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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 May | + | 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 May 15, 2016. |
#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, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | #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, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | ||
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#van den Biggelaar M, Hernández-Fernaud JR, van den Eshof BL, Neilson LJ, Meijer AB, Mertens K, Zanivan S, (2014) "Quantitative phosphoproteomics unveils temporal dynamics of thrombin signaling in human endothelial cells." <i>Blood</i> <b>123</b>(12):e22–36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24501219 24501219]; doi: [https://dx.doi.org/10.1182/blood-2013-12-546036 10.1182/blood-2013-12-546036]; GPMDB: [http://gpmdb.org/data/keyword/24501219 87]. | #van den Biggelaar M, Hernández-Fernaud JR, van den Eshof BL, Neilson LJ, Meijer AB, Mertens K, Zanivan S, (2014) "Quantitative phosphoproteomics unveils temporal dynamics of thrombin signaling in human endothelial cells." <i>Blood</i> <b>123</b>(12):e22–36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24501219 24501219]; doi: [https://dx.doi.org/10.1182/blood-2013-12-546036 10.1182/blood-2013-12-546036]; GPMDB: [http://gpmdb.org/data/keyword/24501219 87]. | ||
#Eguren M, Álvarez-Fernández M, García F, López-Contreras AJ, Fujimitsu K, Yaguchi H, Luque-García JL, Fernández-Capetillo O, Muñoz J, Yamano H, Malumbres M, (2014) "A synthetic lethal interaction between APC/C and topoisomerase poisons uncovered by proteomic screens." <i>Cell Rep</i> <b>6</b>(4):670–83; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24508461 24508461]; doi: [https://dx.doi.org/10.1016/j.celrep.2014.01.017 10.1016/j.celrep.2014.01.017]; GPMDB: [http://gpmdb.org/data/keyword/24508461 119]. | #Eguren M, Álvarez-Fernández M, García F, López-Contreras AJ, Fujimitsu K, Yaguchi H, Luque-García JL, Fernández-Capetillo O, Muñoz J, Yamano H, Malumbres M, (2014) "A synthetic lethal interaction between APC/C and topoisomerase poisons uncovered by proteomic screens." <i>Cell Rep</i> <b>6</b>(4):670–83; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24508461 24508461]; doi: [https://dx.doi.org/10.1016/j.celrep.2014.01.017 10.1016/j.celrep.2014.01.017]; GPMDB: [http://gpmdb.org/data/keyword/24508461 119]. | ||
+ | #Rinschen MM, Wu X, König T, Pisitkun T, Hagmann H, Pahmeyer C, Lamkemeyer T, Kohli P, Schnell N, Schermer B, Dryer S, Brooks BR, Beltrao P, Krueger M, Brinkkoetter PT, Benzing T, (2014) "Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier." <i>J Am Soc Nephrol</i> <b>25</b>(7):1509–22; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24511133 24511133]; doi: [https://dx.doi.org/10.1681/ASN.2013070760 10.1681/ASN.2013070760]; GPMDB: [http://gpmdb.org/data/keyword/24511133 34]. | ||
#Tao D, King JG, Tweedell RE, Jost PJ, Boddey JA, Dinglasan RR, (2014) "The acute transcriptomic and proteomic response of HC-04 hepatoma cells to hepatocyte growth factor and its implications for Plasmodium falciparum sporozoite invasion." <i>Mol Cell Proteomics</i> <b>13</b>(5):1153–64; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24532842 24532842]; doi: [https://dx.doi.org/10.1074/mcp.M113.035584 10.1074/mcp.M113.035584]; GPMDB: [http://gpmdb.org/data/keyword/24532842 51]. | #Tao D, King JG, Tweedell RE, Jost PJ, Boddey JA, Dinglasan RR, (2014) "The acute transcriptomic and proteomic response of HC-04 hepatoma cells to hepatocyte growth factor and its implications for Plasmodium falciparum sporozoite invasion." <i>Mol Cell Proteomics</i> <b>13</b>(5):1153–64; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24532842 24532842]; doi: [https://dx.doi.org/10.1074/mcp.M113.035584 10.1074/mcp.M113.035584]; GPMDB: [http://gpmdb.org/data/keyword/24532842 51]. | ||
