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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 Apr. | + | 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. 22, 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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#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]. | ||
+ | #Yair-Sabag S, Tedeschi V, Vitulano C, Barnea E, Glaser F, Melamed Kadosh D, Taurog JD, Fiorillo MT, Sorrentino R, Admon A, (2018) "The Peptide Repertoire of HLA-B27 may include Ligands with Lysine at P2 Anchor Position." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29393594 29393594]; doi: [https://dx.doi.org/10.1002/pmic.201700249 10.1002/pmic.201700249]; GPMDB: [http://gpmdb.org/data/keyword/29393594 87]. | ||
#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]. | #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]. | ||
+ | #Karayel Ö, Şanal E, Giese SH, Üretmen Kagıalı ZC, Polat AN, Hu CK, Renard BY, Tuncbag N, Özlü N, (2018) "Comparative phosphoproteomic analysis reveals signaling networks regulating monopolar and bipolar cytokinesis." <i>Sci Rep</i> <b>8</b>(1):2269; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29396449 29396449]; doi: [https://dx.doi.org/10.1038/s41598-018-20231-5 10.1038/s41598-018-20231-5]; GPMDB: [http://gpmdb.org/data/keyword/29396449 11]. | ||
+ | #Ikoma M, Gantt S, Casper C, Ogata Y, Zhang Q, Basom R, Dyen MR, Rose TM, Barcy S, (2018) "KSHV oral shedding and plasma viremia result in significant changes in the extracellular tumorigenic miRNA expression profile in individuals infected with the malaria parasite." <i>PLoS One</i> <b>13</b>(2):e0192659; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29425228 29425228]; doi: [https://dx.doi.org/10.1371/journal.pone.0192659 10.1371/journal.pone.0192659]; GPMDB: [http://gpmdb.org/data/keyword/29425228 3]. | ||
#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]. | ||
#De Muyt A, Pyatnitskaya A, Andréani J, Ranjha L, Ramus C, Laureau R, Fernandez-Vega A, Holoch D, Girard E, Govin J, Margueron R, Couté Y, Cejka P, Guérois R, Borde V, (2018) "A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation." <i>Genes Dev</i> <b>32</b>(3-4):283–296; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29440262 29440262]; doi: [https://dx.doi.org/10.1101/gad.308510.117 10.1101/gad.308510.117]; GPMDB: [http://gpmdb.org/data/keyword/29440262 19]. | #De Muyt A, Pyatnitskaya A, Andréani J, Ranjha L, Ramus C, Laureau R, Fernandez-Vega A, Holoch D, Girard E, Govin J, Margueron R, Couté Y, Cejka P, Guérois R, Borde V, (2018) "A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation." <i>Genes Dev</i> <b>32</b>(3-4):283–296; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29440262 29440262]; doi: [https://dx.doi.org/10.1101/gad.308510.117 10.1101/gad.308510.117]; GPMDB: [http://gpmdb.org/data/keyword/29440262 19]. | ||
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#Lan J, Núñez Galindo A, Doecke J, Fowler C, Martins RN, Rainey-Smith SR, Cominetti O, Dayon L, (2018) "Systematic Evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29451788 29451788]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00788 10.1021/acs.jproteome.7b00788]; GPMDB: [http://gpmdb.org/data/keyword/29451788 36]. | #Lan J, Núñez Galindo A, Doecke J, Fowler C, Martins RN, Rainey-Smith SR, Cominetti O, Dayon L, (2018) "Systematic Evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29451788 29451788]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00788 10.1021/acs.jproteome.7b00788]; GPMDB: [http://gpmdb.org/data/keyword/29451788 36]. | ||
#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]. | ||
