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==Data from publications== | ==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 | + | 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 August 1, 2016. |
#Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." <i>Infect Immun</i> <b>57</b>(3):999–1001; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2645217 2645217]; GPMDB: [http://gpmdb.org/data/keyword/2645217 66]. | #Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." <i>Infect Immun</i> <b>57</b>(3):999–1001; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2645217 2645217]; GPMDB: [http://gpmdb.org/data/keyword/2645217 66]. | ||
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#Corradini E, Burgers PP, Plank M, Heck AJ, Scholten A, (2015) "Huntingtin-associated protein 1 (HAP1) is a cGMP-dependent kinase anchoring protein (GKAP) specific for the cGMP-dependent protein kinase Iβ isoform." <i>J Biol Chem</i> <b>290</b>(12):7887–96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25653285 25653285]; doi: [https://dx.doi.org/10.1074/jbc.M114.622613 10.1074/jbc.M114.622613]; GPMDB: [http://gpmdb.org/data/keyword/25653285 6]. | #Corradini E, Burgers PP, Plank M, Heck AJ, Scholten A, (2015) "Huntingtin-associated protein 1 (HAP1) is a cGMP-dependent kinase anchoring protein (GKAP) specific for the cGMP-dependent protein kinase Iβ isoform." <i>J Biol Chem</i> <b>290</b>(12):7887–96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25653285 25653285]; doi: [https://dx.doi.org/10.1074/jbc.M114.622613 10.1074/jbc.M114.622613]; GPMDB: [http://gpmdb.org/data/keyword/25653285 6]. | ||
#Sandin M, Chawade A, Levander F, (2015) "Is label-free LC-MS/MS ready for biomarker discovery?" <i>Proteomics Clin Appl</i> <b>9</b>(3-4):289–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25656266 25656266]; doi: [https://dx.doi.org/10.1002/prca.201400202 10.1002/prca.201400202]; GPMDB: [http://gpmdb.org/data/keyword/25656266 2]. | #Sandin M, Chawade A, Levander F, (2015) "Is label-free LC-MS/MS ready for biomarker discovery?" <i>Proteomics Clin Appl</i> <b>9</b>(3-4):289–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25656266 25656266]; doi: [https://dx.doi.org/10.1002/prca.201400202 10.1002/prca.201400202]; GPMDB: [http://gpmdb.org/data/keyword/25656266 2]. | ||
+ | #Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y, (2015) "Genomic variation. Impact of regulatory variation from RNA to protein." <i>Science</i> <b>347</b>(6222):664–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25657249 25657249]; doi: [https://dx.doi.org/10.1126/science.1260793 10.1126/science.1260793]; GPMDB: [http://gpmdb.org/data/keyword/25657249 2622]. | ||
#Hill RC, Calle EA, Dzieciatkowska M, Niklason LE, Hansen KC, (2015) "Quantification of extracellular matrix proteins from a rat lung scaffold to provide a molecular readout for tissue engineering." <i>Mol Cell Proteomics</i> <b>14</b>(4):961–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25660013 25660013]; doi: [https://dx.doi.org/10.1074/mcp.M114.045260 10.1074/mcp.M114.045260]; GPMDB: [http://gpmdb.org/data/keyword/25660013 60]. | #Hill RC, Calle EA, Dzieciatkowska M, Niklason LE, Hansen KC, (2015) "Quantification of extracellular matrix proteins from a rat lung scaffold to provide a molecular readout for tissue engineering." <i>Mol Cell Proteomics</i> <b>14</b>(4):961–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25660013 25660013]; doi: [https://dx.doi.org/10.1074/mcp.M114.045260 10.1074/mcp.M114.045260]; GPMDB: [http://gpmdb.org/data/keyword/25660013 60]. | ||
