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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 May | + | 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 May 20, 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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#Koch H, Busto ME, Kramer K, Médard G, Kuster B, (2015) "Chemical Proteomics Uncovers EPHA2 as a Mechanism of Acquired Resistance to Small Molecule EGFR Kinase Inhibition." <i>J Proteome Res</i> <b>14</b>(6):2617–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25963923 25963923]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00161 10.1021/acs.jproteome.5b00161]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25963923 18]. | #Koch H, Busto ME, Kramer K, Médard G, Kuster B, (2015) "Chemical Proteomics Uncovers EPHA2 as a Mechanism of Acquired Resistance to Small Molecule EGFR Kinase Inhibition." <i>J Proteome Res</i> <b>14</b>(6):2617–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25963923 25963923]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00161 10.1021/acs.jproteome.5b00161]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25963923 18]. | ||
#Watanabe S, Tan D, Lakshminarasimhan M, Washburn MP, Hong EJ, Walz T, Peterson CL, (2015) "Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C." <i>Nat Commun</i> <b>6</b>:7108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25964121 25964121]; doi: [https://dx.doi.org/10.1038/ncomms8108 10.1038/ncomms8108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25964121 2]. | #Watanabe S, Tan D, Lakshminarasimhan M, Washburn MP, Hong EJ, Walz T, Peterson CL, (2015) "Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C." <i>Nat Commun</i> <b>6</b>:7108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25964121 25964121]; doi: [https://dx.doi.org/10.1038/ncomms8108 10.1038/ncomms8108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25964121 2]. | ||
+ | #Hesketh A, Deery MJ, Hong HJ, (2015) "High-Resolution Mass Spectrometry Based Proteomic Analysis of the Response to Vancomycin-Induced Cell Wall Stress in Streptomyces coelicolor A3(2)." <i>J Proteome Res</i> <b>14</b>(7):2915–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25965010 25965010]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00242 10.1021/acs.jproteome.5b00242]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25965010 3]. | ||
#Xiong Q, Zhang L, Xin L, Gao Y, Peng Y, Tang P, Ge W, (2015) "Proteomic study of different culture medium serum volume fractions on RANKL-dependent RAW264.7 cells differentiating into osteoclasts." <i>Proteome Sci</i> <b>13</b>:16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25969670 25969670]; doi: [https://dx.doi.org/10.1186/s12953-015-0073-6 10.1186/s12953-015-0073-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25969670 1]. | #Xiong Q, Zhang L, Xin L, Gao Y, Peng Y, Tang P, Ge W, (2015) "Proteomic study of different culture medium serum volume fractions on RANKL-dependent RAW264.7 cells differentiating into osteoclasts." <i>Proteome Sci</i> <b>13</b>:16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25969670 25969670]; doi: [https://dx.doi.org/10.1186/s12953-015-0073-6 10.1186/s12953-015-0073-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25969670 1]. | ||
#Oishi N, Duscha S, Boukari H, Meyer M, Xie J, Wei G, Schrepfer T, Roschitzki B, Boettger EC, Schacht J, (2015) "XBP1 mitigates aminoglycoside-induced endoplasmic reticulum stress and neuronal cell death." <i>Cell Death Dis</i> <b>6</b>:e1763; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25973683 25973683]; doi: [https://dx.doi.org/10.1038/cddis.2015.108 10.1038/cddis.2015.108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25973683 1]. | #Oishi N, Duscha S, Boukari H, Meyer M, Xie J, Wei G, Schrepfer T, Roschitzki B, Boettger EC, Schacht J, (2015) "XBP1 mitigates aminoglycoside-induced endoplasmic reticulum stress and neuronal cell death." <i>Cell Death Dis</i> <b>6</b>:e1763; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25973683 25973683]; doi: [https://dx.doi.org/10.1038/cddis.2015.108 10.1038/cddis.2015.108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25973683 1]. | ||