#Kustatscher G, Hégarat N, Wills KL, Furlan C, Bukowski-Wills JC, Hochegger H, Rappsilber J, (2014) "Proteomics of a fuzzy organelle: interphase chromatin." <i>EMBO J</i> <b>33</b>(6):648–64; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24534090 24534090]; doi: [https://dx.doi.org/10.1002/embj.201387614 10.1002/embj.201387614]; GPMDB: [http://gpmdb.org/data/keyword/24534090 519]. | #Kustatscher G, Hégarat N, Wills KL, Furlan C, Bukowski-Wills JC, Hochegger H, Rappsilber J, (2014) "Proteomics of a fuzzy organelle: interphase chromatin." <i>EMBO J</i> <b>33</b>(6):648–64; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24534090 24534090]; doi: [https://dx.doi.org/10.1002/embj.201387614 10.1002/embj.201387614]; GPMDB: [http://gpmdb.org/data/keyword/24534090 519]. | ||
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#Selevsek N, Chang CY, Gillet LC, Navarro P, Bernhardt OM, Reiter L, Cheng LY, Vitek O, Aebersold R, (2015) "Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry." <i>Mol Cell Proteomics</i> <b>14</b>(3):739–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25561506 25561506]; doi: [https://dx.doi.org/10.1074/mcp.M113.035550 10.1074/mcp.M113.035550]; GPMDB: [http://gpmdb.org/data/keyword/25561506 46]. | #Selevsek N, Chang CY, Gillet LC, Navarro P, Bernhardt OM, Reiter L, Cheng LY, Vitek O, Aebersold R, (2015) "Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry." <i>Mol Cell Proteomics</i> <b>14</b>(3):739–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25561506 25561506]; doi: [https://dx.doi.org/10.1074/mcp.M113.035550 10.1074/mcp.M113.035550]; GPMDB: [http://gpmdb.org/data/keyword/25561506 46]. | ||
#Kershaw CJ, Costello JL, Castelli LM, Talavera D, Rowe W, Sims PF, Ashe MP, Hubbard SJ, Pavitt GD, Grant CM, (2015) "The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response." <i>PLoS Genet</i> <b>11</b>(1):e1004903; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25569619 25569619]; doi: [https://dx.doi.org/10.1371/journal.pgen.1004903 10.1371/journal.pgen.1004903]; GPMDB: [http://gpmdb.org/data/keyword/25569619 20]. | #Kershaw CJ, Costello JL, Castelli LM, Talavera D, Rowe W, Sims PF, Ashe MP, Hubbard SJ, Pavitt GD, Grant CM, (2015) "The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response." <i>PLoS Genet</i> <b>11</b>(1):e1004903; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25569619 25569619]; doi: [https://dx.doi.org/10.1371/journal.pgen.1004903 10.1371/journal.pgen.1004903]; GPMDB: [http://gpmdb.org/data/keyword/25569619 20]. | ||
- | #Zappacosta F, Scott GF, Huddleston MJ, Annan RS, (2015) "An optimized platform for hydrophilic interaction chromatography-immobilized metal affinity chromatography enables deep coverage of the rat liver phosphoproteome." <i>J Proteome Res</i> <b>14</b>(2):997–1009; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25575281 25575281]; doi: [https://dx.doi.org/10.1021/pr501025e 10.1021/pr501025e]; GPMDB: [http://gpmdb.org/data/keyword/25575281 | + | #Zappacosta F, Scott GF, Huddleston MJ, Annan RS, (2015) "An optimized platform for hydrophilic interaction chromatography-immobilized metal affinity chromatography enables deep coverage of the rat liver phosphoproteome." <i>J Proteome Res</i> <b>14</b>(2):997–1009; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25575281 25575281]; doi: [https://dx.doi.org/10.1021/pr501025e 10.1021/pr501025e]; GPMDB: [http://gpmdb.org/data/keyword/25575281 42]. |
#Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ, Mann M, (2015) "Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation." <i>Mol Cell Proteomics</i> <b>14</b>(3):658–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25576301 25576301]; doi: [https://dx.doi.org/10.1074/mcp.M114.042812 10.1074/mcp.M114.042812]; GPMDB: [http://gpmdb.org/data/keyword/25576301 40]. | #Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ, Mann M, (2015) "Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation." <i>Mol Cell Proteomics</i> <b>14</b>(3):658–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25576301 25576301]; doi: [https://dx.doi.org/10.1074/mcp.M114.042812 10.1074/mcp.M114.042812]; GPMDB: [http://gpmdb.org/data/keyword/25576301 40]. | ||
#Chiang DY, Lebesgue N, Beavers DL, Alsina KM, Damen JM, Voigt N, Dobrev D, Wehrens XH, Scholten A, (2015) "Alterations in the interactome of serine/threonine protein phosphatase type-1 in atrial fibrillation patients." <i>J Am Coll Cardiol</i> <b>65</b>(2):163–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25593058 25593058]; doi: [https://dx.doi.org/10.1016/j.jacc.2014.10.042 10.1016/j.jacc.2014.10.042]; GPMDB: [http://gpmdb.org/data/keyword/25593058 22]. | #Chiang DY, Lebesgue N, Beavers DL, Alsina KM, Damen JM, Voigt N, Dobrev D, Wehrens XH, Scholten A, (2015) "Alterations in the interactome of serine/threonine protein phosphatase type-1 in atrial fibrillation patients." <i>J Am Coll Cardiol</i> <b>65</b>(2):163–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25593058 25593058]; doi: [https://dx.doi.org/10.1016/j.jacc.2014.10.042 10.1016/j.jacc.2014.10.042]; GPMDB: [http://gpmdb.org/data/keyword/25593058 22]. | ||
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#Coman C, Solari FA, Hentschel A, Sickmann A, Zahedi RP, Ahrends R, (2016) "Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX): A Combinatorial Multimolecular Omics Approach for Systems Biology." <i>Mol Cell Proteomics</i> <b>15</b>(4):1453–66; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26814187 26814187]; doi: [https://dx.doi.org/10.1074/mcp.M115.053702 10.1074/mcp.M115.053702]; GPMDB: [http://gpmdb.org/data/keyword/26814187 68]. | #Coman C, Solari FA, Hentschel A, Sickmann A, Zahedi RP, Ahrends R, (2016) "Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX): A Combinatorial Multimolecular Omics Approach for Systems Biology." <i>Mol Cell Proteomics</i> <b>15</b>(4):1453–66; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26814187 26814187]; doi: [https://dx.doi.org/10.1074/mcp.M115.053702 10.1074/mcp.M115.053702]; GPMDB: [http://gpmdb.org/data/keyword/26814187 68]. | ||
#Bigaud E, Corrales FJ, (2016) "Methylthioadenosine (MTA) Regulates Liver Cells Proteome and Methylproteome: Implications in Liver Biology and Disease." <i>Mol Cell Proteomics</i> <b>15</b>(5):1498–510; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26819315 26819315]; doi: [https://dx.doi.org/10.1074/mcp.M115.055772 10.1074/mcp.M115.055772]; GPMDB: [http://gpmdb.org/data/keyword/26819315 3]. | #Bigaud E, Corrales FJ, (2016) "Methylthioadenosine (MTA) Regulates Liver Cells Proteome and Methylproteome: Implications in Liver Biology and Disease." <i>Mol Cell Proteomics</i> <b>15</b>(5):1498–510; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26819315 26819315]; doi: [https://dx.doi.org/10.1074/mcp.M115.055772 10.1074/mcp.M115.055772]; GPMDB: [http://gpmdb.org/data/keyword/26819315 3]. | ||
+ | #Aubert G, Martin OJ, Horton JL, Lai L, Vega RB, Leone TC, Koves T, Gardell SJ, Krüger M, Hoppel CL, Lewandowski ED, Crawford PA, Muoio DM, Kelly DP, (2016) "The Failing Heart Relies on Ketone Bodies as a Fuel." <i>Circulation</i> <b>133</b>(8):698–705; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26819376 26819376]; doi: [https://dx.doi.org/10.1161/CIRCULATIONAHA.115.017355 10.1161/CIRCULATIONAHA.115.017355]; GPMDB: [http://gpmdb.org/data/keyword/26819376 115]. | ||
