GPMDB Data Sources

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Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.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 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/j.ceb.2007.05.004. 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.
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. GPMDB files: 14.
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.
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. GPMDB files: 230.
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810. Arntzen MØ, Karlskås IL, Skaugen M, Eijsink VG, Mathiesen G, Proteomic Investigation of the Response of Enterococcus faecalis V583 when Cultivated in Urine. PLoS One (2015) 10(4): e0126694; PMID:25915650; doi: 10.1371/journal.pone.0126694. GPMDB files: 24.
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816. Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E, A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. J Proteome Res (2015) 14(7): 2807-18; PMID:25944384; doi: 10.1021/acs.jproteome.5b00315. GPMDB files: 238.
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825. Lee JG, McKinney KQ, Lee YY, Chung HN, Pavlopoulos AJ, Jung KY, Kim WK, Kuroda MJ, Han DK, Hwang S, A draft map of rhesus monkey tissue proteome for biomedical research. PLoS One (2015) 10(5): e0126243; PMID:25974132; doi: 10.1371/journal.pone.0126243. GPMDB files: 19.
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828. Campos A, Díaz R, Martínez-Bartolomé S, Sierra J, Gallardo O, Sabidó E, López-Lucendo M, Ignacio Casal J, Pasquarello C, Scherl A, Chiva C, Borras E, Odena A, Elortza F, Azkargorta M, Ibarrola N, Canals F, Albar JP, Oliveira E, Multicenter experiment for quality control of peptide-centric LC-MS/MS analysis - A longitudinal performance assessment with nLC coupled to orbitrap MS analyzers. J Proteomics (2015) 127(Pt B): 264-74; PMID:25982386; doi: 10.1016/j.jprot.2015.05.012. GPMDB files: 112.
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830. Bennike TB, Carlsen TG, Ellingsen T, Bonderup OK, Glerup H, Bøgsted M, Christiansen G, Birkelund S, Stensballe A, Andersen V, Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies. Inflamm Bowel Dis (2015) 21(9): 2052-67; PMID:25993694; doi: 10.1097/MIB.0000000000000460. GPMDB files: 60.
831. Kharlampieva D, Manuvera V, Podgorny O, Grafskaia E, Kovalchuk S, Pobeguts O, Altukhov I, Govorun V, Lazarev V, Recombinant fragilysin isoforms cause E-cadherin cleavage of intact cells and do not cleave isolated E-cadherin. Microb Pathog (2015) 83-84: 47-56; PMID:25998017; doi: 10.1016/j.micpath.2015.05.003. GPMDB files: 23.
832. Aeberhard L, Banhart S, Fischer M, Jehmlich N, Rose L, Koch S, Laue M, Renard BY, Schmidt F, Heuer D, The Proteome of the Isolated Chlamydia trachomatis Containing Vacuole Reveals a Complex Trafficking Platform Enriched for Retromer Components. PLoS Pathog (2015) 11(6): e1004883; PMID:26042774; doi: 10.1371/journal.ppat.1004883. GPMDB files: 24.
833. Marie P, Labas V, Brionne A, Harichaux G, Hennequet-Antier C, Rodriguez-Navarro AB, Nys Y, Gautron J, Quantitative proteomics provides new insights into chicken eggshell matrix protein functions during the primary events of mineralisation and the active calcification phase. J Proteomics (2015) 126: 140-54; PMID:26049031; doi: 10.1016/j.jprot.2015.05.034. GPMDB files: 180.
834. McCloy RA, Parker BL, Rogers S, Chaudhuri R, Gayevskiy V, Hoffman NJ, Ali N, Watkins DN, Daly RJ, James DE, Lorca T, Castro A, Burgess A, Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs. Mol Cell Proteomics (2015) 14(8): 2194-212; PMID:26055452; doi: 10.1074/mcp.M114.046938. GPMDB files: 29.
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837. Murphy JP, Stepanova E, Everley RA, Paulo JA, Gygi SP, Comprehensive Temporal Protein Dynamics during the Diauxic Shift in Saccharomyces cerevisiae. Mol Cell Proteomics (2015) 14(9): 2454-65; PMID:26077900; doi: 10.1074/mcp.M114.045849. GPMDB files: 66.
838. Wiśniewski JR, Gizak A, Rakus D, Integrating Proteomics and Enzyme Kinetics Reveals Tissue-Specific Types of the Glycolytic and Gluconeogenic Pathways. J Proteome Res (2015) 14(8): 3263-73; PMID:26080680; doi: 10.1021/acs.jproteome.5b00276. GPMDB files: 18.