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#Hospital MA, Jacquel A, Mazed F, Saland E, Larrue C, Mondesir J, Birsen R, Green AS, Lambert M, Sujobert P, Gautier EF, Salnot V, Le Gall M, Decroocq J, Poulain L, Jacque N, Fontenay M, Kosmider O, Récher C, Auberger P, Mayeux P, Bouscary D, Sarry JE, Tamburini J, (2017) "RSK2 is a new Pim2 target with pro-survival functions in FLT3-ITD-positive acute myeloid leukemia." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28914261 28914261]; doi: [https://dx.doi.org/10.1038/leu.2017.284 10.1038/leu.2017.284]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28914261 17]. | #Hospital MA, Jacquel A, Mazed F, Saland E, Larrue C, Mondesir J, Birsen R, Green AS, Lambert M, Sujobert P, Gautier EF, Salnot V, Le Gall M, Decroocq J, Poulain L, Jacque N, Fontenay M, Kosmider O, Récher C, Auberger P, Mayeux P, Bouscary D, Sarry JE, Tamburini J, (2017) "RSK2 is a new Pim2 target with pro-survival functions in FLT3-ITD-positive acute myeloid leukemia." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28914261 28914261]; doi: [https://dx.doi.org/10.1038/leu.2017.284 10.1038/leu.2017.284]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28914261 17]. | ||
#Tain LS, Sehlke R, Jain C, Chokkalingam M, Nagaraj N, Essers P, Rassner M, Grönke S, Froelich J, Dieterich C, Mann M, Alic N, Beyer A, Partridge L, (2017) "A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance." <i>Mol Syst Biol</i> <b>13</b>(9):939; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28916541 28916541]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28916541 92]. | #Tain LS, Sehlke R, Jain C, Chokkalingam M, Nagaraj N, Essers P, Rassner M, Grönke S, Froelich J, Dieterich C, Mann M, Alic N, Beyer A, Partridge L, (2017) "A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance." <i>Mol Syst Biol</i> <b>13</b>(9):939; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28916541 28916541]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28916541 92]. | ||
- | #Mills RJ, Titmarsh DM, Koenig X, Parker BL, Ryall JG, Quaife-Ryan GA, Voges HK, Hodson MP, Ferguson C, Drowley L, Plowright AT, Needham EJ, Wang QD, Gregorevic P, Xin M, Thomas WG, Parton RG, Nielsen LK, Launikonis BS, James DE, Elliott DA, Porrello ER, Hudson JE, (2017) "Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(40):E8372–E8381; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28916735 28916735]; doi: [https://dx.doi.org/10.1073/pnas.1707316114 10.1073/pnas.1707316114]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28916735 | + | #Mills RJ, Titmarsh DM, Koenig X, Parker BL, Ryall JG, Quaife-Ryan GA, Voges HK, Hodson MP, Ferguson C, Drowley L, Plowright AT, Needham EJ, Wang QD, Gregorevic P, Xin M, Thomas WG, Parton RG, Nielsen LK, Launikonis BS, James DE, Elliott DA, Porrello ER, Hudson JE, (2017) "Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(40):E8372–E8381; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28916735 28916735]; doi: [https://dx.doi.org/10.1073/pnas.1707316114 10.1073/pnas.1707316114]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28916735 8]. |
#Martin-Perez M, Villén J, (2017) "Determinants and Regulation of Protein Turnover in Yeast." <i>Cell Syst</i> <b>5</b>(3):283–294.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28918244 28918244]; doi: [https://dx.doi.org/10.1016/j.cels.2017.08.008 10.1016/j.cels.2017.08.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28918244 12]. | #Martin-Perez M, Villén J, (2017) "Determinants and Regulation of Protein Turnover in Yeast." <i>Cell Syst</i> <b>5</b>(3):283–294.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28918244 28918244]; doi: [https://dx.doi.org/10.1016/j.cels.2017.08.008 10.1016/j.cels.2017.08.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28918244 12]. | ||
#Weber A, Elliott PR, Pinto-Fernandez A, Bonham S, Kessler BM, Komander D, El Oualid F, Krappmann D, (2017) "A Linear Diubiquitin-Based Probe for Efficient and Selective Detection of the Deubiquitinating Enzyme OTULIN." <i>Cell Chem Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28919039 28919039]; doi: [https://dx.doi.org/10.1016/j.chembiol.2017.08.006 10.1016/j.chembiol.2017.08.006]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28919039 16]. | #Weber A, Elliott PR, Pinto-Fernandez A, Bonham S, Kessler BM, Komander D, El Oualid F, Krappmann D, (2017) "A Linear Diubiquitin-Based Probe for Efficient and Selective Detection of the Deubiquitinating Enzyme OTULIN." <i>Cell Chem Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28919039 28919039]; doi: [https://dx.doi.org/10.1016/j.chembiol.2017.08.006 10.1016/j.chembiol.2017.08.006]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28919039 16]. | ||
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#Steger M, Diez F, Dhekne HS, Lis P, Nirujogi RS, Karayel O, Tonelli F, Martinez TN, Lorentzen E, Pfeffer SR, Alessi DR, Mann M, (2017) "Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29125462 29125462]; doi: [https://dx.doi.org/10.7554/eLife.31012 10.7554/eLife.31012]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29125462 667]. | #Steger M, Diez F, Dhekne HS, Lis P, Nirujogi RS, Karayel O, Tonelli F, Martinez TN, Lorentzen E, Pfeffer SR, Alessi DR, Mann M, (2017) "Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29125462 29125462]; doi: [https://dx.doi.org/10.7554/eLife.31012 10.7554/eLife.31012]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29125462 667]. | ||
#Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M, (2017) "A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling." <i>Cell Syst</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29128334 29128334]; doi: [https://dx.doi.org/10.1016/j.cels.2017.10.010 10.1016/j.cels.2017.10.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29128334 109]. | #Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M, (2017) "A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling." <i>Cell Syst</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29128334 29128334]; doi: [https://dx.doi.org/10.1016/j.cels.2017.10.010 10.1016/j.cels.2017.10.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29128334 109]. | ||
+ | #Ju Lee H, Bartsch D, Xiao C, Guerrero S, Ahuja G, Schindler C, Moresco JJ, Yates JR 3rd, Gebauer F, Bazzi H, Dieterich C, Kurian L, Vilchez D, (2017) "A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells." <i>Nat Commun</i> <b>8</b>(1):1456; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29129916 29129916]; doi: [https://dx.doi.org/10.1038/s41467-017-01744-5 10.1038/s41467-017-01744-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29129916 6]. | ||
#García-Berrocoso T, Llombart V, Colàs-Campàs L, Hainard A, Licker V, Penalba A, Ramiro L, Simats A, Bustamante A, Martínez-Saez E, Canals F, Sanchez JC, Montaner J, (2017) "Single Cell Immuno-laser Microdissection Coupled to Label-free Proteomics to Reveal the Proteotypes of Human Brain Cells After Ischemia." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133510 29133510]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000419 10.1074/mcp.RA117.000419]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29133510 102]. | #García-Berrocoso T, Llombart V, Colàs-Campàs L, Hainard A, Licker V, Penalba A, Ramiro L, Simats A, Bustamante A, Martínez-Saez E, Canals F, Sanchez JC, Montaner J, (2017) "Single Cell Immuno-laser Microdissection Coupled to Label-free Proteomics to Reveal the Proteotypes of Human Brain Cells After Ischemia." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133510 29133510]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000419 10.1074/mcp.RA117.000419]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29133510 102]. | ||
#Negretti NM, Gourley CR, Clair G, Adkins JN, Konkel ME, (2017) "The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species." <i>Sci Rep</i> <b>7</b>(1):15455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133896 29133896]; doi: [https://dx.doi.org/10.1038/s41598-017-15379-5 10.1038/s41598-017-15379-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29133896 8]. | #Negretti NM, Gourley CR, Clair G, Adkins JN, Konkel ME, (2017) "The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species." <i>Sci Rep</i> <b>7</b>(1):15455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133896 29133896]; doi: [https://dx.doi.org/10.1038/s41598-017-15379-5 10.1038/s41598-017-15379-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29133896 8]. | ||
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#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: [https://gpmdb.thegpm.org/data/keyword/29520031 164]. | #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: [https://gpmdb.thegpm.org/data/keyword/29520031 164]. | ||
#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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/29520855 62]. | ||
- | #Chen JT, Liu CC, Yu JS, Li HH, Lai MC, (2018) "Integrated omics profiling identifies hypoxia-regulated genes in HCT116 colon cancer cells." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29524648 29524648]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.02.031 10.1016/j.jprot.2018.02.031]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29524648 | + | #Chen JT, Liu CC, Yu JS, Li HH, Lai MC, (2018) "Integrated omics profiling identifies hypoxia-regulated genes in HCT116 colon cancer cells." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29524648 29524648]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.02.031 10.1016/j.jprot.2018.02.031]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29524648 4]. |
#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: [https://gpmdb.thegpm.org/data/keyword/29531307 112]. | #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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/29541007 36]. | ||