#Médard G, Pachl F, Ruprecht B, Klaeger S, Heinzlmeir S, Helm D, Qiao H, Ku X, Wilhelm M, Kuehne T, Wu Z, Dittmann A, Hopf C, Kramer K, Kuster B, (2015) "Optimized chemical proteomics assay for kinase inhibitor profiling." <i>J Proteome Res</i> <b>14</b>(3):1574–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25660469 25660469]; doi: [https://dx.doi.org/10.1021/pr5012608 10.1021/pr5012608]; GPMDB: [http://gpmdb.org/data/keyword/25660469 126]. | #Médard G, Pachl F, Ruprecht B, Klaeger S, Heinzlmeir S, Helm D, Qiao H, Ku X, Wilhelm M, Kuehne T, Wu Z, Dittmann A, Hopf C, Kramer K, Kuster B, (2015) "Optimized chemical proteomics assay for kinase inhibitor profiling." <i>J Proteome Res</i> <b>14</b>(3):1574–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25660469 25660469]; doi: [https://dx.doi.org/10.1021/pr5012608 10.1021/pr5012608]; GPMDB: [http://gpmdb.org/data/keyword/25660469 126]. | ||
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#Moche M, Schlüter R, Bernhardt J, Plate K, Riedel K, Hecker M, Becher D, (2015) "Time-Resolved Analysis of Cytosolic and Surface-Associated Proteins of Staphylococcus aureus HG001 under Planktonic and Biofilm Conditions." <i>J Proteome Res</i> <b>14</b>(9):3804–22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26152824 26152824]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00148 10.1021/acs.jproteome.5b00148]; GPMDB: [http://gpmdb.org/data/keyword/26152824 924]. | #Moche M, Schlüter R, Bernhardt J, Plate K, Riedel K, Hecker M, Becher D, (2015) "Time-Resolved Analysis of Cytosolic and Surface-Associated Proteins of Staphylococcus aureus HG001 under Planktonic and Biofilm Conditions." <i>J Proteome Res</i> <b>14</b>(9):3804–22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26152824 26152824]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00148 10.1021/acs.jproteome.5b00148]; GPMDB: [http://gpmdb.org/data/keyword/26152824 924]. | ||
#Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R, (2015) "An open-source computational and data resource to analyze digital maps of immunopeptidomes." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26154972 26154972]; doi: [https://dx.doi.org/10.7554/eLife.07661 10.7554/eLife.07661]; GPMDB: [http://gpmdb.org/data/keyword/26154972 70]. | #Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R, (2015) "An open-source computational and data resource to analyze digital maps of immunopeptidomes." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26154972 26154972]; doi: [https://dx.doi.org/10.7554/eLife.07661 10.7554/eLife.07661]; GPMDB: [http://gpmdb.org/data/keyword/26154972 70]. | ||
+ | #Stroud DA, Maher MJ, Lindau C, Vögtle FN, Frazier AE, Surgenor E, Mountford H, Singh AP, Bonas M, Oeljeklaus S, Warscheid B, Meisinger C, Thorburn DR, Ryan MT, (2015) "COA6 is a mitochondrial complex IV assembly factor critical for biogenesis of mtDNA-encoded COX2." <i>Hum Mol Genet</i> <b>24</b>(19):5404–15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26160915 26160915]; doi: [https://dx.doi.org/10.1093/hmg/ddv265 10.1093/hmg/ddv265]; GPMDB: [http://gpmdb.org/data/keyword/26160915 14]. | ||
#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, (2015) "Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project." <i>J Proteome Res</i> <b>14</b>(9):3606–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26168773 26168773]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00170 10.1021/acs.jproteome.5b00170]; GPMDB: [http://gpmdb.org/data/keyword/26168773 63]. | #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, (2015) "Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project." <i>J Proteome Res</i> <b>14</b>(9):3606–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26168773 26168773]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00170 10.1021/acs.jproteome.5b00170]; GPMDB: [http://gpmdb.org/data/keyword/26168773 63]. | ||