839. Mui MZ, Zhou Y, Blanchette P, Chughtai N, Knight JF, Gruosso T, Papadakis AI, Huang S, Park M, Gingras AC, Branton PE, The Human Adenovirus Type 5 E4orf4 Protein Targets Two Phosphatase Regulators of the Hippo Signaling Pathway. J Virol (2015) 89(17): 8855-70; PMID:26085163; doi: 10.1128/JVI.03710-14. GPMDB files: 16.
840. Cehofski LJ, Kruse A, Kjærgaard B, Stensballe A, Honoré B, Vorum H, Proteins involved in focal adhesion signaling pathways are differentially regulated in experimental branch retinal vein occlusion. Exp Eye Res (2015) 138: 87-95; PMID:26086079; doi: 10.1016/j.exer.2015.06.011. GPMDB files: 48.
841. Stebbing J, Zhang H, Xu Y, Grothey A, Ajuh P, Angelopoulos N, Giamas G, Characterization of the Tyrosine Kinase-Regulated Proteome in Breast Cancer by Combined use of RNA interference (RNAi) and Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) Quantitative Proteomics. Mol Cell Proteomics (2015) 14(9): 2479-92; PMID:26089344; doi: 10.1074/mcp.M115.048090. GPMDB files: 370.
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843. Barco RA, Emerson D, Sylvan JB, Orcutt BN, Jacobson Meyers ME, Ramírez GA, Zhong JD, Edwards KJ, New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph. Appl Environ Microbiol (2015) 81(17): 5927-37; PMID:26092463; doi: 10.1128/AEM.01374-15. GPMDB files: 28.
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849. Uebbing S, Konzer A, Xu L, Backström N, Brunström B, Bergquist J, Ellegren H, Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken. Mol Biol Evol (2015) 32(10): 2716-25; PMID:26108680; doi: 10.1093/molbev/msv147. GPMDB files: 30.
850. Zhu M, Wu G, Li YX, Stevens JK, Fan CX, Spang A, Dong MQ, Serum- and Glucocorticoid-Inducible Kinase-1 (SGK-1) Plays a Role in Membrane Trafficking in Caenorhabditis elegans. PLoS One (2015) 10(6): e0130778; PMID:26115433; doi: 10.1371/journal.pone.0130778. GPMDB files: 2.
851. Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, Lin ZY, Lopez MF, Loppnau P, Miersch S, Nguyen T, Olsen JB, Paduch M, Ravichandran M, Seitova A, Vadali G, Vogelsang MS, Whiteaker JR, Zhong G, Zhong N, Zhao L, Aebersold R, Arrowsmith CH, Emili A, Frappier L, Gingras AC, Gstaiger M, Paulovich AG, Koide S, Kossiakoff AA, Sidhu SS, Wodak SJ, Gräslund S, Greenblatt JF, Edwards AM, Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat Methods (2015) 12(8): 725-31; PMID:26121405; doi: 10.1038/nmeth.3472. GPMDB files: 1220.
852. Cardona M, López JA, Serafín A, Rongvaux A, Inserte J, García-Dorado D, Flavell R, Llovera M, Cañas X, Vázquez J, Sanchis D, Executioner Caspase-3 and 7 Deficiency Reduces Myocyte Number in the Developing Mouse Heart. PLoS One (2015) 10(6): e0131411; PMID:26121671; doi: 10.1371/journal.pone.0131411. GPMDB files: 8.
853. Herbst FA, Danielsen HN, Wimmer R, Nielsen PH, Dueholm MS, Label-free quantification reveals major proteomic changes in Pseudomonas putida F1 during the exponential growth phase. Proteomics (2015) 15(18): 3244-52; PMID:26122999; doi: 10.1002/pmic.201400482. GPMDB files: 16.
854. Sghaier H, Hezbri K, Ghodhbane-Gtari F, Pujic P, Sen A, Daffonchio D, Boudabous A, Tisa LS, Klenk HP, Armengaud J, Normand P, Gtari M, Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes. ISME J (2016) 10(1): 21-9; PMID:26125681; doi: 10.1038/ismej.2015.108. GPMDB files: 9.