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#Sanz-Bravo A, Alvarez-Navarro C, Martín-Esteban A, Barnea E, Admon A, López de Castro JA, (2018) "Ranking the contribution of ankylosing spondylitis-associated ERAP1 polymorphisms to shaping the HLA-B*27 peptidome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29632046 29632046]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000565 10.1074/mcp.RA117.000565]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29632046 15]. | #Sanz-Bravo A, Alvarez-Navarro C, Martín-Esteban A, Barnea E, Admon A, López de Castro JA, (2018) "Ranking the contribution of ankylosing spondylitis-associated ERAP1 polymorphisms to shaping the HLA-B*27 peptidome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29632046 29632046]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000565 10.1074/mcp.RA117.000565]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29632046 15]. | ||
#Johnston D, Malo Estepa I, Ebhardt HA, Crowe MA, Diskin MG, (2018) "Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle." <i>Theriogenology</i> <b>114</b>:301–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29677633 29677633]; doi: [https://dx.doi.org/10.1016/j.theriogenology.2018.04.008 10.1016/j.theriogenology.2018.04.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29677633 63]. | #Johnston D, Malo Estepa I, Ebhardt HA, Crowe MA, Diskin MG, (2018) "Differences in the bovine milk whey proteome between early pregnancy and the estrous cycle." <i>Theriogenology</i> <b>114</b>:301–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29677633 29677633]; doi: [https://dx.doi.org/10.1016/j.theriogenology.2018.04.008 10.1016/j.theriogenology.2018.04.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29677633 63]. | ||
+ | #Komov L, Kadosh DM, Barnea E, Milner E, Hendler A, Admon A, (2018) "Cell Surface MHC Class I Expression is Limited by the Availability of Peptide-Receptive 'Empty' Molecules Rather than by the Supply of Peptide Ligands." <i>Proteomics</i> <b></b>:e1700248; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29707912 29707912]; doi: [https://dx.doi.org/10.1002/pmic.201700248 10.1002/pmic.201700248]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29707912 35]. | ||
#Rosting C, Yu J, Cooper HJ, (2018) "High Field Asymmetric Waveform Ion Mobility Spectrometry in Nontargeted Bottom-up Proteomics of Dried Blood Spots." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29707944 29707944]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00746 10.1021/acs.jproteome.7b00746]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29707944 42]. | #Rosting C, Yu J, Cooper HJ, (2018) "High Field Asymmetric Waveform Ion Mobility Spectrometry in Nontargeted Bottom-up Proteomics of Dried Blood Spots." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29707944 29707944]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00746 10.1021/acs.jproteome.7b00746]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29707944 42]. | ||
#Chen X, Yu C, Gao J, Zhu H, Cui B, Zhang T, Zhou Y, Liu Q, He H, Xiao R, Huang R, Xie H, Gao D, Zhou H, (2018) "A novel USP9X substrate TTK contributes to tumorigenesis in non-small-cell lung cancer." <i>Theranostics</i> <b>8</b>(9):2348–2360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29721084 29721084]; doi: [https://dx.doi.org/10.7150/thno.22901 10.7150/thno.22901]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29721084 1]. | #Chen X, Yu C, Gao J, Zhu H, Cui B, Zhang T, Zhou Y, Liu Q, He H, Xiao R, Huang R, Xie H, Gao D, Zhou H, (2018) "A novel USP9X substrate TTK contributes to tumorigenesis in non-small-cell lung cancer." <i>Theranostics</i> <b>8</b>(9):2348–2360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29721084 29721084]; doi: [https://dx.doi.org/10.7150/thno.22901 10.7150/thno.22901]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29721084 1]. | ||
- | #Meier F, Geyer PE, Virreira Winter S, Cox J, Mann M, (2018) "BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29735998 29735998]; doi: [https://dx.doi.org/10.1038/s41592-018-0003-5 10.1038/s41592-018-0003-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29735998 | + | #Meier F, Geyer PE, Virreira Winter S, Cox J, Mann M, (2018) "BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29735998 29735998]; doi: [https://dx.doi.org/10.1038/s41592-018-0003-5 10.1038/s41592-018-0003-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29735998 60]. |
+ | #Seltmann K, Meyer M, Sulcova J, Kockmann T, Wehkamp U, Weidinger S, Auf dem Keller U, Werner S, (2018) "Humidity-regulated CLCA2 protects the epidermis from hyperosmotic stress." <i>Sci Transl Med</i> <b>10</b>(440):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29743348 29743348]; doi: [https://dx.doi.org/10.1126/scitranslmed.aao4650 10.1126/scitranslmed.aao4650]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29743348 24]. |
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 May 20, 2018.