#Kristensen TN, Kjeldal H, Schou MF, Nielsen JL, (2016) "Proteomic data reveal a physiological basis for costs and benefits associated with thermal acclimation." <i>J Exp Biol</i> <b>219</b>(Pt 7):969–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26823104 26823104]; doi: [https://dx.doi.org/10.1242/jeb.132696 10.1242/jeb.132696]; GPMDB: [http://gpmdb.org/data/keyword/26823104 9]. | #Kristensen TN, Kjeldal H, Schou MF, Nielsen JL, (2016) "Proteomic data reveal a physiological basis for costs and benefits associated with thermal acclimation." <i>J Exp Biol</i> <b>219</b>(Pt 7):969–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26823104 26823104]; doi: [https://dx.doi.org/10.1242/jeb.132696 10.1242/jeb.132696]; GPMDB: [http://gpmdb.org/data/keyword/26823104 9]. | ||
#Steger M, Tonelli F, Ito G, Davies P, Trost M, Vetter M, Wachter S, Lorentzen E, Duddy G, Wilson S, Baptista MA, Fiske BK, Fell MJ, Morrow JA, Reith AD, Alessi DR, Mann M, (2016) "Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26824392 26824392]; doi: [https://dx.doi.org/10.7554/eLife.12813 10.7554/eLife.12813]; GPMDB: [http://gpmdb.org/data/keyword/26824392 216]. | #Steger M, Tonelli F, Ito G, Davies P, Trost M, Vetter M, Wachter S, Lorentzen E, Duddy G, Wilson S, Baptista MA, Fiske BK, Fell MJ, Morrow JA, Reith AD, Alessi DR, Mann M, (2016) "Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26824392 26824392]; doi: [https://dx.doi.org/10.7554/eLife.12813 10.7554/eLife.12813]; GPMDB: [http://gpmdb.org/data/keyword/26824392 216]. | ||
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#Long B, Muhamad R, Yan G, Yu J, Fan Q, Wang Z, Li X, Purnomoadi A, Achmadi J, Yan X, (2016) "Quantitative proteomics analysis reveals glutamine deprivation activates fatty acid β-oxidation pathway in HepG2 cells." <i>Amino Acids</i> <b>48</b>(5):1297–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26837383 26837383]; doi: [https://dx.doi.org/10.1007/s00726-016-2182-7 10.1007/s00726-016-2182-7]; GPMDB: [http://gpmdb.org/data/keyword/26837383 1]. | #Long B, Muhamad R, Yan G, Yu J, Fan Q, Wang Z, Li X, Purnomoadi A, Achmadi J, Yan X, (2016) "Quantitative proteomics analysis reveals glutamine deprivation activates fatty acid β-oxidation pathway in HepG2 cells." <i>Amino Acids</i> <b>48</b>(5):1297–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26837383 26837383]; doi: [https://dx.doi.org/10.1007/s00726-016-2182-7 10.1007/s00726-016-2182-7]; GPMDB: [http://gpmdb.org/data/keyword/26837383 1]. | ||
#Iwamoto N, D'Alessandro LA, Depner S, Hahn B, Kramer BA, Lucarelli P, Vlasov A, Stepath M, Böhm ME, Deharde D, Damm G, Seehofer D, Lehmann WD, Klingmüller U, Schilling M, (2016) "Context-specific flow through the MEK/ERK module produces cell- and ligand-specific patterns of ERK single and double phosphorylation." <i>Sci Signal</i> <b>9</b>(413):ra13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26838549 26838549]; doi: [https://dx.doi.org/10.1126/scisignal.aab1967 10.1126/scisignal.aab1967]; GPMDB: [http://gpmdb.org/data/keyword/26838549 66]. | #Iwamoto N, D'Alessandro LA, Depner S, Hahn B, Kramer BA, Lucarelli P, Vlasov A, Stepath M, Böhm ME, Deharde D, Damm G, Seehofer D, Lehmann WD, Klingmüller U, Schilling M, (2016) "Context-specific flow through the MEK/ERK module produces cell- and ligand-specific patterns of ERK single and double phosphorylation." <i>Sci Signal</i> <b>9</b>(413):ra13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26838549 26838549]; doi: [https://dx.doi.org/10.1126/scisignal.aab1967 10.1126/scisignal.aab1967]; GPMDB: [http://gpmdb.org/data/keyword/26838549 66]. | ||
