GPMDB Data Sources

From TheGPMWiki
Revision as of 17:08, 13 January 2016 by WikiSysop (Talk | contribs)
Jump to: navigation, search

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Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.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 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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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/
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  69. Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ, HUPO Test Sample Working Group, A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat Methods (2009) 6(6): 423-30; PMID:19448641; doi: 10.1038/nmeth.1333.
  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.
  71. Sprung RW Jr, Brock JW, Tanksley JP, Li M, Washington MK, Slebos RJ, Liebler DC, Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol Cell Proteomics (2009) 8(8): 1988-98; PMID:19467989; doi: 10.1074/mcp.M800518-MCP200.
  72. Burkard ME, Maciejowski J, Rodriguez-Bravo V, Repka M, Lowery DM, Clauser KR, Zhang C, Shokat KM, Carr SA, Yaffe MB, Jallepalli PV, Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells. PLoS Biol (2009) 7(5): e1000111; PMID:19468302; doi: 10.1371/journal.pbio.1000111.
  73. () ; PMID:.
  74. Ma ZQ, Dasari S, Chambers MC, Litton MD, Sobecki SM, Zimmerman LJ, Halvey PJ, Schilling B, Drake PM, Gibson BW, Tabb DL, IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering. J Proteome Res (2009) 8(8): 3872-81; PMID:19522537; doi: 10.1021/pr900360j.
  75. Shi L, Chowdhury SM, Smallwood HS, Yoon H, Mottaz-Brewer HM, Norbeck AD, McDermott JE, Clauss TR, Heffron F, Smith RD, Adkins JN, Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica. Infect Immun (2009) 77(8): 3227-33; PMID:19528222; doi: 10.1128/IAI.00063-09.
  76. Cox B, Kotlyar M, Evangelou AI, Ignatchenko V, Ignatchenko A, Whiteley K, Jurisica I, Adamson SL, Rossant J, Kislinger T, Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology. Mol Syst Biol (2009) 5: 279; PMID:19536202; doi: 10.1038/msb.2009.37.
  77. Kentsis A, Lin YY, Kurek K, Calicchio M, Wang YY, Monigatti F, Campagne F, Lee R, Horwitz B, Steen H, Bachur R, Discovery and validation of urine markers of acute pediatric appendicitis using high-accuracy mass spectrometry. Ann Emerg Med (2010) 55(1): 62-70.e4; PMID:19556024; doi: 10.1016/j.annemergmed.2009.04.020.
  78. Lau NC, Kolkman A, van Schaik FM, Mulder KW, Pijnappel WW, Heck AJ, Timmers HT, Human Ccr4-Not complexes contain variable deadenylase subunits. Biochem J (2009) 422(3): 443-53; PMID:19558367; doi: 10.1042/BJ20090500.
  79. Zivanovic Y, Armengaud J, Lagorce A, Leplat C, Guérin P, Dutertre M, Anthouard V, Forterre P, Wincker P, Confalonieri F, Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol (2009) 10(6): R70; PMID:19558674; doi: 10.1186/gb-2009-10-6-r70.
  80. Alev C, Shinmyozu K, McIntyre BA, Sheng G, Genomic organization of zebra finch alpha and beta globin genes and their expression in primitive and definitive blood in comparison with globins in chicken. Dev Genes Evol (2009) 219(7): 353-60; PMID:19609557; doi: 10.1007/s00427-009-0294-8.
  81. Izquierdo L, Schulz BL, Rodrigues JA, Güther ML, Procter JB, Barton GJ, Aebi M, Ferguson MA, Distinct donor and acceptor specificities of Trypanosoma brucei oligosaccharyltransferases. EMBO J (2009) 28(17): 2650-61; PMID:19629045; doi: 10.1038/emboj.2009.203.
  82. Van Hoof D, Muñoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J, Phosphorylation dynamics during early differentiation of human embryonic stem cells. Cell Stem Cell (2009) 5(2): 214-26; PMID:19664995; doi: 10.1016/j.stem.2009.05.021.
  83. Tebbe A, Schmidt A, Konstantinidis K, Falb M, Bisle B, Klein C, Aivaliotis M, Kellermann J, Siedler F, Pfeiffer F, Lottspeich F, Oesterhelt D, Life-style changes of a halophilic archaeon analyzed by quantitative proteomics. Proteomics (2009) 9(15): 3843-55; PMID:19670246; doi: 10.1002/pmic.200800944.
  84. Casado-Vela J, Rodriguez-Suarez E, Iloro I, Ametzazurra A, Alkorta N, García-Velasco JA, Matorras R, Prieto B, González S, Nagore D, Simón L, Elortza F, Comprehensive proteomic analysis of human endometrial fluid aspirate. J Proteome Res (2009) 8(10): 4622-32; PMID:19670903; doi: 10.1021/pr9004426.
