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| | 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. | | 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. |
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| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/12177431' target='_gpmdb'>498</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/15362891' target='_gpmdb'>6</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/15561729' target='_gpmdb'>1</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/15619294' target='_gpmdb'>37</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/15822933' target='_gpmdb'>4</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/16118637' target='_gpmdb'>30</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/16446289' target='_gpmdb'>75</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/16470658' target='_gpmdb'>1603</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/16674103' target='_gpmdb'>3</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/16804162' target='_gpmdb'>32</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/16927433' target='_gpmdb'>296</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/16964243' target='_gpmdb'>31</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/16969339' target='_gpmdb'>27</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/17164401' target='_gpmdb'>314</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/17189379' target='_gpmdb'>1</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/17203963' target='_gpmdb'>176</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/17242355' target='_gpmdb'>1</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/17326674' target='_gpmdb'>10</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/17431180' target='_gpmdb'>2</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/17446864' target='_gpmdb'>24</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/17450130' target='_gpmdb'>1907</a>. |
| - | #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. | + | #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: <a href='http://gpmdb.org/data/keyword/17519225' target='_gpmdb'>2299</a>. |
| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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| - | #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.
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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.
The following public data repositories are checked daily for new suitable raw data for reanalysis:
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.
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.
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.
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.