+ | #Tong M, Kleffmann T, Pradhan S, Johansson CL, DeSousa J, Stone PR, James JL, Chen Q, Chamley LW, (2016) "Proteomic characterization of macro-, micro- and nano-extracellular vesicles derived from the same first trimester placenta: relevance for feto-maternal communication." <i>Hum Reprod</i> <b>31</b>(4):687–99; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26839151 26839151]; doi: [https://dx.doi.org/10.1093/humrep/dew004 10.1093/humrep/dew004]; GPMDB: [http://gpmdb.org/data/keyword/26839151 3]. | ||
#Huang H, Yoo CY, Bindbeutel R, Goldsworthy J, Tielking A, Alvarez S, Naldrett MJ, Evans BS, Chen M, Nusinow DA, (2016) "PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis." <i>Elife</i> <b>5</b>:e13292; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26839287 26839287]; doi: [https://dx.doi.org/10.7554/eLife.13292 10.7554/eLife.13292]; GPMDB: [http://gpmdb.org/data/keyword/26839287 9]. | #Huang H, Yoo CY, Bindbeutel R, Goldsworthy J, Tielking A, Alvarez S, Naldrett MJ, Evans BS, Chen M, Nusinow DA, (2016) "PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis." <i>Elife</i> <b>5</b>:e13292; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26839287 26839287]; doi: [https://dx.doi.org/10.7554/eLife.13292 10.7554/eLife.13292]; GPMDB: [http://gpmdb.org/data/keyword/26839287 9]. | ||
#Thorpe CT, Peffers MJ, Simpson D, Halliwell E, Screen HR, Clegg PD, (2016) "Anatomical heterogeneity of tendon: Fascicular and interfascicular tendon compartments have distinct proteomic composition." <i>Sci Rep</i> <b>6</b>:20455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26842662 26842662]; doi: [https://dx.doi.org/10.1038/srep20455 10.1038/srep20455]; GPMDB: [http://gpmdb.org/data/keyword/26842662 20]. | #Thorpe CT, Peffers MJ, Simpson D, Halliwell E, Screen HR, Clegg PD, (2016) "Anatomical heterogeneity of tendon: Fascicular and interfascicular tendon compartments have distinct proteomic composition." <i>Sci Rep</i> <b>6</b>:20455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26842662 26842662]; doi: [https://dx.doi.org/10.1038/srep20455 10.1038/srep20455]; GPMDB: [http://gpmdb.org/data/keyword/26842662 20]. | ||
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#Xu B, Tian R, Wang X, Zhan S, Wang R, Guo Y, Ge W, (2016) "Protein profile changes in the frontotemporal lobes in human severe traumatic brain injury." <i>Brain Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067185 27067185]; doi: [https://dx.doi.org/10.1016/j.brainres.2016.04.008 10.1016/j.brainres.2016.04.008]; GPMDB: [http://gpmdb.org/data/keyword/27067185 20]. | #Xu B, Tian R, Wang X, Zhan S, Wang R, Guo Y, Ge W, (2016) "Protein profile changes in the frontotemporal lobes in human severe traumatic brain injury." <i>Brain Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067185 27067185]; doi: [https://dx.doi.org/10.1016/j.brainres.2016.04.008 10.1016/j.brainres.2016.04.008]; GPMDB: [http://gpmdb.org/data/keyword/27067185 20]. | ||
#Rider MA, Hurwitz SN, Meckes DG Jr, (2016) "ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles." <i>Sci Rep</i> <b>6</b>:23978; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27068479 27068479]; doi: [https://dx.doi.org/10.1038/srep23978 10.1038/srep23978]; GPMDB: [http://gpmdb.org/data/keyword/27068479 3]. | #Rider MA, Hurwitz SN, Meckes DG Jr, (2016) "ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles." <i>Sci Rep</i> <b>6</b>:23978; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27068479 27068479]; doi: [https://dx.doi.org/10.1038/srep23978 10.1038/srep23978]; GPMDB: [http://gpmdb.org/data/keyword/27068479 3]. | ||
