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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 August | + | 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 8, 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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#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 40]. |
#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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#Taha MK, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane AE, Frosch M, Hellenbrand W, Hong E, Parent du Châtelet I, Prior K, Harmsen D, Vogel U, (2016) "Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men." <i>PLoS One</i> <b>11</b>(5):e0154047; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27167067 27167067]; doi: [https://dx.doi.org/10.1371/journal.pone.0154047 10.1371/journal.pone.0154047]; GPMDB: [http://gpmdb.org/data/keyword/27167067 12]. | #Taha MK, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane AE, Frosch M, Hellenbrand W, Hong E, Parent du Châtelet I, Prior K, Harmsen D, Vogel U, (2016) "Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men." <i>PLoS One</i> <b>11</b>(5):e0154047; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27167067 27167067]; doi: [https://dx.doi.org/10.1371/journal.pone.0154047 10.1371/journal.pone.0154047]; GPMDB: [http://gpmdb.org/data/keyword/27167067 12]. | ||
#Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG, (2016) "Proteomic investigation of the secretome of Cellvibrio japonicus during growth on chitin." <i>Proteomics</i> <b>16</b>(13):1904–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27169553 27169553]; doi: [https://dx.doi.org/10.1002/pmic.201500419 10.1002/pmic.201500419]; GPMDB: [http://gpmdb.org/data/keyword/27169553 18]. | #Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG, (2016) "Proteomic investigation of the secretome of Cellvibrio japonicus during growth on chitin." <i>Proteomics</i> <b>16</b>(13):1904–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27169553 27169553]; doi: [https://dx.doi.org/10.1002/pmic.201500419 10.1002/pmic.201500419]; GPMDB: [http://gpmdb.org/data/keyword/27169553 18]. | ||
- | #Rao SR, Flores-Rodriguez N, Page SL, Wong C, Robinson PJ, Chircop M, (2016) "The | + | #Rao SR, Flores-Rodriguez N, Page SL, Wong C, Robinson PJ, Chircop M, (2016) "The Clathrin-dependent Spindle Proteome." <i>Mol Cell Proteomics</i> <b>15</b>(8):2537–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27174698 27174698]; doi: [https://dx.doi.org/10.1074/mcp.M115.054809 10.1074/mcp.M115.054809]; GPMDB: [http://gpmdb.org/data/keyword/27174698 130]. |
#Gupta I, Villanyi Z, Kassem S, Hughes C, Panasenko OO, Steinmetz LM, Collart MA, (2016) "Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex." <i>Cell Rep</i> <b>15</b>(8):1782–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27184853 27184853]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.04.055 10.1016/j.celrep.2016.04.055]; GPMDB: [http://gpmdb.org/data/keyword/27184853 4]. | #Gupta I, Villanyi Z, Kassem S, Hughes C, Panasenko OO, Steinmetz LM, Collart MA, (2016) "Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex." <i>Cell Rep</i> <b>15</b>(8):1782–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27184853 27184853]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.04.055 10.1016/j.celrep.2016.04.055]; GPMDB: [http://gpmdb.org/data/keyword/27184853 4]. | ||
#Kliuchnikova AA, Samokhina NI, Ilina IY, Karpov DS, Pyatnitskiy MA, Kuznetsova KG, Toropygin IY, Kochergin SA, Alekseev IB, Zgoda VG, Archakov AI, Moshkovskii SA, (2016) "Human aqueous humor proteome in cataract, glaucoma, and pseudoexfoliation syndrome." <i>Proteomics</i> <b>16</b>(13):1938–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193151 27193151]; doi: [https://dx.doi.org/10.1002/pmic.201500423 10.1002/pmic.201500423]; GPMDB: [http://gpmdb.org/data/keyword/27193151 86]. | #Kliuchnikova AA, Samokhina NI, Ilina IY, Karpov DS, Pyatnitskiy MA, Kuznetsova KG, Toropygin IY, Kochergin SA, Alekseev IB, Zgoda VG, Archakov AI, Moshkovskii SA, (2016) "Human aqueous humor proteome in cataract, glaucoma, and pseudoexfoliation syndrome." <i>Proteomics</i> <b>16</b>(13):1938–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193151 27193151]; doi: [https://dx.doi.org/10.1002/pmic.201500423 10.1002/pmic.201500423]; GPMDB: [http://gpmdb.org/data/keyword/27193151 86]. | ||