855. Carapito C, Lane L, Benama M, Opsomer A, Mouton-Barbosa E, Garrigues L, Gonzalez de Peredo A, Burel A, Bruley C, Gateau A, Bouyssié D, Jaquinod M, Cianferani S, Burlet-Schiltz O, Van Dorsselaer A, Garin J, Vandenbrouck Y, Computational and Mass-Spectrometry-Based Workflow for the Discovery and Validation of Missing Human Proteins: Application to Chromosomes 2 and 14. J Proteome Res (2015) 14(9): 3621-34; PMID:26132440; doi: 10.1021/pr5010345. GPMDB files: 58.
856. Dislich B, Wohlrab F, Bachhuber T, Müller SA, Kuhn PH, Hogl S, Meyer-Luehmann M, Lichtenthaler SF, Label-free Quantitative Proteomics of Mouse Cerebrospinal Fluid Detects β-Site APP Cleaving Enzyme (BACE1) Protease Substrates In Vivo. Mol Cell Proteomics (2015) 14(10): 2550-63; PMID:26139848; doi: 10.1074/mcp.M114.041533. GPMDB files: 26.
857. Swaney DL, Rodríguez-Mias RA, Villén J, Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover. EMBO Rep (2015) 16(9): 1131-44; PMID:26142280; doi: 10.15252/embr.201540298. GPMDB files: 56.
858. Su N, Zhang C, Zhang Y, Wang Z, Fan F, Zhao M, Wu F, Gao Y, Li Y, Chen L, Tian M, Zhang T, Wen B, Sensang N, Xiong Z, Wu S, Liu S, Yang P, Zhen B, Zhu Y, He F, Xu P, Special Enrichment Strategies Greatly Increase the Efficiency of Missing Proteins Identification from Regular Proteome Samples. J Proteome Res (2015) 14(9): 3680-92; PMID:26144840; doi: 10.1021/acs.jproteome.5b00481. GPMDB files: 428.
859. Ajeian JN, Horton ER, Astudillo P, Byron A, Askari JA, Millon-Frémillon A, Knight D, Kimber SJ, Humphries MJ, Humphries JD, Proteomic analysis of integrin-associated complexes from mesenchymal stem cells. Proteomics Clin Appl (2016) 10(1): 51-7; PMID:26147903; doi: 10.1002/prca.201500033. GPMDB files: 177.
860. Hoover H, Li J, Marchese J, Rothwell C, Borawoski J, Jeffery DA, Gaither LA, Finkel N, Quantitative Proteomic Verification of Membrane Proteins as Potential Therapeutic Targets Located in the 11q13 Amplicon in Cancers. J Proteome Res (2015) 14(9): 3670-9; PMID:26151158; doi: 10.1021/acs.jproteome.5b00508. GPMDB files: 27.
861. Huber RJ, O'Day DH, Proteomic profiling of the extracellular matrix (slime sheath) of Dictyostelium discoideum. Proteomics (2015) 15(19): 3315-9; PMID:26152465; doi: 10.1002/pmic.201500143. GPMDB files: 23.
862. Moche M, Schlüter R, Bernhardt J, Plate K, Riedel K, Hecker M, Becher D, Time-Resolved Analysis of Cytosolic and Surface-Associated Proteins of Staphylococcus aureus HG001 under Planktonic and Biofilm Conditions. J Proteome Res (2015) 14(9): 3804-22; PMID:26152824; doi: 10.1021/acs.jproteome.5b00148. GPMDB files: 924.
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864. Jumeau F, Com E, Lane L, Duek P, Lagarrigue M, Lavigne R, Guillot L, Rondel K, Gateau A, Melaine N, Guével B, Sergeant N, Mitchell V, Pineau C, Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project. J Proteome Res (2015) 14(9): 3606-20; PMID:26168773; doi: 10.1021/acs.jproteome.5b00170. GPMDB files: 63.
865. Schiller HB, Fernandez IE, Burgstaller G, Schaab C, Scheltema RA, Schwarzmayr T, Strom TM, Eickelberg O, Mann M, Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair. Mol Syst Biol (2015) 11(7): 819; PMID:26174933. GPMDB files: 228.
866. Morley S, You S, Pollan S, Choi J, Zhou B, Hager MH, Steadman K, Spinelli C, Rajendran K, Gertych A, Kim J, Adam RM, Yang W, Krishnan R, Knudsen BS, Di Vizio D, Freeman MR, Regulation of microtubule dynamics by DIAPH3 influences amoeboid tumor cell mechanics and sensitivity to taxanes. Sci Rep (2015) 5: 12136; PMID:26179371; doi: 10.1038/srep12136. GPMDB files: 16.