+ | #Barallobre-Barreiro J, Oklu R, Lynch M, Fava M, Baig F, Yin X, Barwari T, Potier DN, Albadawi H, Jahangiri M, Porter KE, Watkins MT, Misra S, Stoughton J, Mayr M, (2016) "Extracellular Matrix Remodeling in Response to Venous Hypertension: Proteomics of Human Varicose Veins." <i>Cardiovasc Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27068509 27068509]; doi: [https://dx.doi.org/10.1093/cvr/cvw075 10.1093/cvr/cvw075]; GPMDB: [http://gpmdb.org/data/keyword/27068509 12]. | ||
#Sarhan AR, Patel TR, Creese AJ, Tomlinson MG, Hellberg C, Heath JK, Hotchin NA, Cunningham DL, (2016) "Regulation of platelet derived growth factor signalling by LAR protein tyrosine phosphatase: a quantitative phosphoproteomics study." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27074791 27074791]; doi: [https://dx.doi.org/10.1074/mcp.M115.053652 10.1074/mcp.M115.053652]; GPMDB: [http://gpmdb.org/data/keyword/27074791 17]. | #Sarhan AR, Patel TR, Creese AJ, Tomlinson MG, Hellberg C, Heath JK, Hotchin NA, Cunningham DL, (2016) "Regulation of platelet derived growth factor signalling by LAR protein tyrosine phosphatase: a quantitative phosphoproteomics study." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27074791 27074791]; doi: [https://dx.doi.org/10.1074/mcp.M115.053652 10.1074/mcp.M115.053652]; GPMDB: [http://gpmdb.org/data/keyword/27074791 17]. | ||
#Lochmatter C, Fischer R, Charles PD, Yu Z, Powrie F, Kessler BM, (2016) "Integrative Phosphoproteomics Links IL-23R Signaling with Metabolic Adaptation in Lymphocytes." <i>Sci Rep</i> <b>6</b>:24491; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27080861 27080861]; doi: [https://dx.doi.org/10.1038/srep24491 10.1038/srep24491]; GPMDB: [http://gpmdb.org/data/keyword/27080861 7]. | #Lochmatter C, Fischer R, Charles PD, Yu Z, Powrie F, Kessler BM, (2016) "Integrative Phosphoproteomics Links IL-23R Signaling with Metabolic Adaptation in Lymphocytes." <i>Sci Rep</i> <b>6</b>:24491; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27080861 27080861]; doi: [https://dx.doi.org/10.1038/srep24491 10.1038/srep24491]; GPMDB: [http://gpmdb.org/data/keyword/27080861 7]. | ||
#Arts IS, Vertommen D, Baldin F, Laloux G, Collet JF, (2016) "Comprehensively characterizing the thioredoxin interactome in vivo highlights the central role played by this ubiquitous oxidoreductase in redox control." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27081212 27081212]; doi: [https://dx.doi.org/10.1074/mcp.M115.056440 10.1074/mcp.M115.056440]; GPMDB: [http://gpmdb.org/data/keyword/27081212 103]. | #Arts IS, Vertommen D, Baldin F, Laloux G, Collet JF, (2016) "Comprehensively characterizing the thioredoxin interactome in vivo highlights the central role played by this ubiquitous oxidoreductase in redox control." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27081212 27081212]; doi: [https://dx.doi.org/10.1074/mcp.M115.056440 10.1074/mcp.M115.056440]; GPMDB: [http://gpmdb.org/data/keyword/27081212 103]. | ||
- | #Tape CJ, Ling S, Dimitriadi M, McMahon KM, Worboys JD, Leong HS, Norrie IC, Miller CJ, Poulogiannis G, Lauffenburger DA, Jørgensen C, (2016) "Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation." <i>Cell</i> <b>165</b>(4):910– | + | #Tape CJ, Ling S, Dimitriadi M, McMahon KM, Worboys JD, Leong HS, Norrie IC, Miller CJ, Poulogiannis G, Lauffenburger DA, Jørgensen C, (2016) "Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation." <i>Cell</i> <b>165</b>(4):910–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27087446 27087446]; doi: [https://dx.doi.org/10.1016/j.cell.2016.03.029 10.1016/j.cell.2016.03.029]; GPMDB: [http://gpmdb.org/data/keyword/27087446 374]. |