+ | #Eckersley A, Mellody KT, Pilkington S, Griffiths CEM, Watson REB, O'Cualain R, Baldock C, Knight D, Sherratt MJ, (2018) "Structural and compositional diversity of fibrillin microfibrils in human tissues." <i>J Biol Chem</i> <b>293</b>(14):5117–5133; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29453284 29453284]; doi: [https://dx.doi.org/10.1074/jbc.RA117.001483 10.1074/jbc.RA117.001483]; GPMDB: [http://gpmdb.org/data/keyword/29453284 19]. | ||
#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]. | #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]. | ||
+ | #Velez G, Machlab DA, Tang PH, Sun Y, Tsang SH, Bassuk AG, Mahajan VB, (2018) "Proteomic analysis of the human retina reveals region-specific susceptibilities to metabolic- and oxidative stress-related diseases." <i>PLoS One</i> <b>13</b>(2):e0193250; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29466423 29466423]; doi: [https://dx.doi.org/10.1371/journal.pone.0193250 10.1371/journal.pone.0193250]; GPMDB: [http://gpmdb.org/data/keyword/29466423 9]. | ||
#Laria AE, Messineo S, Arcidiacono B, Varano M, Chiefari E, Semple RK, Rocha N, Russo D, Cuda G, Gaspari M, Brunetti A, Foti DP, (2018) "Secretome Analysis of Hypoxia-Induced 3T3-L1 Adipocytes Uncovers Novel Proteins Potentially Involved in Obesity." <i>Proteomics</i> <b>18</b>(7):e1700260; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29466620 29466620]; doi: [https://dx.doi.org/10.1002/pmic.201700260 10.1002/pmic.201700260]; GPMDB: [http://gpmdb.org/data/keyword/29466620 8]. | #Laria AE, Messineo S, Arcidiacono B, Varano M, Chiefari E, Semple RK, Rocha N, Russo D, Cuda G, Gaspari M, Brunetti A, Foti DP, (2018) "Secretome Analysis of Hypoxia-Induced 3T3-L1 Adipocytes Uncovers Novel Proteins Potentially Involved in Obesity." <i>Proteomics</i> <b>18</b>(7):e1700260; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29466620 29466620]; doi: [https://dx.doi.org/10.1002/pmic.201700260 10.1002/pmic.201700260]; GPMDB: [http://gpmdb.org/data/keyword/29466620 8]. | ||
#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]. | ||
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#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]. | #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 132]. |
#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 | + | #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 112]. |
#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]. | #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]. | ||
#Savitski MM, Zinn N, Faelth-Savitski M, Poeckel D, Gade S, Becher I, Muelbaier M, Wagner AJ, Strohmer K, Werner T, Melchert S, Petretich M, Rutkowska A, Vappiani J, Franken H, Steidel M, Sweetman GM, Gilan O, Lam EYN, Dawson MA, Prinjha RK, Grandi P, Bergamini G, Bantscheff M, (2018) "Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis." <i>Cell</i> <b>173</b>(1):260–274.e25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29551266 29551266]; doi: [https://dx.doi.org/10.1016/j.cell.2018.02.030 10.1016/j.cell.2018.02.030]; GPMDB: [http://gpmdb.org/data/keyword/29551266 5]. | #Savitski MM, Zinn N, Faelth-Savitski M, Poeckel D, Gade S, Becher I, Muelbaier M, Wagner AJ, Strohmer K, Werner T, Melchert S, Petretich M, Rutkowska A, Vappiani J, Franken H, Steidel M, Sweetman GM, Gilan O, Lam EYN, Dawson MA, Prinjha RK, Grandi P, Bergamini G, Bantscheff M, (2018) "Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis." <i>Cell</i> <b>173</b>(1):260–274.e25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29551266 29551266]; doi: [https://dx.doi.org/10.1016/j.cell.2018.02.030 10.1016/j.cell.2018.02.030]; GPMDB: [http://gpmdb.org/data/keyword/29551266 5]. | ||
+ | #Salunkhe V, De Cuyper IM, Papadopoulos P, van der Meer PF, Daal BB, Villa-Fajardo M, de Korte D, van den Berg TK, Gutiérrez L, (2018) "A comprehensive proteomics study on platelet concentrates: Platelet proteome, storage time and Mirasol pathogen reduction technology." <i>Platelets</i> <b></b>:1–12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29553857 29553857]; doi: [https://dx.doi.org/10.1080/09537104.2018.1447658 10.1080/09537104.2018.1447658]; GPMDB: [http://gpmdb.org/data/keyword/29553857 27]. | ||