  85. Charles RC, Harris JB, Chase MR, Lebrun LM, Sheikh A, LaRocque RC, Logvinenko T, Rollins SM, Tarique A, Hohmann EL, Rosenberg I, Krastins B, Sarracino DA, Qadri F, Calderwood SB, Ryan ET, Comparative proteomic analysis of the PhoP regulon in Salmonella enterica serovar Typhi versus Typhimurium. PLoS One (2009) 4(9): e6994; PMID:19746165; doi: 10.1371/journal.pone.0006994.
  86. Pottiez G, Flahaut C, Cecchelli R, Karamanos Y, Understanding the blood-brain barrier using gene and protein expression profiling technologies. Brain Res Rev (2009) 62(1): 83-98; PMID:19770003; doi: 10.1016/j.brainresrev.2009.09.004.
  87. Boersema PJ, Foong LY, Ding VM, Lemeer S, van Breukelen B, Philp R, Boekhorst J, Snel B, den Hertog J, Choo AB, Heck AJ, In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling. Mol Cell Proteomics (2010) 9(1): 84-99; PMID:19770167; doi: 10.1074/mcp.M900291-MCP200.
  88. Ozlü N, Monigatti F, Renard BY, Field CM, Steen H, Mitchison TJ, Steen JJ, Binding partner switching on microtubules and aurora-B in the mitosis to cytokinesis transition. Mol Cell Proteomics (2010) 9(2): 336-50; PMID:19786723; doi: 10.1074/mcp.M900308-MCP200.
  89. Johansen E, Schilling B, Lerch M, Niles RK, Liu H, Li B, Allen S, Hall SC, Witkowska HE, Regnier FE, Gibson BW, Fisher SJ, Drake PM, A lectin HPLC method to enrich selectively-glycosylated peptides from complex biological samples. J Vis Exp (2009) ; PMID:19798022; doi: 10.3791/1398.
  90. Hahn CK, Berchuck JE, Ross KN, Kakoza RM, Clauser K, Schinzel AC, Ross L, Galinsky I, Davis TN, Silver SJ, Root DE, Stone RM, DeAngelo DJ, Carroll M, Hahn WC, Carr SA, Golub TR, Kung AL, Stegmaier K, Proteomic and genetic approaches identify Syk as an AML target. Cancer Cell (2009) 16(4): 281-94; PMID:19800574; doi: 10.1016/j.ccr.2009.08.018.
  91. Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA, Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A (2009) 106(38): 16428-33; PMID:19805315; doi: 10.1073/pnas.0905240106.
  92. Tunica DG, Yin X, Sidibe A, Stegemann C, Nissum M, Zeng L, Brunet M, Mayr M, Proteomic analysis of the secretome of human umbilical vein endothelial cells using a combination of free-flow electrophoresis and nanoflow LC-MS/MS. Proteomics (2009) 9(21): 4991-6; PMID:19810032; doi: 10.1002/pmic.200900065.
  93. Mathivanan S, Lim JW, Tauro BJ, Ji H, Moritz RL, Simpson RJ, Proteomics analysis of A33 immunoaffinity-purified exosomes released from the human colon tumor cell line LIM1215 reveals a tissue-specific protein signature. Mol Cell Proteomics (2010) 9(2): 197-208; PMID:19837982; doi: 10.1074/mcp.M900152-MCP200.
  94. Baudet M, Ortet P, Gaillard JC, Fernandez B, Guérin P, Enjalbal C, Subra G, de Groot A, Barakat M, Dedieu A, Armengaud J, Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. Mol Cell Proteomics (2010) 9(2): 415-26; PMID:19875382; doi: 10.1074/mcp.M900359-MCP200.
  95. Pitteri SJ, JeBailey L, Faça VM, Thorpe JD, Silva MA, Ireton RC, Horton MB, Wang H, Pruitt LC, Zhang Q, Cheng KH, Urban N, Hanash SM, Dinulescu DM, Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery. PLoS One (2009) 4(11): e7916; PMID:19936259; doi: 10.1371/journal.pone.0007916.
  96. Bilodeau N, Fiset A, Boulanger MC, Bhardwaj S, Winstall E, Lavoie JN, Faure RL, Proteomic analysis of Src family kinases signaling complexes in Golgi/endosomal fractions using a site-selective anti-phosphotyrosine antibody: identification of LRP1-insulin receptor complexes. J Proteome Res (2010) 9(2): 708-17; PMID:19947650; doi: 10.1021/pr900481b.
  97. Mathias RA, Chen YS, Wang B, Ji H, Kapp EA, Moritz RL, Zhu HJ, Simpson RJ, Extracellular remodelling during oncogenic Ras-induced epithelial-mesenchymal transition facilitates MDCK cell migration. J Proteome Res (2010) 9(2): 1007-19; PMID:19954229; doi: 10.1021/pr900907g.
  98. Lau TY, Power KA, Dijon S, de Gardelle I, McDonnell S, Duffy MJ, Pennington SR, Gallagher WM, Prioritization of candidate protein biomarkers from an in vitro model system of breast tumor progression toward clinical verification. J Proteome Res (2010) 9(3): 1450-9; PMID:20000743; doi: 10.1021/pr900989q.