#Schiller HB, Fernandez IE, Burgstaller G, Schaab C, Scheltema RA, Schwarzmayr T, Strom TM, Eickelberg O, Mann M, (2015) "Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair." <i>Mol Syst Biol</i> <b>11</b>(7):819; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26174933 26174933]; GPMDB: [http://gpmdb.org/data/keyword/26174933 228]. | #Schiller HB, Fernandez IE, Burgstaller G, Schaab C, Scheltema RA, Schwarzmayr T, Strom TM, Eickelberg O, Mann M, (2015) "Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair." <i>Mol Syst Biol</i> <b>11</b>(7):819; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26174933 26174933]; GPMDB: [http://gpmdb.org/data/keyword/26174933 228]. | ||
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#Kieselbach T, Zijnge V, Granström E, Oscarsson J, (2015) "Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles." <i>PLoS One</i> <b>10</b>(9):e0138591; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26381655 26381655]; doi: [https://dx.doi.org/10.1371/journal.pone.0138591 10.1371/journal.pone.0138591]; GPMDB: [http://gpmdb.org/data/keyword/26381655 5]. | #Kieselbach T, Zijnge V, Granström E, Oscarsson J, (2015) "Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles." <i>PLoS One</i> <b>10</b>(9):e0138591; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26381655 26381655]; doi: [https://dx.doi.org/10.1371/journal.pone.0138591 10.1371/journal.pone.0138591]; GPMDB: [http://gpmdb.org/data/keyword/26381655 5]. | ||
#Goris T, Schiffmann CL, Gadkari J, Schubert T, Seifert J, Jehmlich N, von Bergen M, Diekert G, (2015) "Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates." <i>Sci Rep</i> <b>5</b>:13794; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26387727 26387727]; doi: [https://dx.doi.org/10.1038/srep13794 10.1038/srep13794]; GPMDB: [http://gpmdb.org/data/keyword/26387727 36]. | #Goris T, Schiffmann CL, Gadkari J, Schubert T, Seifert J, Jehmlich N, von Bergen M, Diekert G, (2015) "Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates." <i>Sci Rep</i> <b>5</b>:13794; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26387727 26387727]; doi: [https://dx.doi.org/10.1038/srep13794 10.1038/srep13794]; GPMDB: [http://gpmdb.org/data/keyword/26387727 36]. | ||
- | #Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R, (2015) "Kinome-wide decoding of network-attacking mutations rewiring cancer signaling." <i>Cell</i> <b>163</b>(1):202–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26388441 26388441]; doi: [https://dx.doi.org/10.1016/j.cell.2015.08.056 10.1016/j.cell.2015.08.056]; GPMDB: [http://gpmdb.org/data/keyword/26388441 | + | #Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R, (2015) "Kinome-wide decoding of network-attacking mutations rewiring cancer signaling." <i>Cell</i> <b>163</b>(1):202–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26388441 26388441]; doi: [https://dx.doi.org/10.1016/j.cell.2015.08.056 10.1016/j.cell.2015.08.056]; GPMDB: [http://gpmdb.org/data/keyword/26388441 12]. |
#Paulo JA, O'Connell JD, Gaun A, Gygi SP, (2015) "Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae." <i>Mol Biol Cell</i> <b>26</b>(22):4063–74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26399295 26399295]; doi: [https://dx.doi.org/10.1091/mbc.E15-07-0499 10.1091/mbc.E15-07-0499]; GPMDB: [http://gpmdb.org/data/keyword/26399295 1]. | #Paulo JA, O'Connell JD, Gaun A, Gygi SP, (2015) "Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae." <i>Mol Biol Cell</i> <b>26</b>(22):4063–74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26399295 26399295]; doi: [https://dx.doi.org/10.1091/mbc.E15-07-0499 10.1091/mbc.E15-07-0499]; GPMDB: [http://gpmdb.org/data/keyword/26399295 1]. | ||