#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]. | #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]. | ||
#Saei AA, Sabatier P, Güler Tokat Ü, Chernobrovkin A, Pirmoradian M, Zubarev RA, (2018) "Comparative proteomics of dying and surviving cancer cells improves the identification of drug targets and sheds light on cell life/death decisions." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29572246 29572246]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000610 10.1074/mcp.RA118.000610]; GPMDB: [http://gpmdb.org/data/keyword/29572246 90]. | #Saei AA, Sabatier P, Güler Tokat Ü, Chernobrovkin A, Pirmoradian M, Zubarev RA, (2018) "Comparative proteomics of dying and surviving cancer cells improves the identification of drug targets and sheds light on cell life/death decisions." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29572246 29572246]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000610 10.1074/mcp.RA118.000610]; GPMDB: [http://gpmdb.org/data/keyword/29572246 90]. | ||
- | #Haller C, Chaskar P, Piccand J, Cominetti O, Macron C, Dayon L, Kraus MR, (2018) "Insights into islet differentiation and maturation through proteomic characterization of a human iPSC-derived pancreatic endocrine model." <i>Proteomics Clin Appl</i> <b></b>:e1600173; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29578310 29578310]; doi: [https://dx.doi.org/10.1002/prca.201600173 10.1002/prca.201600173]; GPMDB: [http://gpmdb.org/data/keyword/29578310 | + | #Haller C, Chaskar P, Piccand J, Cominetti O, Macron C, Dayon L, Kraus MR, (2018) "Insights into islet differentiation and maturation through proteomic characterization of a human iPSC-derived pancreatic endocrine model." <i>Proteomics Clin Appl</i> <b></b>:e1600173; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29578310 29578310]; doi: [https://dx.doi.org/10.1002/prca.201600173 10.1002/prca.201600173]; GPMDB: [http://gpmdb.org/data/keyword/29578310 218]. |
#Klont F, Bras L, Wolters JC, Ongay S, Bischoff R, Halmos GB, Horvatovich P, (2018) "Assessment of Sample Preparation Bias in Mass Spectrometry-Based Proteomics." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29608294 29608294]; doi: [https://dx.doi.org/10.1021/acs.analchem.8b00600 10.1021/acs.analchem.8b00600]; GPMDB: [http://gpmdb.org/data/keyword/29608294 80]. | #Klont F, Bras L, Wolters JC, Ongay S, Bischoff R, Halmos GB, Horvatovich P, (2018) "Assessment of Sample Preparation Bias in Mass Spectrometry-Based Proteomics." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29608294 29608294]; doi: [https://dx.doi.org/10.1021/acs.analchem.8b00600 10.1021/acs.analchem.8b00600]; GPMDB: [http://gpmdb.org/data/keyword/29608294 80]. | ||
#Bostanci N, Selevsek N, Wolski W, Grossmann J, Bao K, Wahlander A, Trachsel C, Schlapbach R, Özturk VÖ, Afacan B, Emingil G, Belibasakis GN, (2018) "Targeted proteomics guided by label-free global proteome analysis in saliva reveal transition signatures from health to periodontal disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29610270 29610270]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000718 10.1074/mcp.RA118.000718]; GPMDB: [http://gpmdb.org/data/keyword/29610270 54]. | #Bostanci N, Selevsek N, Wolski W, Grossmann J, Bao K, Wahlander A, Trachsel C, Schlapbach R, Özturk VÖ, Afacan B, Emingil G, Belibasakis GN, (2018) "Targeted proteomics guided by label-free global proteome analysis in saliva reveal transition signatures from health to periodontal disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29610270 29610270]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000718 10.1074/mcp.RA118.000718]; GPMDB: [http://gpmdb.org/data/keyword/29610270 54]. |
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. 22, 2018.