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==Data from publications== | ==Data from publications== | ||
- | The following is a list of 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 list of 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 Apr. 1, 2018. |
#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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#Cosme J, Guo H, Hadipour-Lakmehsari S, Emili A, Gramolini AO, (2017) "Hypoxia-Induced Changes in the Fibroblast Secretome, Exosome, and Whole-Cell Proteome Using Cultured, Cardiac-Derived Cells Isolated from Neonatal Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28641008 28641008]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00144 10.1021/acs.jproteome.7b00144]; GPMDB: [http://gpmdb.org/data/keyword/28641008 39]. | #Cosme J, Guo H, Hadipour-Lakmehsari S, Emili A, Gramolini AO, (2017) "Hypoxia-Induced Changes in the Fibroblast Secretome, Exosome, and Whole-Cell Proteome Using Cultured, Cardiac-Derived Cells Isolated from Neonatal Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28641008 28641008]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00144 10.1021/acs.jproteome.7b00144]; GPMDB: [http://gpmdb.org/data/keyword/28641008 39]. | ||
#Belmont J, Gu T, Mudd A, Salomon AR, (2017) "A PLC-γ1 Feedback Pathway Regulates Lck Substrate Phosphorylation at the T-Cell Receptor and SLP-76 Complex." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28644030 28644030]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01026 10.1021/acs.jproteome.6b01026]; GPMDB: [http://gpmdb.org/data/keyword/28644030 60]. | #Belmont J, Gu T, Mudd A, Salomon AR, (2017) "A PLC-γ1 Feedback Pathway Regulates Lck Substrate Phosphorylation at the T-Cell Receptor and SLP-76 Complex." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28644030 28644030]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01026 10.1021/acs.jproteome.6b01026]; GPMDB: [http://gpmdb.org/data/keyword/28644030 60]. | ||
+ | #Henriet E, Abou Hammoud A, Dupuy JW, Dartigues B, Ezzoukry Z, Dugot-Senant N, Leste-Lasserre T, Pallares-Lupon N, Nikolski M, Le Bail B, Blanc JF, Balabaud C, Bioulac-Sage P, Raymond AA, Saltel F, (2017) "Argininosuccinate synthase 1 (ASS1): A marker of unclassified hepatocellular adenoma and high bleeding risk." <i>Hepatology</i> <b>66</b>(6):2016–2028; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28646562 28646562]; doi: [https://dx.doi.org/10.1002/hep.29336 10.1002/hep.29336]; GPMDB: [http://gpmdb.org/data/keyword/28646562 124]. | ||
#Gu Y, Albuquerque CP, Braas D, Zhang W, Villa GR, Bi J, Ikegami S, Masui K, Gini B, Yang H, Gahman TC, Shiau AK, Cloughesy TF, Christofk HR, Zhou H, Guan KL, Mischel PS, (2017) "mTORC2 Regulates Amino Acid Metabolism in Cancer by Phosphorylation of the Cystine-Glutamate Antiporter xCT." <i>Mol Cell</i> <b>67</b>(1):128–138.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28648777 28648777]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.05.030 10.1016/j.molcel.2017.05.030]; GPMDB: [http://gpmdb.org/data/keyword/28648777 2]. | #Gu Y, Albuquerque CP, Braas D, Zhang W, Villa GR, Bi J, Ikegami S, Masui K, Gini B, Yang H, Gahman TC, Shiau AK, Cloughesy TF, Christofk HR, Zhou H, Guan KL, Mischel PS, (2017) "mTORC2 Regulates Amino Acid Metabolism in Cancer by Phosphorylation of the Cystine-Glutamate Antiporter xCT." <i>Mol Cell</i> <b>67</b>(1):128–138.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28648777 28648777]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.05.030 10.1016/j.molcel.2017.05.030]; GPMDB: [http://gpmdb.org/data/keyword/28648777 2]. | ||