#Liu T, Tian CF, Chen WX, (2015) "Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase." <i>PLoS One</i> <b>10</b>(9):e0139143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26401955 26401955]; doi: [https://dx.doi.org/10.1371/journal.pone.0139143 10.1371/journal.pone.0139143]; GPMDB: [http://gpmdb.org/data/keyword/26401955 2]. | #Liu T, Tian CF, Chen WX, (2015) "Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase." <i>PLoS One</i> <b>10</b>(9):e0139143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26401955 26401955]; doi: [https://dx.doi.org/10.1371/journal.pone.0139143 10.1371/journal.pone.0139143]; GPMDB: [http://gpmdb.org/data/keyword/26401955 2]. | ||
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#Yu J, Storer BE, Kushekhar K, Abu Zaid M, Zhang Q, Gafken PR, Ogata Y, Martin PJ, Flowers ME, Hansen JA, Arora M, Cutler C, Jagasia M, Pidala J, Hamilton BK, Chen GL, Pusic I, Lee SJ, Paczesny S, (2016) "Biomarker Panel for Chronic Graft-Versus-Host Disease." <i>J Clin Oncol</i> <b>34</b>(22):2583–90; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27217465 27217465]; doi: [https://dx.doi.org/10.1200/JCO.2015.65.9615 10.1200/JCO.2015.65.9615]; GPMDB: [http://gpmdb.org/data/keyword/27217465 3]. | #Yu J, Storer BE, Kushekhar K, Abu Zaid M, Zhang Q, Gafken PR, Ogata Y, Martin PJ, Flowers ME, Hansen JA, Arora M, Cutler C, Jagasia M, Pidala J, Hamilton BK, Chen GL, Pusic I, Lee SJ, Paczesny S, (2016) "Biomarker Panel for Chronic Graft-Versus-Host Disease." <i>J Clin Oncol</i> <b>34</b>(22):2583–90; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27217465 27217465]; doi: [https://dx.doi.org/10.1200/JCO.2015.65.9615 10.1200/JCO.2015.65.9615]; GPMDB: [http://gpmdb.org/data/keyword/27217465 3]. | ||
#Wang B, Pfeiffer MJ, Drexler HC, Fuellen G, Boiani M, (2016) "Proteomic Analysis of Mouse Oocytes Identifies PRMT7 as a Reprogramming Factor that Replaces SOX2 in the Induction of Pluripotent Stem Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27225728 27225728]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01083 10.1021/acs.jproteome.5b01083]; GPMDB: [http://gpmdb.org/data/keyword/27225728 14]. | #Wang B, Pfeiffer MJ, Drexler HC, Fuellen G, Boiani M, (2016) "Proteomic Analysis of Mouse Oocytes Identifies PRMT7 as a Reprogramming Factor that Replaces SOX2 in the Induction of Pluripotent Stem Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27225728 27225728]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01083 10.1021/acs.jproteome.5b01083]; GPMDB: [http://gpmdb.org/data/keyword/27225728 14]. | ||
+ | #Lobas AA, Karpov DS, Kopylov AT, Solovyeva EM, Ivanov MV, Ilina IY, Lazarev VN, Kuznetsova KG, Ilgisonis EV, Zgoda VG, Gorshkov MV, Moshkovskii SA, (2016) "Exome-based proteogenomics of HEK-293 human cell line: Coding genomic variants identified at the level of shotgun proteome." <i>Proteomics</i> <b>16</b>(14):1980–91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27233776 27233776]; doi: [https://dx.doi.org/10.1002/pmic.201500349 10.1002/pmic.201500349]; GPMDB: [http://gpmdb.org/data/keyword/27233776 7]. | ||