+ | #Stoehr A, Yang Y, Patel S, Evangelista AM, Aponte A, Wang G, Liu P, Boylston J, Kloner PH, Lin Y, Gucek M, Zhu J, Murphy E, (2016) "Prolyl hydroxylation regulates protein degradation, synthesis and splicing in human induced pluripotent stem cell-derived cardiomyocytes." <i>Cardiovasc Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27095734 27095734]; doi: [https://dx.doi.org/10.1093/cvr/cvw081 10.1093/cvr/cvw081]; GPMDB: [http://gpmdb.org/data/keyword/27095734 12]. | ||
#Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M, (2016) "Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27107777 27107777]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.03.049 10.1016/j.jprot.2016.03.049]; GPMDB: [http://gpmdb.org/data/keyword/27107777 163]. | #Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M, (2016) "Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27107777 27107777]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.03.049 10.1016/j.jprot.2016.03.049]; GPMDB: [http://gpmdb.org/data/keyword/27107777 163]. | ||
- | #Larance M, Kirkwood KJ, Tinti M, Murillo AB, Ferguson MA, Lamond AI, (2016) "Global Membrane Protein Interactome Analysis using In vivo Crosslinking and MS-based Protein Correlation Profiling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27114452 27114452]; doi: [https://dx.doi.org/10.1074/mcp.O115.055467 10.1074/mcp.O115.055467]; GPMDB: [http://gpmdb.org/data/keyword/27114452 | + | #Larance M, Kirkwood KJ, Tinti M, Murillo AB, Ferguson MA, Lamond AI, (2016) "Global Membrane Protein Interactome Analysis using In vivo Crosslinking and MS-based Protein Correlation Profiling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27114452 27114452]; doi: [https://dx.doi.org/10.1074/mcp.O115.055467 10.1074/mcp.O115.055467]; GPMDB: [http://gpmdb.org/data/keyword/27114452 396]. |
- | #Laghmani K, Beck BB, Yang SS, Seaayfan E, Wenzel A, Reusch B, Vitzthum H, Priem D, Demaretz S, Bergmann K, Duin LK, Göbel H, Mache C, Thiele H, Bartram MP, Dombret C, Altmüller J, Nürnberg P, Benzing T, Levtchenko E, Seyberth HW, Klaus G, Yigit G, Lin SH, Timmer A, de Koning TJ, Scherjon SA, Schlingmann KP, Bertrand MJ, Rinschen MM, de Backer O, Konrad M, Kömhoff M, (2016) "Polyhydramnios, Transient Antenatal Bartter's Syndrome, and MAGED2 Mutations." <i>N Engl J Med</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27120771 27120771]; doi: [https://dx.doi.org/10.1056/NEJMoa1507629 10.1056/NEJMoa1507629]; GPMDB: [http://gpmdb.org/data/keyword/27120771 21]. | + | #Laghmani K, Beck BB, Yang SS, Seaayfan E, Wenzel A, Reusch B, Vitzthum H, Priem D, Demaretz S, Bergmann K, Duin LK, Göbel H, Mache C, Thiele H, Bartram MP, Dombret C, Altmüller J, Nürnberg P, Benzing T, Levtchenko E, Seyberth HW, Klaus G, Yigit G, Lin SH, Timmer A, de Koning TJ, Scherjon SA, Schlingmann KP, Bertrand MJ, Rinschen MM, de Backer O, Konrad M, Kömhoff M, (2016) "Polyhydramnios, Transient Antenatal Bartter's Syndrome, and MAGED2 Mutations." <i>N Engl J Med</i> <b>374</b>(19):1853–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27120771 27120771]; doi: [https://dx.doi.org/10.1056/NEJMoa1507629 10.1056/NEJMoa1507629]; GPMDB: [http://gpmdb.org/data/keyword/27120771 21]. |
+ | #Hoehenwarter W, Mönchgesang S, Neumann S, Majovsky P, Abel S, Müller J, (2016) "Comparative expression profiling reveals a role of the root apoplast in local phosphate response." <i>BMC Plant Biol</i> <b>16</b>(1):106; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27121119 27121119]; doi: [https://dx.doi.org/10.1186/s12870-016-0790-8 10.1186/s12870-016-0790-8]; GPMDB: [http://gpmdb.org/data/keyword/27121119 23]. | ||