#Flury V, Georgescu PR, Iesmantavicius V, Shimada Y, Kuzdere T, Braun S, Bühler M, (2017) "The Histone Acetyltransferase Mst2 Protects Active Chromatin from Epigenetic Silencing by Acetylating the Ubiquitin Ligase Brl1." <i>Mol Cell</i> <b>67</b>(2):294–307.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28648780 28648780]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.05.026 10.1016/j.molcel.2017.05.026]; GPMDB: [http://gpmdb.org/data/keyword/28648780 50]. | #Flury V, Georgescu PR, Iesmantavicius V, Shimada Y, Kuzdere T, Braun S, Bühler M, (2017) "The Histone Acetyltransferase Mst2 Protects Active Chromatin from Epigenetic Silencing by Acetylating the Ubiquitin Ligase Brl1." <i>Mol Cell</i> <b>67</b>(2):294–307.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28648780 28648780]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.05.026 10.1016/j.molcel.2017.05.026]; GPMDB: [http://gpmdb.org/data/keyword/28648780 50]. | ||
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#Grossegesse M, Doellinger J, Fritsch A, Laue M, Piesker J, Schaade L, Nitsche A, (2018) "Global ubiquitination analysis reveals extensive modification and proteasomal degradation of cowpox virus proteins, but preservation of viral cores." <i>Sci Rep</i> <b>8</b>(1):1807; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29379051 29379051]; doi: [https://dx.doi.org/10.1038/s41598-018-20130-9 10.1038/s41598-018-20130-9]; GPMDB: [http://gpmdb.org/data/keyword/29379051 16]. | #Grossegesse M, Doellinger J, Fritsch A, Laue M, Piesker J, Schaade L, Nitsche A, (2018) "Global ubiquitination analysis reveals extensive modification and proteasomal degradation of cowpox virus proteins, but preservation of viral cores." <i>Sci Rep</i> <b>8</b>(1):1807; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29379051 29379051]; doi: [https://dx.doi.org/10.1038/s41598-018-20130-9 10.1038/s41598-018-20130-9]; GPMDB: [http://gpmdb.org/data/keyword/29379051 16]. | ||
#Hawkins AG, Basrur V, da Veiga Leprevost F, Pedersen E, Sperring C, Nesvizhskii AI, Lawlor ER, (2018) "The Ewing sarcoma secretome and its response to activation of Wnt/beta-catenin signaling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29386236 29386236]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000596 10.1074/mcp.RA118.000596]; GPMDB: [http://gpmdb.org/data/keyword/29386236 12]. | #Hawkins AG, Basrur V, da Veiga Leprevost F, Pedersen E, Sperring C, Nesvizhskii AI, Lawlor ER, (2018) "The Ewing sarcoma secretome and its response to activation of Wnt/beta-catenin signaling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29386236 29386236]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000596 10.1074/mcp.RA118.000596]; GPMDB: [http://gpmdb.org/data/keyword/29386236 12]. | ||
+ | #La Favor JD, Fu Z, Venkatraman V, Bivalacqua TJ, Van Eyk JE, Burnett AL, (2018) "Molecular Profile of Priapism Associated with Low Nitric Oxide Bioavailability." <i>J Proteome Res</i> <b>17</b>(3):1031–1040; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29394072 29394072]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00657 10.1021/acs.jproteome.7b00657]; GPMDB: [http://gpmdb.org/data/keyword/29394072 12]. | ||