#Lodrini M, Poschmann G, Schmidt V, Wünschel J, Dreidax D, Witt O, Höfer T, Meyer HE, Stühler K, Eggert A, Deubzer HE, (2016) "Minichromosome Maintenance Complex Is a Critical Node in the miR-183 Signaling Network of MYCN-Amplified Neuroblastoma Cells." <i>J Proteome Res</i> <b>15</b>(7):2178–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27239679 27239679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00134 10.1021/acs.jproteome.6b00134]; GPMDB: [http://gpmdb.org/data/keyword/27239679 12]. | #Lodrini M, Poschmann G, Schmidt V, Wünschel J, Dreidax D, Witt O, Höfer T, Meyer HE, Stühler K, Eggert A, Deubzer HE, (2016) "Minichromosome Maintenance Complex Is a Critical Node in the miR-183 Signaling Network of MYCN-Amplified Neuroblastoma Cells." <i>J Proteome Res</i> <b>15</b>(7):2178–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27239679 27239679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00134 10.1021/acs.jproteome.6b00134]; GPMDB: [http://gpmdb.org/data/keyword/27239679 12]. | ||
#Bullen JW, Tchernyshyov I, Holewinski RJ, DeVine L, Wu F, Venkatraman V, Kass DL, Cole RN, Van Eyk J, Semenza GL, (2016) "Protein kinase A-dependent phosphorylation stimulates the transcriptional activity of hypoxia-inducible factor 1." <i>Sci Signal</i> <b>9</b>(430):ra56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27245613 27245613]; doi: [https://dx.doi.org/10.1126/scisignal.aaf0583 10.1126/scisignal.aaf0583]; GPMDB: [http://gpmdb.org/data/keyword/27245613 14]. | #Bullen JW, Tchernyshyov I, Holewinski RJ, DeVine L, Wu F, Venkatraman V, Kass DL, Cole RN, Van Eyk J, Semenza GL, (2016) "Protein kinase A-dependent phosphorylation stimulates the transcriptional activity of hypoxia-inducible factor 1." <i>Sci Signal</i> <b>9</b>(430):ra56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27245613 27245613]; doi: [https://dx.doi.org/10.1126/scisignal.aaf0583 10.1126/scisignal.aaf0583]; GPMDB: [http://gpmdb.org/data/keyword/27245613 14]. | ||
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#Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of novel pancreatic ductal adenocarcinoma subtypes by global phosphotyrosine profiling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [http://gpmdb.org/data/keyword/27259358 112]. | #Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of novel pancreatic ductal adenocarcinoma subtypes by global phosphotyrosine profiling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [http://gpmdb.org/data/keyword/27259358 112]. | ||
#Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W, (2016) "Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2]. | #Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W, (2016) "Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2]. | ||
+ | #Gnad F, Doll S, Song K, Stokes MP, Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M, (2016) "Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms." <i>Proteomics</i> <b>16</b>(14):1998–2004; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27273156 27273156]; doi: [https://dx.doi.org/10.1002/pmic.201600119 10.1002/pmic.201600119]; GPMDB: [http://gpmdb.org/data/keyword/27273156 56]. | ||
+ | #Gnad F, Wallin J, Edgar K, Doll S, Arnott D, Robillard L, Kirkpatrick DS, Stokes MP, Vijapurkar U, Hatzivassiliou G, Friedman LS, Belvin M, (2016) "Quantitative phosphoproteomic analysis of the PI3K-regulated signaling network." <i>Proteomics</i> <b>16</b>(14):1992–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27282143 27282143]; doi: [https://dx.doi.org/10.1002/pmic.201600118 10.1002/pmic.201600118]; GPMDB: [http://gpmdb.org/data/keyword/27282143 72]. | ||