#Eyckerman S, Titeca K, Van Quickelberghe E, Cloots E, Verhee A, Samyn N, De Ceuninck L, Timmerman E, De Sutter D, Lievens S, Van Calenbergh S, Gevaert K, Tavernier J, (2016) "Trapping mammalian protein complexes in viral particles." <i>Nat Commun</i> <b>7</b>:11416; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27122307 27122307]; doi: [https://dx.doi.org/10.1038/ncomms11416 10.1038/ncomms11416]; GPMDB: [http://gpmdb.org/data/keyword/27122307 58]. | #Eyckerman S, Titeca K, Van Quickelberghe E, Cloots E, Verhee A, Samyn N, De Ceuninck L, Timmerman E, De Sutter D, Lievens S, Van Calenbergh S, Gevaert K, Tavernier J, (2016) "Trapping mammalian protein complexes in viral particles." <i>Nat Commun</i> <b>7</b>:11416; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27122307 27122307]; doi: [https://dx.doi.org/10.1038/ncomms11416 10.1038/ncomms11416]; GPMDB: [http://gpmdb.org/data/keyword/27122307 58]. | ||
+ | #Ono M, Yamada K, Bensaddek D, Afzal V, Biddlestone J, Ortmann B, Mudie S, Boivin V, Scott MS, Rocha S, Lamond AI, (2016) "Enhanced snoMEN Vectors Facilitate Establishment of GFP-HIF-1α Protein Replacement Human Cell Lines." <i>PLoS One</i> <b>11</b>(4):e0154759; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27128805 27128805]; doi: [https://dx.doi.org/10.1371/journal.pone.0154759 10.1371/journal.pone.0154759]; GPMDB: [http://gpmdb.org/data/keyword/27128805 72]. | ||
#Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M, (2015) "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats." <i>Cell Syst</i> <b>1</b>(3):224–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27135913 27135913]; doi: [https://dx.doi.org/10.1016/j.cels.2015.08.012 10.1016/j.cels.2015.08.012]; GPMDB: [http://gpmdb.org/data/keyword/27135913 190]. | #Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M, (2015) "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats." <i>Cell Syst</i> <b>1</b>(3):224–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27135913 27135913]; doi: [https://dx.doi.org/10.1016/j.cels.2015.08.012 10.1016/j.cels.2015.08.012]; GPMDB: [http://gpmdb.org/data/keyword/27135913 190]. | ||
+ | #Ulrich V, Rotllan N, Araldi E, Luciano A, Skroblin P, Abonnenc M, Perrotta P, Yin X, Bauer A, Leslie KL, Zhang P, Aryal B, Montgomery RL, Thum T, Martin K, Suarez Y, Mayr M, Fernandez-Hernando C, Sessa WC, (2016) "Chronic miR-29 antagonism promotes favorable plaque remodeling in atherosclerotic mice." <i>EMBO Mol Med</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27137489 27137489]; doi: [https://dx.doi.org/10.15252/emmm.201506031 10.15252/emmm.201506031]; GPMDB: [http://gpmdb.org/data/keyword/27137489 120]. | ||
+ | #Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE, (2016) "Proteomics-driven antigen discovery for development of vaccines against gonorrhea." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141096 27141096]; doi: [https://dx.doi.org/10.1074/mcp.M116.058800 10.1074/mcp.M116.058800]; GPMDB: [http://gpmdb.org/data/keyword/27141096 3]. | ||
+ | #Dørum S, Steinsbø Ø, Bergseng E, Arntzen MØ, de Souza GA, Sollid LM, (2016) "Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes." <i>Sci Rep</i> <b>6</b>:25565; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27146306 27146306]; doi: [https://dx.doi.org/10.1038/srep25565 10.1038/srep25565]; GPMDB: [http://gpmdb.org/data/keyword/27146306 27]. | ||
+ | #Jhingan GD, Kumari S, Jamwal SV, Kalam H, Arora D, Jain N, KrishnaKumaar L, Samal A, Rao KV, Kumar D, Nandicoori VK, (2016) "Comparative proteomic analyses of avirulent, virulent and clinical strains of Mycobacterium tuberculosis identifies strain-specific patterns." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27151218 27151218]; doi: [https://dx.doi.org/10.1074/jbc.M115.666123 10.1074/jbc.M115.666123]; GPMDB: [http://gpmdb.org/data/keyword/27151218 16]. |
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 May 15, 2016.