelou AI, Ignatchenko A, Agochiya M, Brown TJ, Ringuette MJ, Jurisica I, Kislinger T, Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT). Mol Biosyst (2008) 4(7): 762-73; PMID:18563251; doi: 10.1039/b717542f. GPMDB files: 252.
  42. Schimmel J, Larsen KM, Matic I, van Hagen M, Cox J, Mann M, Andersen JS, Vertegaal AC, The ubiquitin-proteasome system is a key component of the SUMO-2/3 cycle. Mol Cell Proteomics (2008) 7(11): 2107-22; PMID:18565875; doi: 10.1074/mcp.M800025-MCP200. GPMDB files: 5.
  43. Yu MJ, Pisitkun T, Wang G, Aranda JF, Gonzales PA, Tchapyjnikov D, Shen RF, Alonso MA, Knepper MA, Large-scale quantitative LC-MS/MS analysis of detergent-resistant membrane proteins from rat renal collecting duct. Am J Physiol Cell Physiol (2008) 295(3): C661-78; PMID:18596208; doi: 10.1152/ajpcell.90650.2007. GPMDB files: 137.
  44. Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, Hill DE, Vidal M, Evans JG, Thorburn DR, Carr SA, Mootha VK, A mitochondrial protein compendium elucidates complex I disease biology. Cell (2008) 134(1): 112-23; PMID:18614015; doi: 10.1016/j.cell.2008.06.016. GPMDB files: 274.
  45. Merrihew GE, Davis C, Ewing B, Williams G, Käll L, Frewen BE, Noble WS, Green P, Thomas JH, MacCoss MJ, Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res (2008) 18(10): 1660-9; PMID:18653799; doi: 10.1101/gr.077644.108. GPMDB files: 369.
  46. Dix MM, Simon GM, Cravatt BF, Global mapping of the topography and magnitude of proteolytic events in apoptosis. Cell (2008) 134(4): 679-91; PMID:18724940; doi: 10.1016/j.cell.2008.06.038. GPMDB files: 178.
  47. Kline KG, Frewen B, Bristow MR, Maccoss MJ, Wu CC, High quality catalog of proteotypic peptides from human heart. J Proteome Res (2008) 7(11): 5055-61; PMID:18803417; doi: 10.1021/pr800239e. GPMDB files: 96.
  48. de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Fröhlich F, Walther TC, Mann M, Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature (2008) 455(7217): 1251-4; PMID:18820680; doi: 10.1038/nature07341. GPMDB files: 505.
  49. Liao L, Park SK, Xu T, Vanderklish P, Yates JR 3rd, Quantitative proteomic analysis of primary neurons reveals diverse changes in synaptic protein content in fmr1 knockout mice. Proc Natl Acad Sci U S A (2008) 105(40): 15281-6; PMID:18829439; doi: 10.1073/pnas.0804678105. GPMDB files: 15.
  50. Lin MK, Lee YJ, Lough TJ, Phinney BS, Lucas WJ, Analysis of the pumpkin phloem proteome provides insights into angiosperm sieve tube function. Mol Cell Proteomics (2009) 8(2): 343-56; PMID:18936055; doi: 10.1074/mcp.M800420-MCP200. GPMDB files: 346.
  51. Slebos RJ, Brock JW, Winters NF, Stuart SR, Martinez MA, Li M, Chambers MC, Zimmerman LJ, Ham AJ, Tabb DL, Liebler DC, Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry. J Proteome Res (2008) 7(12): 5286-94; PMID:18939861; doi: 10.1021/pr8004666. GPMDB files: 346.
  52. Mittler G, Butter F, Mann M, A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genome Res (2009) 19(2): 284-93; PMID:19015324; doi: 10.1101/gr.081711.108. GPMDB files: 7.
  53. Codreanu SG, Zhang B, Sobecki SM, Billheimer DD, Liebler DC, Global analysis of protein damage by the lipid electrophile 4-hydroxy-2-nonenal. Mol Cell Proteomics (2009) 8(4): 670-80; PMID:19054759; doi: 10.1074/mcp.M800070-MCP200. GPMDB files: 168.
  54. Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI, Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. J Proteome Res (2009) 8(2): 887-99; PMID:19072539; doi: 10.1021/pr800535h. GPMDB files: 18.
  55. Du J, Bernasconi P, Clauser KR, Mani DR, Finn SP, Beroukhim R, Burns M, Julian B, Peng XP, Hieronymus H, Maglathlin RL, Lewis TA, Liau LM, Nghiemphu P, Mellinghoff IK, Louis DN, Loda M, Carr SA, Kung AL, Golub TR, Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy. Nat Biotechnol (2009) 27(1): 77-83; PMID:19098899; doi: 10.1038/nbt.1513. GPMDB files: 36.