#Prendergast L, Müller S, Liu Y, Huang H, Dingli F, Loew D, Vassias I, Patel DJ, Sullivan KF, Almouzni G, (2016) "The CENP-T/-W complex is a binding partner of the histone chaperone FACT." <i>Genes Dev</i> <b>30</b>(11):1313–26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27284163 27284163]; doi: [https://dx.doi.org/10.1101/gad.275073.115 10.1101/gad.275073.115]; GPMDB: [http://gpmdb.org/data/keyword/27284163 47]. | #Prendergast L, Müller S, Liu Y, Huang H, Dingli F, Loew D, Vassias I, Patel DJ, Sullivan KF, Almouzni G, (2016) "The CENP-T/-W complex is a binding partner of the histone chaperone FACT." <i>Genes Dev</i> <b>30</b>(11):1313–26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27284163 27284163]; doi: [https://dx.doi.org/10.1101/gad.275073.115 10.1101/gad.275073.115]; GPMDB: [http://gpmdb.org/data/keyword/27284163 47]. | ||
#Wiśniewski JR, Mann M, (2016) "A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting." <i>J Proteome Res</i> <b>15</b>(7):2321–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27297043 27297043]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00403 10.1021/acs.jproteome.6b00403]; GPMDB: [http://gpmdb.org/data/keyword/27297043 64]. | #Wiśniewski JR, Mann M, (2016) "A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting." <i>J Proteome Res</i> <b>15</b>(7):2321–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27297043 27297043]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00403 10.1021/acs.jproteome.6b00403]; GPMDB: [http://gpmdb.org/data/keyword/27297043 64]. | ||
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#Ashford P, Hernandez A, Greco TM, Buch A, Sodeik B, Cristea IM, Grunewald K, Shepherd A, Topf M, (2016) "HVint: A strategy for identifying novel protein-protein interactions in herpes simplex virus type 1." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27384951 27384951]; doi: [https://dx.doi.org/10.1074/mcp.M116.058552 10.1074/mcp.M116.058552]; GPMDB: [http://gpmdb.org/data/keyword/27384951 19]. | #Ashford P, Hernandez A, Greco TM, Buch A, Sodeik B, Cristea IM, Grunewald K, Shepherd A, Topf M, (2016) "HVint: A strategy for identifying novel protein-protein interactions in herpes simplex virus type 1." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27384951 27384951]; doi: [https://dx.doi.org/10.1074/mcp.M116.058552 10.1074/mcp.M116.058552]; GPMDB: [http://gpmdb.org/data/keyword/27384951 19]. | ||
#Picariello G, Addeo F, Ferranti P, Nocerino R, Paparo L, Passariello A, Dallas DC, Robinson RC, Barile D, Canani RB, (2016) "Antibody-independent identification of bovine milk-derived peptides in breast-milk." <i>Food Funct</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27396729 27396729]; doi: [https://dx.doi.org/10.1039/c6fo00731g 10.1039/c6fo00731g]; GPMDB: [http://gpmdb.org/data/keyword/27396729 12]. | #Picariello G, Addeo F, Ferranti P, Nocerino R, Paparo L, Passariello A, Dallas DC, Robinson RC, Barile D, Canani RB, (2016) "Antibody-independent identification of bovine milk-derived peptides in breast-milk." <i>Food Funct</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27396729 27396729]; doi: [https://dx.doi.org/10.1039/c6fo00731g 10.1039/c6fo00731g]; GPMDB: [http://gpmdb.org/data/keyword/27396729 12]. | ||
- | #Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M, (2016) "Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development." <i>Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27397507 27397507]; doi: [https://dx.doi.org/10.1016/j.cell.2016.06.015 10.1016/j.cell.2016.06.015]; GPMDB: [http://gpmdb.org/data/keyword/27397507 18]. | + | #Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M, (2016) "Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development." <i>Cell</i> <b>166</b>(3):664–678; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27397507 27397507]; doi: [https://dx.doi.org/10.1016/j.cell.2016.06.015 10.1016/j.cell.2016.06.015]; GPMDB: [http://gpmdb.org/data/keyword/27397507 18]. |