#Sandow JJ, Rainczuk A, Infusini G, Makanji M, Bilandzic M, Wilson AL, Fairweather N, Stanton PG, Garama D, Gough D, Jobling TW, Webb AI, Stephens AN, (2018) "Discovery and Validation of Novel Protein Biomarkers in Ovarian Cancer Patient Urine." <i>Proteomics Clin Appl</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29426060 29426060]; doi: [https://dx.doi.org/10.1002/prca.201700135 10.1002/prca.201700135]; GPMDB: [http://gpmdb.org/data/keyword/29426060 10]. | #Sandow JJ, Rainczuk A, Infusini G, Makanji M, Bilandzic M, Wilson AL, Fairweather N, Stanton PG, Garama D, Gough D, Jobling TW, Webb AI, Stephens AN, (2018) "Discovery and Validation of Novel Protein Biomarkers in Ovarian Cancer Patient Urine." <i>Proteomics Clin Appl</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29426060 29426060]; doi: [https://dx.doi.org/10.1002/prca.201700135 10.1002/prca.201700135]; GPMDB: [http://gpmdb.org/data/keyword/29426060 10]. | ||
#Schanzenbächer CT, Langer JD, Schuman EM, (2018) "Time- and polarity-dependent proteomic changes associated with homeostatic scaling at central synapses." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29447110 29447110]; doi: [https://dx.doi.org/10.7554/eLife.33322 10.7554/eLife.33322]; GPMDB: [http://gpmdb.org/data/keyword/29447110 78]. | #Schanzenbächer CT, Langer JD, Schuman EM, (2018) "Time- and polarity-dependent proteomic changes associated with homeostatic scaling at central synapses." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29447110 29447110]; doi: [https://dx.doi.org/10.7554/eLife.33322 10.7554/eLife.33322]; GPMDB: [http://gpmdb.org/data/keyword/29447110 78]. | ||
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#Bergmann TJ, Fregno I, Fumagalli F, Rinaldi A, Bertoni F, Boersema PJ, Picotti P, Molinari M, (2018) "Chemical stresses fail to mimic the unfolded protein response resulting from luminal load with unfolded polypeptides." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29453283 29453283]; doi: [https://dx.doi.org/10.1074/jbc.RA117.001484 10.1074/jbc.RA117.001484]; GPMDB: [http://gpmdb.org/data/keyword/29453283 39]. | #Bergmann TJ, Fregno I, Fumagalli F, Rinaldi A, Bertoni F, Boersema PJ, Picotti P, Molinari M, (2018) "Chemical stresses fail to mimic the unfolded protein response resulting from luminal load with unfolded polypeptides." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29453283 29453283]; doi: [https://dx.doi.org/10.1074/jbc.RA117.001484 10.1074/jbc.RA117.001484]; GPMDB: [http://gpmdb.org/data/keyword/29453283 39]. | ||
#Das CK, Linder B, Bonn F, Rothweiler F, Dikic I, Michaelis M, Cinatl J, Mandal M, Kögel D, (2018) "BAG3 Overexpression and Cytoprotective Autophagy Mediate Apoptosis Resistance in Chemoresistant Breast Cancer Cells." <i>Neoplasia</i> <b>20</b>(3):263–279; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29462756 29462756]; doi: [https://dx.doi.org/10.1016/j.neo.2018.01.001 10.1016/j.neo.2018.01.001]; GPMDB: [http://gpmdb.org/data/keyword/29462756 12]. | #Das CK, Linder B, Bonn F, Rothweiler F, Dikic I, Michaelis M, Cinatl J, Mandal M, Kögel D, (2018) "BAG3 Overexpression and Cytoprotective Autophagy Mediate Apoptosis Resistance in Chemoresistant Breast Cancer Cells." <i>Neoplasia</i> <b>20</b>(3):263–279; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29462756 29462756]; doi: [https://dx.doi.org/10.1016/j.neo.2018.01.001 10.1016/j.neo.2018.01.001]; GPMDB: [http://gpmdb.org/data/keyword/29462756 12]. | ||
+ | #Smestad J, Hamidi O, Wang L, Holte MN, Khazal FA, Erber L, Chen Y, Maher LJ 3rd, (2018) "Characterization and metabolic synthetic lethal testing in a new model of SDH-loss familial pheochromocytoma and paraganglioma." <i>Oncotarget</i> <b>9</b>(5):6109–6127; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29464059 29464059]; doi: [https://dx.doi.org/10.18632/oncotarget.23639 10.18632/oncotarget.23639]; GPMDB: [http://gpmdb.org/data/keyword/29464059 20]. | ||