  56. Glatter T, Wepf A, Aebersold R, Gstaiger M, An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol (2009) 5: 237; PMID:19156129; doi: 10.1038/msb.2008.75. GPMDB files: 62.
  57. Bivi N, Bereszczak JZ, Romanello M, Zeef LA, Delneri D, Quadrifoglio F, Moro L, Brancia FL, Tell G, Transcriptome and proteome analysis of osteocytes treated with nitrogen-containing bisphosphonates. J Proteome Res (2009) 8(3): 1131-42; PMID:19226166; doi: 10.1021/pr8005606. GPMDB files: 10.
  58. Pieper R, Huang ST, Clark DJ, Robinson JM, Alami H, Parmar PP, Suh MJ, Kuntumalla S, Bunai CL, Perry RD, Fleischmann RD, Peterson SN, Integral and peripheral association of proteins and protein complexes with Yersinia pestis inner and outer membranes. Proteome Sci (2009) 7: 5; PMID:19228400; doi: 10.1186/1477-5956-7-5. GPMDB files: 376.
  59. de Sousa Abreu R, Sanchez-Diaz PC, Vogel C, Burns SC, Ko D, Burton TL, Vo DT, Chennasamudaram S, Le SY, Shapiro BA, Penalva LO, Genomic analyses of musashi1 downstream targets show a strong association with cancer-related processes. J Biol Chem (2009) 284(18): 12125-35; PMID:19258308; doi: 10.1074/jbc.M809605200. GPMDB files: 14.
  60. Mathias RA, Wang B, Ji H, Kapp EA, Moritz RL, Zhu HJ, Simpson RJ, Secretome-based proteomic profiling of Ras-transformed MDCK cells reveals extracellular modulators of epithelial-mesenchymal transition. J Proteome Res (2009) 8(6): 2827-37; PMID:19296674; doi: 10.1021/pr8010974. GPMDB files: 98.
  61. Boersema PJ, Raijmakers R, Lemeer S, Mohammed S, Heck AJ, Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat Protoc (2009) 4(4): 484-94; PMID:19300442; doi: 10.1038/nprot.2009.21. GPMDB files: 3.
  62. Ramakrishnan SR, Vogel C, Prince JT, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP, Wang R, Integrating shotgun proteomics and mRNA expression data to improve protein identification. Bioinformatics (2009) 25(11): 1397-403; PMID:19318424; doi: 10.1093/bioinformatics/btp168. GPMDB files: 8.
  63. Rudomin EL, Carr SA, Jaffe JD, Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx). J Proteome Res (2009) 8(6): 3154-60; PMID:19344186; doi: 10.1021/pr801017a. GPMDB files: 11.
  64. Steiling K, Kadar AY, Bergerat A, Flanigon J, Sridhar S, Shah V, Ahmad QR, Brody JS, Lenburg ME, Steffen M, Spira A, Comparison of proteomic and transcriptomic profiles in the bronchial airway epithelium of current and never smokers. PLoS One (2009) 4(4): e5043; PMID:19357784; doi: 10.1371/journal.pone.0005043. GPMDB files: 589.
  65. Hjelmervik TO, Jonsson R, Bolstad AI, The minor salivary gland proteome in Sjögren's syndrome. Oral Dis (2009) 15(5): 342-53; PMID:19364392; doi: 10.1111/j.1601-0825.2009.01531.x. GPMDB files: 2.
  66. Zanivan S, Gnad F, Wickström SA, Geiger T, Macek B, Cox J, Fässler R, Mann M, Solid tumor proteome and phosphoproteome analysis by high resolution mass spectrometry. J Proteome Res (2008) 7(12): 5314-26; PMID:19367708. GPMDB files: 20.
  67. Reiland S, Messerli G, Baerenfaller K, Gerrits B, Endler A, Grossmann J, Gruissem W, Baginsky S, Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol (2009) 150(2): 889-903; PMID:19376835; doi: 10.1104/pp.109.138677. GPMDB files: 13.
  68. Parker KC, Walsh RJ, Salajegheh M, Amato AA, Krastins B, Sarracino DA, Greenberg SA, Characterization of human skeletal muscle biopsy samples using shotgun proteomics. J Proteome Res (2009) 8(7): 3265-77; PMID:19382779; doi: 10.1021/pr800873q. GPMDB files: 36.
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  70. Fernández E, Collins MO, Uren RT, Kopanitsa MV, Komiyama NH, Croning MD, Zografos L, Armstrong JD, Choudhary JS, Grant SG, Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins. Mol Syst Biol (2009) 5: 269; PMID:19455133; doi: 10.1038/msb.2009.27. GPMDB files: 70.
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