- | #Shraibman B, Melamed Kadosh D, Barnea E, Admon A, (2016) "HLA peptides derived from tumor antigens induced by inhibition of DNA methylation for development of drug-facilitated immunotherapy." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27412690 27412690]; doi: [https://dx.doi.org/10.1074/mcp.M116.060350 10.1074/mcp.M116.060350]; GPMDB: [http://gpmdb.org/data/keyword/27412690 | + | #Shraibman B, Melamed Kadosh D, Barnea E, Admon A, (2016) "HLA peptides derived from tumor antigens induced by inhibition of DNA methylation for development of drug-facilitated immunotherapy." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27412690 27412690]; doi: [https://dx.doi.org/10.1074/mcp.M116.060350 10.1074/mcp.M116.060350]; GPMDB: [http://gpmdb.org/data/keyword/27412690 60]. |
#Müller S, Balaz M, Stefanicka P, Varga L, Amri EZ, Ukropec J, Wollscheid B, Wolfrum C, (2016) "Proteomic Analysis of Human Brown Adipose Tissue Reveals Utilization of Coupled and Uncoupled Energy Expenditure Pathways." <i>Sci Rep</i> <b>6</b>:30030; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418403 27418403]; doi: [https://dx.doi.org/10.1038/srep30030 10.1038/srep30030]; GPMDB: [http://gpmdb.org/data/keyword/27418403 32]. | #Müller S, Balaz M, Stefanicka P, Varga L, Amri EZ, Ukropec J, Wollscheid B, Wolfrum C, (2016) "Proteomic Analysis of Human Brown Adipose Tissue Reveals Utilization of Coupled and Uncoupled Energy Expenditure Pathways." <i>Sci Rep</i> <b>6</b>:30030; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418403 27418403]; doi: [https://dx.doi.org/10.1038/srep30030 10.1038/srep30030]; GPMDB: [http://gpmdb.org/data/keyword/27418403 32]. | ||
+ | #Petrera A, Kern U, Linz D, Gomez-Auli A, Hohl M, Gassenhuber J, Sadowski T, Schilling O, (2016) "Proteomic Profiling of Cardiomyocyte-Specific Cathepsin A Overexpression Links Cathepsin A to the Oxidative Stress Response." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432266 27432266]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00413 10.1021/acs.jproteome.6b00413]; GPMDB: [http://gpmdb.org/data/keyword/27432266 3]. | ||
+ | #Zhou Y, Xiong L, Zhang Y, Yu R, Jiang X, Xu G, (2016) "Quantitative proteomics identifies myoferlin as a novel regulator of A Disintegrin and Metalloproteinase 12 in HeLa cells." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432471 27432471]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.07.015 10.1016/j.jprot.2016.07.015]; GPMDB: [http://gpmdb.org/data/keyword/27432471 14]. | ||
+ | #Suárez-Cortes P, Sharma V, Bertuccini L, Costa G, Bannerman NL, Sannella AR, Williamson K, Klemba M, Levashina EA, Lasonder E, Alano P, (2016) "Comparative proteomics and functional analysis reveal a role of P. falciparum osmiophilic bodies in malaria parasite transmission." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432909 27432909]; doi: [https://dx.doi.org/10.1074/mcp.M116.060681 10.1074/mcp.M116.060681]; GPMDB: [http://gpmdb.org/data/keyword/27432909 162]. | ||
+ | #Vandenbrouck Y, Lane L, Carapito C, Duek P, Rondel K, Bruley C, Macron C, Gonzalez de Peredo A, Couté Y, Chaoui K, Com E, Gateau A, Hesse AM, Marcellin M, Mear L, Mouton-Barbosa E, Robin T, Burlet-Schiltz O, Cianférani S, Ferro M, Freour T, Lindskog C, Garin J, Pineau C, (2016) "Looking for missing proteins in the proteome of human spermatozoa: an update." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27444420 27444420]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00400 10.1021/acs.jproteome.6b00400]; GPMDB: [http://gpmdb.org/data/keyword/27444420 108]. |
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.
Contents |
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 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 August 1, 2016.