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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 July 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: [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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#Brockmeyer C, Paster W, Pepper D, Tan CP, Trudgian DC, McGowan S, Fu G, Gascoigne NR, Acuto O, Salek M, (2011) "T cell receptor (TCR)-induced tyrosine phosphorylation dynamics identifies THEMIS as a new TCR signalosome component." <i>J Biol Chem</i> <b>286</b>(9):7535–47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21189249 21189249]; doi: [https://dx.doi.org/10.1074/jbc.M110.201236 10.1074/jbc.M110.201236]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21189249 4]. | #Brockmeyer C, Paster W, Pepper D, Tan CP, Trudgian DC, McGowan S, Fu G, Gascoigne NR, Acuto O, Salek M, (2011) "T cell receptor (TCR)-induced tyrosine phosphorylation dynamics identifies THEMIS as a new TCR signalosome component." <i>J Biol Chem</i> <b>286</b>(9):7535–47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21189249 21189249]; doi: [https://dx.doi.org/10.1074/jbc.M110.201236 10.1074/jbc.M110.201236]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21189249 4]. | ||
#Manes NP, Dong L, Zhou W, Du X, Reghu N, Kool AC, Choi D, Bailey CL, Petricoin EF 3rd, Liotta LA, Popov SG, (2011) "Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry." <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.000927; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21189417 21189417]; doi: [https://dx.doi.org/10.1074/mcp.M110.000927 10.1074/mcp.M110.000927]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21189417 133]. | #Manes NP, Dong L, Zhou W, Du X, Reghu N, Kool AC, Choi D, Bailey CL, Petricoin EF 3rd, Liotta LA, Popov SG, (2011) "Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry." <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.000927; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21189417 21189417]; doi: [https://dx.doi.org/10.1074/mcp.M110.000927 10.1074/mcp.M110.000927]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21189417 133]. | ||
+ | #Chornoguz O, Grmai L, Sinha P, Artemenko KA, Zubarev RA, Ostrand-Rosenberg S, (2011) "Proteomic pathway analysis reveals inflammation increases myeloid-derived suppressor cell resistance to apoptosis." <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.002980; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21191032 21191032]; doi: [https://dx.doi.org/10.1074/mcp.M110.002980 10.1074/mcp.M110.002980]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21191032 6]. | ||
#Hansson J, Panchaud A, Favre L, Bosco N, Mansourian R, Benyacoub J, Blum S, Jensen ON, Kussmann M, (2011) "Time-resolved quantitative proteome analysis of in vivo intestinal development." <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.005231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21191033 21191033]; doi: [https://dx.doi.org/10.1074/mcp.M110.005231 10.1074/mcp.M110.005231]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21191033 48]. | #Hansson J, Panchaud A, Favre L, Bosco N, Mansourian R, Benyacoub J, Blum S, Jensen ON, Kussmann M, (2011) "Time-resolved quantitative proteome analysis of in vivo intestinal development." <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.005231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21191033 21191033]; doi: [https://dx.doi.org/10.1074/mcp.M110.005231 10.1074/mcp.M110.005231]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21191033 48]. | ||
#Singh SK, Lakshmi MG, Saxena S, Swamy CV, Idris MM, (2011) "Proteome profile of zebrafish caudal fin based on one-dimensional gel electrophoresis LCMS/MS and two-dimensional gel electrophoresis MALDI MS/MS analysis." <i>J Sep Sci</i> <b>34</b>(2):225–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21246729 21246729]; doi: [https://dx.doi.org/10.1002/jssc.201000626 10.1002/jssc.201000626]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21246729 17]. | #Singh SK, Lakshmi MG, Saxena S, Swamy CV, Idris MM, (2011) "Proteome profile of zebrafish caudal fin based on one-dimensional gel electrophoresis LCMS/MS and two-dimensional gel electrophoresis MALDI MS/MS analysis." <i>J Sep Sci</i> <b>34</b>(2):225–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21246729 21246729]; doi: [https://dx.doi.org/10.1002/jssc.201000626 10.1002/jssc.201000626]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/21246729 17]. | ||