867. Feng S, Powell SM, Wilson R, Bowman JP, Proteomic Insight into Functional Changes of Proteorhodopsin-Containing Bacterial Species Psychroflexus torquis under Different Illumination and Salinity Levels. J Proteome Res (2015) 14(9): 3848-58; PMID:26179671; doi: 10.1021/acs.jproteome.5b00241. GPMDB files: 72.
868. Selvan LD, Sreenivasamurthy SK, Kumar S, Yelamanchi SD, Madugundu AK, Anil AK, Renuse S, Nair BG, Gowda H, Mathur PP, Satishchandra P, Shankar SK, Mahadevan A, Keshava Prasad TS, Characterization of host response to Cryptococcus neoformans through quantitative proteomic analysis of cryptococcal meningitis co-infected with HIV. Mol Biosyst (2015) 11(9): 2529-40; PMID:26181685; doi: 10.1039/c5mb00187k. GPMDB files: 1.
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870. Bish R, Cuevas-Polo N, Cheng Z, Hambardzumyan D, Munschauer M, Landthaler M, Vogel C, Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins. Biomolecules (2015) 5(3): 1441-66; PMID:26184334; doi: 10.3390/biom5031441. GPMDB files: 50.
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942. Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H, Beli P, ATR inhibition rewires cellular signaling networks induced by replication stress. Proteomics (2015) ; PMID:26572502; doi: 10.1002/pmic.201500172. GPMDB files: 20.
943. Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE, The effect of microbial colonization on the host proteome varies by gastrointestinal location. ISME J (2015) ; PMID:26574685; doi: 10.1038/ismej.2015.187. GPMDB files: 45.
944. Latos PA, Sienerth AR, Murray A, Senner CE, Muto M, Ikawa M, Oxley D, Burge S, Cox BJ, Hemberger M, Elf5-centered transcription factor hub controls trophoblast stem cell self-renewal and differentiation through stoichiometry-sensitive shifts in target gene networks. Genes Dev (2015) 29(23): 2435-48; PMID:26584622; doi: 10.1101/gad.268821.115. GPMDB files: 6.
945. Cundiff JK, McConnell EJ, Lohe KJ, Maria SD, McMahon RJ, Zhang Q, Sensing Small Changes in Protein Abundance: Stimulation of Caco-2 Cells by Human Whey Proteins. J Proteome Res (2016) 15(1): 125-43; PMID:26586228; doi: 10.1021/acs.jproteome.5b00597. GPMDB files: 16.
946. Kudelko M, Chan CW, Sharma R, Yao Q, Lau E, Chu IK, Cheah KS, Tanner JA, Chan D, Label-Free Quantitative Proteomics Reveals Survival Mechanisms Developed by Hypertrophic Chondrocytes under ER Stress. J Proteome Res (2016) 15(1): 86-99; PMID:26587667; doi: 10.1021/acs.jproteome.5b00537. GPMDB files: 30.
947. Dammeier S, Nahnsen S, Veit J, Wehner F, Ueffing M, Kohlbacher O, Mass-Spectrometry-Based Proteomics Reveals Organ-Specific Expression Patterns To Be Used as Forensic Evidence. J Proteome Res (2016) 15(1): 182-92; PMID:26593679; doi: 10.1021/acs.jproteome.5b00704. GPMDB files: 88.
948. Basak T, Vega-Montoto L, Zimmerman LJ, Tabb DL, Hudson BG, Vanacore RM, Comprehensive Characterization of Glycosylation and Hydroxylation of Basement Membrane Collagen IV by High-Resolution Mass Spectrometry. J Proteome Res (2016) 15(1): 245-58; PMID:26593852; doi: 10.1021/acs.jproteome.5b00767. GPMDB files: 26.
949. Broncel M, Serwa RA, Bunney TD, Katan M, Tate EW, Global profiling of HYPE mediated AMPylation through a chemical proteomic approach. Mol Cell Proteomics (2015) ; PMID:26604261; doi: 10.1074/mcp.O115.054429. GPMDB files: 56.
950. Pankow S, Bamberger C, Calzolari D, Martínez-Bartolomé S, Lavallée-Adam M, Balch WE, Yates JR 3rd, ∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis. Nature (2015) 528(7583): 510-6; PMID:26618866; doi: 10.1038/nature15729. GPMDB files: 56.
951. Kennedy JJ, Yan P, Zhao L, Ivey RG, Voytovich UJ, Moore HD, Lin C, Pogosova-Agadjanyan EL, Stirewalt DL, Reding KW, Whiteaker JR, Paulovich AG, Immobilized metal affinity chromatography coupled to multiple reaction monitoring enables reproducible quantification of phospho-signaling. Mol Cell Proteomics (2015) ; PMID:26621847; doi: 10.1074/mcp.O115.054940. GPMDB files: 114.