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#Yang W, Jackson B, Zhang H, (2016) "Identification of glycoproteins associated with HIV latently infected cells using quantitative glycoproteomics." <i>Proteomics</i> <b>16</b>(13):1872–80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27195445 27195445]; doi: [https://dx.doi.org/10.1002/pmic.201500215 10.1002/pmic.201500215]; GPMDB: [http://gpmdb.org/data/keyword/27195445 12]. | #Yang W, Jackson B, Zhang H, (2016) "Identification of glycoproteins associated with HIV latently infected cells using quantitative glycoproteomics." <i>Proteomics</i> <b>16</b>(13):1872–80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27195445 27195445]; doi: [https://dx.doi.org/10.1002/pmic.201500215 10.1002/pmic.201500215]; GPMDB: [http://gpmdb.org/data/keyword/27195445 12]. | ||
#Liang W, Ward LJ, Karlsson H, Ljunggren SA, Li W, Lindahl M, Yuan XM, (2016) "Distinctive proteomic profiles among different regions of human carotid plaques in men and women." <i>Sci Rep</i> <b>6</b>:26231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27198765 27198765]; doi: [https://dx.doi.org/10.1038/srep26231 10.1038/srep26231]; GPMDB: [http://gpmdb.org/data/keyword/27198765 60]. | #Liang W, Ward LJ, Karlsson H, Ljunggren SA, Li W, Lindahl M, Yuan XM, (2016) "Distinctive proteomic profiles among different regions of human carotid plaques in men and women." <i>Sci Rep</i> <b>6</b>:26231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27198765 27198765]; doi: [https://dx.doi.org/10.1038/srep26231 10.1038/srep26231]; GPMDB: [http://gpmdb.org/data/keyword/27198765 60]. | ||
- | #Virant-Klun I, Leicht S, Hughes C, Krijgsveld J, (2016) "Identification of | + | #Virant-Klun I, Leicht S, Hughes C, Krijgsveld J, (2016) "Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes." <i>Mol Cell Proteomics</i> <b>15</b>(8):2616–27; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27215607 27215607]; doi: [https://dx.doi.org/10.1074/mcp.M115.056887 10.1074/mcp.M115.056887]; GPMDB: [http://gpmdb.org/data/keyword/27215607 18]. |
#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]. | ||
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#Patella F, Neilson LJ, Athineos D, Erami Z, Anderson KI, Blyth K, Ryan KM, Zanivan S, (2016) "In-Depth Proteomics Identifies a Role for Autophagy in Controlling Reactive Oxygen Species Mediated Endothelial Permeability." <i>J Proteome Res</i> <b>15</b>(7):2187–97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27246970 27246970]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00166 10.1021/acs.jproteome.6b00166]; GPMDB: [http://gpmdb.org/data/keyword/27246970 25]. | #Patella F, Neilson LJ, Athineos D, Erami Z, Anderson KI, Blyth K, Ryan KM, Zanivan S, (2016) "In-Depth Proteomics Identifies a Role for Autophagy in Controlling Reactive Oxygen Species Mediated Endothelial Permeability." <i>J Proteome Res</i> <b>15</b>(7):2187–97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27246970 27246970]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00166 10.1021/acs.jproteome.6b00166]; GPMDB: [http://gpmdb.org/data/keyword/27246970 25]. | ||
#Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC, (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [http://gpmdb.org/data/keyword/27251275 1265]. | #Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC, (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [http://gpmdb.org/data/keyword/27251275 1265]. | ||
- | #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 | + | #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> <b>15</b>(8):2671–85; 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, 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]. | ||
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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> <b>166</b>(3):664– | + | #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):664–78; 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 60]. | #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]. | #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]. | + | #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> <b>148</b>:94–104; 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]. | #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]. | #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]. | ||
+ | #Thomsen MS, Birkelund S, Burkhart A, Stensballe A, Moos T, (2016) "Synthesis and deposition of basement membrane proteins by primary brain capillary endothelial cells in a murine model of the blood-brain barrier." <i>J Neurochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27456748 27456748]; doi: [https://dx.doi.org/10.1111/jnc.13747 10.1111/jnc.13747]; GPMDB: [http://gpmdb.org/data/keyword/27456748 12]. | ||
+ | #Liu Z, Wang F, Chen J, Zhou Y, Zou H, (2016) "Modulating the selectivity of affinity absorbents to multi-phosphopeptides by a competitive substitution strategy." <i>J Chromatogr A</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27470094 27470094]; doi: [https://dx.doi.org/10.1016/j.chroma.2016.07.042 10.1016/j.chroma.2016.07.042]; GPMDB: [http://gpmdb.org/data/keyword/27470094 9]. |
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 8, 2016.