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#Elmasri WA, Zhu R, Peng W, Al-Hariri M, Kobeissy F, Tran P, Hamood AN, Hegazy MF, Paré PW, Mechref Y, (2017) "Multitargeted Flavonoid Inhibition of the Pathogenic Bacterium Staphylococcus aureus: A Proteomic Characterization." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28541047 28541047]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00137 10.1021/acs.jproteome.7b00137]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28541047 12]. | #Elmasri WA, Zhu R, Peng W, Al-Hariri M, Kobeissy F, Tran P, Hamood AN, Hegazy MF, Paré PW, Mechref Y, (2017) "Multitargeted Flavonoid Inhibition of the Pathogenic Bacterium Staphylococcus aureus: A Proteomic Characterization." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28541047 28541047]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00137 10.1021/acs.jproteome.7b00137]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28541047 12]. | ||
#Fijalkowska D, Verbruggen S, Ndah E, Jonckheere V, Menschaert G, Van Damme P, (2017) "eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs." <i>Nucleic Acids Res</i> <b>45</b>(13):7997–8013; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28541577 28541577]; doi: [https://dx.doi.org/10.1093/nar/gkx469 10.1093/nar/gkx469]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28541577 19]. | #Fijalkowska D, Verbruggen S, Ndah E, Jonckheere V, Menschaert G, Van Damme P, (2017) "eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs." <i>Nucleic Acids Res</i> <b>45</b>(13):7997–8013; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28541577 28541577]; doi: [https://dx.doi.org/10.1093/nar/gkx469 10.1093/nar/gkx469]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28541577 19]. | ||
+ | #Hakimi O, Ternette N, Murphy R, Kessler BM, Carr A, (2017) "A quantitative label-free analysis of the extracellular proteome of human supraspinatus tendon reveals damage to the pericellular and elastic fibre niches in torn and aged tissue." <i>PLoS One</i> <b>12</b>(5):e0177656; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28542244 28542244]; doi: [https://dx.doi.org/10.1371/journal.pone.0177656 10.1371/journal.pone.0177656]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28542244 116]. | ||
#Kume K, Cantwell H, Neumann FR, Jones AW, Snijders AP, Nurse P, (2017) "A systematic genomic screen implicates nucleocytoplasmic transport and membrane growth in nuclear size control." <i>PLoS Genet</i> <b>13</b>(5):e1006767; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28545058 28545058]; doi: [https://dx.doi.org/10.1371/journal.pgen.1006767 10.1371/journal.pgen.1006767]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28545058 192]. | #Kume K, Cantwell H, Neumann FR, Jones AW, Snijders AP, Nurse P, (2017) "A systematic genomic screen implicates nucleocytoplasmic transport and membrane growth in nuclear size control." <i>PLoS Genet</i> <b>13</b>(5):e1006767; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28545058 28545058]; doi: [https://dx.doi.org/10.1371/journal.pgen.1006767 10.1371/journal.pgen.1006767]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28545058 192]. | ||
#Meier SM, Kreutz D, Winter L, Klose MHM, Cseh K, Weiss T, Bileck A, Alte B, Mader JC, Jana S, Chatterjee A, Bhattacharyya A, Hejl M, Jakupec MA, Heffeter P, Berger W, Hartinger CG, Keppler BK, Wiche G, Gerner C, (2017) "An Organoruthenium Anticancer Agent Shows Unexpected Target Selectivity For Plectin." <i>Angew Chem Int Ed Engl</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28547791 28547791]; doi: [https://dx.doi.org/10.1002/anie.201702242 10.1002/anie.201702242]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28547791 4]. | #Meier SM, Kreutz D, Winter L, Klose MHM, Cseh K, Weiss T, Bileck A, Alte B, Mader JC, Jana S, Chatterjee A, Bhattacharyya A, Hejl M, Jakupec MA, Heffeter P, Berger W, Hartinger CG, Keppler BK, Wiche G, Gerner C, (2017) "An Organoruthenium Anticancer Agent Shows Unexpected Target Selectivity For Plectin." <i>Angew Chem Int Ed Engl</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28547791 28547791]; doi: [https://dx.doi.org/10.1002/anie.201702242 10.1002/anie.201702242]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28547791 4]. | ||
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#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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/29610270 54]. | ||
#Sipilä KH, Drushinin K, Rappu P, Jokinen J, Salminen TA, Salo AM, Käpylä J, Myllyharju J, Heino J, (2018) "Proline hydroxylation in collagen supports integrin binding by two distinct mechanisms." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29615493 29615493]; doi: [https://dx.doi.org/10.1074/jbc.RA118.002200 10.1074/jbc.RA118.002200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29615493 54]. | #Sipilä KH, Drushinin K, Rappu P, Jokinen J, Salminen TA, Salo AM, Käpylä J, Myllyharju J, Heino J, (2018) "Proline hydroxylation in collagen supports integrin binding by two distinct mechanisms." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29615493 29615493]; doi: [https://dx.doi.org/10.1074/jbc.RA118.002200 10.1074/jbc.RA118.002200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29615493 54]. | ||