  99. Chalkley RJ, Medzihradszky KF, Lynn AJ, Baker PR, Burlingame AL, Statistical analysis of Peptide electron transfer dissociation fragmentation mass spectrometry. Anal Chem (2010) 82(2): 579-84; PMID:20028093; doi: 10.1021/ac9018582.
  100. Yin X, Cuello F, Mayr U, Hao Z, Hornshaw M, Ehler E, Avkiran M, Mayr M, Proteomics analysis of the cardiac myofilament subproteome reveals dynamic alterations in phosphatase subunit distribution. Mol Cell Proteomics (2010) 9(3): 497-509; PMID:20037178; doi: 10.1074/mcp.M900275-MCP200.
  101. Friso G, Majeran W, Huang M, Sun Q, van Wijk KJ, Reconstruction of metabolic pathways, protein expression, and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts: large-scale quantitative proteomics using the first maize genome assembly. Plant Physiol (2010) 152(3): 1219-50; PMID:20089766; doi: 10.1104/pp.109.152694.
  102. Gant-Branum RL, Broussard JA, Mahsut A, Webb DJ, McLean JA, Identification of phosphorylation sites within the signaling adaptor APPL1 by mass spectrometry. J Proteome Res (2010) 9(3): 1541-8; PMID:20095645; doi: 10.1021/pr901043e.
  103. Paweletz CP, Wiener MC, Bondarenko AY, Yates NA, Song Q, Liaw A, Lee AY, Hunt BT, Henle ES, Meng F, Sleph HF, Holahan M, Sankaranarayanan S, Simon AJ, Settlage RE, Sachs JR, Shearman M, Sachs AB, Cook JJ, Hendrickson RC, Application of an end-to-end biomarker discovery platform to identify target engagement markers in cerebrospinal fluid by high resolution differential mass spectrometry. J Proteome Res (2010) 9(3): 1392-401; PMID:20095649; doi: 10.1021/pr900925d.
  104. Guo X, Shen J, Xia Z, Zhang R, Zhang P, Zhao C, Xing J, Chen L, Chen W, Lin M, Huo R, Su B, Zhou Z, Sha J, Proteomic analysis of proteins involved in spermiogenesis in mouse. J Proteome Res (2010) 9(3): 1246-56; PMID:20099899; doi: 10.1021/pr900735k.
  105. Chaerkady R, Kerr CL, Kandasamy K, Marimuthu A, Gearhart JD, Pandey A, Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics (2010) 10(7): 1359-73; PMID:20104618; doi: 10.1002/pmic.200900483.
  106. Burgess EF, Ham AJ, Tabb DL, Billheimer D, Roth BJ, Chang SS, Cookson MS, Hinton TJ, Cheek KL, Hill S, Pietenpol JA, Prostate cancer serum biomarker discovery through proteomic analysis of alpha-2 macroglobulin protein complexes. Proteomics Clin Appl (2008) 2(9): 1223; PMID:20107526; doi: 10.1002/prca.200780073.
  107. Swaney DL, Wenger CD, Coon JJ, Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J Proteome Res (2010) 9(3): 1323-9; PMID:20113005; doi: 10.1021/pr900863u.
  108. Rinschen MM, Yu MJ, Wang G, Boja ES, Hoffert JD, Pisitkun T, Knepper MA, Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor-dependent signaling pathways in renal collecting duct cells. Proc Natl Acad Sci U S A (2010) 107(8): 3882-7; PMID:20139300; doi: 10.1073/pnas.0910646107.
  109. Looso M, Borchardt T, Krüger M, Braun T, Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry. Mol Cell Proteomics (2010) 9(6): 1157-66; PMID:20139370; doi: 10.1074/mcp.M900426-MCP200.
  110. Tomazella GG, daSilva I, Thomé CH, Greene LJ, Koehler CJ, Thiede B, Wiker HG, de Souza GA, Analysis of detergent-insoluble and whole cell lysate fractions of resting neutrophils using high-resolution mass spectrometry. J Proteome Res (2010) 9(4): 2030-6; PMID:20158270; doi: 10.1021/pr1000253.
  111. Sharma K, Kumar C, Kéri G, Breitkopf SB, Oppermann FS, Daub H, Quantitative analysis of kinase-proximal signaling in lipopolysaccharide-induced innate immune response. J Proteome Res (2010) 9(5): 2539-49; PMID:20222745; doi: 10.1021/pr901192p.
  112. Baiges I, Palmfeldt J, Bladé C, Gregersen N, Arola L, Lipogenesis is decreased by grape seed proanthocyanidins according to liver proteomics of rats fed a high fat diet. Mol Cell Proteomics (2010) 9(7): 1499-513; PMID:20332082; doi: 10.1074/mcp.M000055-MCP201.
Personal tools