#O'Loughlin T, Masters TA, Buss F, (2018) "The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29467281 29467281]; doi: [https://dx.doi.org/10.15252/embr.201744884 10.15252/embr.201744884]; GPMDB: [http://gpmdb.org/data/keyword/29467281 34]. | #O'Loughlin T, Masters TA, Buss F, (2018) "The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29467281 29467281]; doi: [https://dx.doi.org/10.15252/embr.201744884 10.15252/embr.201744884]; GPMDB: [http://gpmdb.org/data/keyword/29467281 34]. | ||
#Di Costanzo A, Del Gaudio N, Conte L, Dell'Aversana C, Vermeulen M, de Thé H, Migliaccio A, Nebbioso A, Altucci L, (2018) "The HDAC inhibitor SAHA regulates CBX2 stability via a SUMO-triggered ubiquitin-mediated pathway in leukemia." <i>Oncogene</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29467492 29467492]; doi: [https://dx.doi.org/10.1038/s41388-018-0143-1 10.1038/s41388-018-0143-1]; GPMDB: [http://gpmdb.org/data/keyword/29467492 6]. | #Di Costanzo A, Del Gaudio N, Conte L, Dell'Aversana C, Vermeulen M, de Thé H, Migliaccio A, Nebbioso A, Altucci L, (2018) "The HDAC inhibitor SAHA regulates CBX2 stability via a SUMO-triggered ubiquitin-mediated pathway in leukemia." <i>Oncogene</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29467492 29467492]; doi: [https://dx.doi.org/10.1038/s41388-018-0143-1 10.1038/s41388-018-0143-1]; GPMDB: [http://gpmdb.org/data/keyword/29467492 6]. | ||
#Zhan Y, Marchand CH, Maes A, Mauries A, Sun Y, Dhaliwal JS, Uniacke J, Arragain S, Jiang H, Gold ND, Martin VJJ, Lemaire SD, Zerges W, (2018) "Pyrenoid functions revealed by proteomics in Chlamydomonas reinhardtii." <i>PLoS One</i> <b>13</b>(2):e0185039; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29481573 29481573]; doi: [https://dx.doi.org/10.1371/journal.pone.0185039 10.1371/journal.pone.0185039]; GPMDB: [http://gpmdb.org/data/keyword/29481573 16]. | #Zhan Y, Marchand CH, Maes A, Mauries A, Sun Y, Dhaliwal JS, Uniacke J, Arragain S, Jiang H, Gold ND, Martin VJJ, Lemaire SD, Zerges W, (2018) "Pyrenoid functions revealed by proteomics in Chlamydomonas reinhardtii." <i>PLoS One</i> <b>13</b>(2):e0185039; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29481573 29481573]; doi: [https://dx.doi.org/10.1371/journal.pone.0185039 10.1371/journal.pone.0185039]; GPMDB: [http://gpmdb.org/data/keyword/29481573 16]. | ||
#Zeiner PS, Zinke J, Kowalewski DJ, Bernatz S, Tichy J, Ronellenfitsch MW, Thorsen F, Berger A, Forster MT, Muller A, Steinbach JP, Beschorner R, Wischhusen J, Kvasnicka HM, Plate KH, Stefanović S, Weide B, Mittelbronn M, Harter PN, (2018) "CD74 regulates complexity of tumor cell HLA class II peptidome in brain metastasis and is a positive prognostic marker for patient survival." <i>Acta Neuropathol Commun</i> <b>6</b>(1):18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29490700 29490700]; doi: [https://dx.doi.org/10.1186/s40478-018-0521-5 10.1186/s40478-018-0521-5]; GPMDB: [http://gpmdb.org/data/keyword/29490700 20]. | #Zeiner PS, Zinke J, Kowalewski DJ, Bernatz S, Tichy J, Ronellenfitsch MW, Thorsen F, Berger A, Forster MT, Muller A, Steinbach JP, Beschorner R, Wischhusen J, Kvasnicka HM, Plate KH, Stefanović S, Weide B, Mittelbronn M, Harter PN, (2018) "CD74 regulates complexity of tumor cell HLA class II peptidome in brain metastasis and is a positive prognostic marker for patient survival." <i>Acta Neuropathol Commun</i> <b>6</b>(1):18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29490700 29490700]; doi: [https://dx.doi.org/10.1186/s40478-018-0521-5 10.1186/s40478-018-0521-5]; GPMDB: [http://gpmdb.org/data/keyword/29490700 20]. | ||