952. Urfer M, Bogdanovic J, Lo Monte F, Moehle K, Zerbe K, Omasits U, Ahrens CH, Pessi G, Eberl L, Robinson JA, A Peptidomimetic Antibiotic Targets Outer Membrane Proteins and Disrupts Selectively the Outer Membrane in Escherichia coli. J Biol Chem (2015) ; PMID:26627837; doi: 10.1074/jbc.M115.691725. GPMDB files: 59.
953. Krogager TP, Nielsen LV, Kahveci D, Dyrlund TF, Scavenius C, Sanggaard KW, Enghild JJ, Hepatocytes respond differently to major dietary trans fatty acid isomers, elaidic acid and trans-vaccenic acid. Proteome Sci (2015) 13: 31; PMID:26628894; doi: 10.1186/s12953-015-0084-3. GPMDB files: 95.
954. Xu B, Xiong F, Tian R, Zhan S, Gao Y, Qiu W, Wang R, Ge W, Ma C, Temporal lobe in human aging: A quantitative protein profiling study of samples from Chinese Human Brain Bank. Exp Gerontol (2015) 73: 31-41; PMID:26631761; doi: 10.1016/j.exger.2015.11.016. GPMDB files: 1.
955. Aguado BA, Wu JJ, Azarin SM, Nanavati D, Rao SS, Bushnell GG, Medicherla CB, Shea LD, Secretome identification of immune cell factors mediating metastatic cell homing. Sci Rep (2015) 5: 17566; PMID:26634905; doi: 10.1038/srep17566. GPMDB files: 6.
956. Padden J, Ahrens M, Kälsch J, Bertram S, Megger DA, Bracht T, Eisenacher M, Kocabayoglu P, Meyer HE, Sipos B, Baba HA, Sitek B, Immunohistochemical Markers Distinguishing Cholangiocellular Carcinoma from Pancreatic Ductal Adenocarcinoma Discovered by Proteomic Analysis of Microdissected Cells. Mol Cell Proteomics (2015) ; PMID:26644413; doi: 10.1074/mcp.M115.054585. GPMDB files: 66.
957. Kasvandik S, Samuel K, Peters M, Eimre M, Peet N, Roost AM, Padrik L, Paju K, Peil L, Salumets A, Deep Quantitative Proteomics Reveals Extensive Metabolic Reprogramming and Cancer-Like Changes of Ectopic Endometriotic Stromal Cells. J Proteome Res (2015) ; PMID:26654049; doi: 10.1021/acs.jproteome.5b00965. GPMDB files: 21.
958. Farina F, Gaillard J, Guérin C, Couté Y, Sillibourne J, Blanchoin L, Théry M, The centrosome is an actin-organizing centre. Nat Cell Biol (2016) 18(1): 65-75; PMID:26655833; doi: 10.1038/ncb3285. GPMDB files: 2.
959. Giguère SS, Guise AJ, Jean Beltran PM, Joshi PM, Greco TM, Quach OL, Kong J, Cristea IM, The proteomic profile of deleted in breast cancer 1 (DBC1) interactions points to a multi-faceted regulation of gene expression. Mol Cell Proteomics (2015) ; PMID:26657080; doi: 10.1074/mcp.M115.054619. GPMDB files: 109.
960. Su S, Zhu X, Lin L, Chen X, Wang Y, Zi J, Dong Y, Xie Y, Zhu Y, Zhang J, Zhu J, Xu D, Xu N, Lou X, Liu S, Lowering endogenous cathepsin D abundance results in ROS accumulation and cell senescence. Mol Cell Proteomics (2015) ; PMID:26657266; doi: 10.1074/mcp.M115.050179. GPMDB files: 154.
961. Chen M, Hu Y, Liu J, Wu Q, Zhang C, Yu J, Xiao J, Wei F, Wu J, Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome. Sci Rep (2015) 5: 18019; PMID:26658305; doi: 10.1038/srep18019. GPMDB files: 36.
962. Mizuno Y, Nagano-Shoji M, Kubo S, Kawamura Y, Yoshida A, Kawasaki H, Nishiyama M, Yoshida M, Kosono S, Altered acetylation and succinylation profiles in Corynebacterium glutamicum in response to conditions inducing glutamate overproduction. Microbiologyopen (2015) ; PMID:26663479; doi: 10.1002/mbo3.320. GPMDB files: 10.
963. Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC, The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast. Nucleic Acids Res (2015) ; PMID:26682798; doi: 10.1093/nar/gkv1473. GPMDB files: 4.
964. Rudney JD, Jagtap PD, Reilly CS, Chen R, Markowski TW, Higgins L, Johnson JE, Griffin TJ, Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries. Microbiome (2015) 3(1): 69; PMID:26684897; doi: 10.1186/s40168-015-0136-z. GPMDB files: 24.
965. Debaisieux S, Encheva V, Chakravarty P, Snijders AP, Schiavo G, Analysis of signaling endosome composition and dynamics using SILAC in embryonic stem cell-derived neurons. Mol Cell Proteomics (2015) ; PMID:26685126; doi: 10.1074/mcp.M115.051649. GPMDB files: 28.
966. Oberbach A, Adams V, Schlichting N, Heinrich M, Kullnick Y, Lehmann S, Lehmann S, Feder S, Correia JC, Mohr FW, Völker U, Jehmlich N, Proteome profiles of HDL particles of patients with chronic heart failure are associated with immune response and also include bacteria proteins. Clin Chim Acta (2015) 453: 114-122; PMID:26688386; doi: 10.1016/j.cca.2015.12.005. GPMDB files: 10.
967. Eitzinger N, Wagner V, Weisheit W, Geimer S, Boness D, Kreimer G, Mittag M, Proteomic Analysis of a Fraction with Intact Eyespots of Chlamydomonas reinhardtii and Assignment of Protein Methylation. Front Plant Sci (2015) 6: 1085; PMID:26697039; doi: 10.3389/fpls.2015.01085. GPMDB files: 128.
968. Kozlov SV, Waardenberg AJ, Engholm-Keller K, Arthur JW, Graham ME, Lavin MF, ROS-activated ATM-dependent phosphorylation of cytoplasmic substrates identified by large scale phosphoproteomics screen. Mol Cell Proteomics (2015) ; PMID:26699800; doi: 10.1074/mcp.M115.055723. GPMDB files: 141.
969. Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L, Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome. Proteomics (2015) ; PMID:26702875; doi: 10.1002/pmic.201500187. GPMDB files: 2.
970. Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S, Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains. Mol Cell (2016) 61(1): 125-37; PMID:26711008; doi: 10.1016/j.molcel.2015.11.016. GPMDB files: 44.
971. Bigenzahn JW, Fauster A, Rebsamen M, Kandasamy RK, Scorzoni S, Vladimer GI, Mueller AC, Gstaiger M, Zuber J, Bennett KL, Superti-Furga G, An inducible retroviral expression system for tandem affinity purification mass-spectrometry-based proteomics identifies MLKL as an HSP90 client. Mol Cell Proteomics (2015) ; PMID:26714523; doi: 10.1074/mcp.O115.055350. GPMDB files: 16.
972. Bode D, Yu L, Tate P, Pardo M, Choudhary JS, Characterisation of two distinct Nucleosome Remodelling and Deacetylase Complex (NuRD) assemblies in embryonic stem cells. Mol Cell Proteomics (2015) ; PMID:26714524; doi: 10.1074/mcp.M115.053207. GPMDB files: 179.
973. Li Q, Chang Z, Oliveira G, Xiong M, Smith LM, Frey BL, Welham NV, Protein turnover during in vitro tissue engineering. Biomaterials (2015) 81: 104-113; PMID:26724458; doi: 10.1016/j.biomaterials.2015.12.004. GPMDB files: 66.
974. Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T, Proteomic maps of breast cancer subtypes. Nat Commun (2016) 7: 10259; PMID:26725330; doi: 10.1038/ncomms10259. GPMDB files: 207.
975. Guo Z, Kong Q, Liu C, Zhang S, Zou L, Yan F, Whitmire JK, Xiong Y, Chen X, Wan YY, DCAF1 controls T-cell function via p53-dependent and -independent mechanisms. Nat Commun (2016) 7: 10307; PMID:26728942; doi: 10.1038/ncomms10307. GPMDB files: 118.
976. Clark DJ, Fondrie WE, Yang A, Mao L, Triple SILAC quantitative proteomic analysis reveals differential abundance of cell signaling proteins between normal and lung cancer-derived exosomes. J Proteomics (2015) ; PMID:26739763; doi: 10.1016/j.jprot.2015.12.023. GPMDB files: 3.