+ | #Olsson N, Schultz LM, Zhang L, Khodadoust MS, Narayan R, Czerwinski DK, Levy R, Elias JE, (2018) "T-cell immunopeptidomes reveal cell subtype surface markers derived from intracellular proteins." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29493099 29493099]; doi: [https://dx.doi.org/10.1002/pmic.201700410 10.1002/pmic.201700410]; GPMDB: [http://gpmdb.org/data/keyword/29493099 30]. | ||
#Goel RK, Paczkowska M, Reimand J, Napper S, Lukong KE, (2018) "Phosphoproteomics analysis identifies novel candidate substrates of the non-receptor tyrosine kinase, SRMS." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29496907 29496907]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000643 10.1074/mcp.RA118.000643]; GPMDB: [http://gpmdb.org/data/keyword/29496907 4]. | #Goel RK, Paczkowska M, Reimand J, Napper S, Lukong KE, (2018) "Phosphoproteomics analysis identifies novel candidate substrates of the non-receptor tyrosine kinase, SRMS." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29496907 29496907]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000643 10.1074/mcp.RA118.000643]; GPMDB: [http://gpmdb.org/data/keyword/29496907 4]. | ||
#Azimi A, Caramuta S, Seashore-Ludlow B, Boström J, Robinson JL, Edfors F, Tuominen R, Kemper K, Krijgsman O, Peeper DS, Nielsen J, Hansson J, Egyhazi Brage S, Altun M, Uhlen M, Maddalo G, (2018) "Targeting CDK2 overcomes melanoma resistance against BRAF and Hsp90 inhibitors." <i>Mol Syst Biol</i> <b>14</b>(3):e7858; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29507054 29507054]; GPMDB: [http://gpmdb.org/data/keyword/29507054 16]. | #Azimi A, Caramuta S, Seashore-Ludlow B, Boström J, Robinson JL, Edfors F, Tuominen R, Kemper K, Krijgsman O, Peeper DS, Nielsen J, Hansson J, Egyhazi Brage S, Altun M, Uhlen M, Maddalo G, (2018) "Targeting CDK2 overcomes melanoma resistance against BRAF and Hsp90 inhibitors." <i>Mol Syst Biol</i> <b>14</b>(3):e7858; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29507054 29507054]; GPMDB: [http://gpmdb.org/data/keyword/29507054 16]. | ||
+ | #Lanoix J, Durette C, Courcelles M, Cossette É, Comtois-Marotte S, Hardy MP, Côté C, Perreault C, Thibault P, (2018) "Comparison of the MHC I Immunopeptidome Repertoire of B-Cell Lymphoblasts using Two Isolation Methods." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29508533 29508533]; doi: [https://dx.doi.org/10.1002/pmic.201700251 10.1002/pmic.201700251]; GPMDB: [http://gpmdb.org/data/keyword/29508533 48]. | ||
#Carette X, Platig J, Young DC, Helmel M, Young AT, Wang Z, Potluri LP, Moody CS, Zeng J, Prisic S, Paulson JN, Muntel J, Madduri AVR, Velarde J, Mayfield JA, Locher C, Wang T, Quackenbush J, Rhee KY, Moody DB, Steen H, Husson RN, (2018) "Multisystem Analysis of <i>Mycobacterium tuberculosis</i> Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface." <i>MBio</i> <b>9</b>(2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29511081 29511081]; doi: [https://dx.doi.org/10.1128/mBio.02333-17 10.1128/mBio.02333-17]; GPMDB: [http://gpmdb.org/data/keyword/29511081 48]. | #Carette X, Platig J, Young DC, Helmel M, Young AT, Wang Z, Potluri LP, Moody CS, Zeng J, Prisic S, Paulson JN, Muntel J, Madduri AVR, Velarde J, Mayfield JA, Locher C, Wang T, Quackenbush J, Rhee KY, Moody DB, Steen H, Husson RN, (2018) "Multisystem Analysis of <i>Mycobacterium tuberculosis</i> Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface." <i>MBio</i> <b>9</b>(2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29511081 29511081]; doi: [https://dx.doi.org/10.1128/mBio.02333-17 10.1128/mBio.02333-17]; GPMDB: [http://gpmdb.org/data/keyword/29511081 48]. | ||
- | #Ge S, Xia X, Ding C, Zhen B, Zhou Q, Feng J, Yuan J, Chen R, Li Y, Ge Z, Ji J, Zhang L, Wang J, Li Z, Lai Y, Hu Y, Li Y, Li Y, Gao J, Chen L, Xu J, Zhang C, Jung SY, Choi JM, Jain A, Liu M, Song L, Liu W, Guo G, Gong T, Huang Y, Qiu Y, Huang W, Shi T, Zhu W, Wang Y, He F, Shen L, Qin J, (2018) "A proteomic landscape of diffuse-type gastric cancer." <i>Nat Commun</i> <b>9</b>(1):1012; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29520031 29520031]; doi: [https://dx.doi.org/10.1038/s41467-018-03121-2 10.1038/s41467-018-03121-2]; GPMDB: [http://gpmdb.org/data/keyword/29520031 | + | #Ge S, Xia X, Ding C, Zhen B, Zhou Q, Feng J, Yuan J, Chen R, Li Y, Ge Z, Ji J, Zhang L, Wang J, Li Z, Lai Y, Hu Y, Li Y, Li Y, Gao J, Chen L, Xu J, Zhang C, Jung SY, Choi JM, Jain A, Liu M, Song L, Liu W, Guo G, Gong T, Huang Y, Qiu Y, Huang W, Shi T, Zhu W, Wang Y, He F, Shen L, Qin J, (2018) "A proteomic landscape of diffuse-type gastric cancer." <i>Nat Commun</i> <b>9</b>(1):1012; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29520031 29520031]; doi: [https://dx.doi.org/10.1038/s41467-018-03121-2 10.1038/s41467-018-03121-2]; GPMDB: [http://gpmdb.org/data/keyword/29520031 95]. |
#Ojalill M, Rappu P, Siljamäki E, Taimen P, Boström P, Heino J, (2018) "The composition of prostate core matrisome in vivo and in vitro unveiled by mass spectrometric analysis." <i>Prostate</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29520855 29520855]; doi: [https://dx.doi.org/10.1002/pros.23503 10.1002/pros.23503]; GPMDB: [http://gpmdb.org/data/keyword/29520855 62]. | #Ojalill M, Rappu P, Siljamäki E, Taimen P, Boström P, Heino J, (2018) "The composition of prostate core matrisome in vivo and in vitro unveiled by mass spectrometric analysis." <i>Prostate</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29520855 29520855]; doi: [https://dx.doi.org/10.1002/pros.23503 10.1002/pros.23503]; GPMDB: [http://gpmdb.org/data/keyword/29520855 62]. | ||
+ | #Deeke SA, Starr AE, Ning Z, Ahmadi S, Zhang X, Mayne J, Chiang CK, Singleton R, Benchimol EI, Mack DR, Stintzi A, Figeys D, (2018) "Mucosal-luminal interface proteomics reveals biomarkers of pediatric inflammatory bowel disease-associated colitis." <i>Am J Gastroenterol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29531307 29531307]; doi: [https://dx.doi.org/10.1038/s41395-018-0024-9 10.1038/s41395-018-0024-9]; GPMDB: [http://gpmdb.org/data/keyword/29531307 25]. | ||
+ | #Zila N, Bileck A, Muqaku B, Janker L, Eichhoff OM, Cheng PF, Dummer R, Levesque MP, Gerner C, Paulitschke V, (2018) "Proteomics-based insights into mitogen-activated protein kinase inhibitor resistance of cerebral melanoma metastases." <i>Clin Proteomics</i> <b>15</b>:13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29541007 29541007]; doi: [https://dx.doi.org/10.1186/s12014-018-9189-x 10.1186/s12014-018-9189-x]; GPMDB: [http://gpmdb.org/data/keyword/29541007 36]. | ||
+ | #Liang P, Zhu W, Lan T, Tao Q, (2018) "Detection of salivary protein biomarkers of saliva secretion disorder in a primary Sjögren syndrome murine model." <i>J Pharm Biomed Anal</i> <b>154</b>:252–262; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29558726 29558726]; doi: [https://dx.doi.org/10.1016/j.jpba.2018.03.023 10.1016/j.jpba.2018.03.023]; GPMDB: [http://gpmdb.org/data/keyword/29558726 2]. |
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 be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
The following is a list of 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 Apr. 1, 2018.