+ | #Lim S, Kim D, Ju S, Shin S, Cho IJ, Park SH, Grailhe R, Lee C, Kim YK, (2018) "Glioblastoma-secreted soluble CD44 activates tau pathology in the brain." <i>Exp Mol Med</i> <b>50</b>(4):5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29622771 29622771]; doi: [https://dx.doi.org/10.1038/s12276-017-0008-7 10.1038/s12276-017-0008-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29622771 2]. | ||
#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]. | ||
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#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]. | #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]. | #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]. | ||
+ | #Aslebagh R, Channaveerappa D, Arcaro KF, Darie CC, (2018) "Comparative two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of human milk to identify dysregulated proteins in breast cancer." <i>Electrophoresis</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29756217 29756217]; doi: [https://dx.doi.org/10.1002/elps.201800025 10.1002/elps.201800025]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29756217 62]. | ||
#Gaviard C, Broutin I, Cosette P, De E, Jouenne T, Hardouin J, (2018) "Lysine succinylation and acetylation in Pseudomonas aeruginosa." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29770699 29770699]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00210 10.1021/acs.jproteome.8b00210]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29770699 24]. | #Gaviard C, Broutin I, Cosette P, De E, Jouenne T, Hardouin J, (2018) "Lysine succinylation and acetylation in Pseudomonas aeruginosa." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29770699 29770699]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00210 10.1021/acs.jproteome.8b00210]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29770699 24]. | ||
#Di Lorenzo G, Voltolini Velho R, Winter D, Thelen M, Ahmadi S, Schweizer M, De Pace R, Cornils K, Yorgan TA, Grüb S, Hermans-Borgmeyer I, Schinke T, Müller-Loennies S, Braulke T, Pohl S, (2018) "Lysosomal proteome and secretome analysis identifies missorted enzymes and their non-degraded substrates in mucolipidosis III mouse cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29773673 29773673]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000720 10.1074/mcp.RA118.000720]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29773673 30]. | #Di Lorenzo G, Voltolini Velho R, Winter D, Thelen M, Ahmadi S, Schweizer M, De Pace R, Cornils K, Yorgan TA, Grüb S, Hermans-Borgmeyer I, Schinke T, Müller-Loennies S, Braulke T, Pohl S, (2018) "Lysosomal proteome and secretome analysis identifies missorted enzymes and their non-degraded substrates in mucolipidosis III mouse cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29773673 29773673]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000720 10.1074/mcp.RA118.000720]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29773673 30]. | ||
#Wang H, Cheng Q, Li X, Hu F, Han L, Zhang H, Li L, Ge J, Ying X, Guo X, Wang Q, (2018) "Loss of TIGAR induces oxidative stress and meiotic defects in oocytes from obese mice." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29776966 29776966]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000620 10.1074/mcp.RA118.000620]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29776966 9]. | #Wang H, Cheng Q, Li X, Hu F, Han L, Zhang H, Li L, Ge J, Ying X, Guo X, Wang Q, (2018) "Loss of TIGAR induces oxidative stress and meiotic defects in oocytes from obese mice." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29776966 29776966]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000620 10.1074/mcp.RA118.000620]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29776966 9]. | ||
+ | #Ternette N, Olde Nordkamp MJM, Müller J, Anderson AP, Nicastri A, Hill AVS, Kessler BM, Li D, (2018) "Immunopeptidomic Profiling of HLA-A2-Positive Triple Negative Breast Cancer Identifies Potential Immunotherapy Target Antigens." <i>Proteomics</i> <b>18</b>(12):e1700465; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29786170 29786170]; doi: [https://dx.doi.org/10.1002/pmic.201700465 10.1002/pmic.201700465]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29786170 66]. | ||
#Löffler MW, Kowalewski DJ, Backert L, Bernhardt J, Adam P, Schuster H, Dengler F, Backes D, Kopp HG, Beckert S, Wagner S, Königsrainer I, Kohlbacher O, Kanz L, Königsrainer A, Rammensee HG, Stevanovic S, Haen SP, (2018) "Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation." <i>Cancer Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29789417 29789417]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-17-1745 10.1158/0008-5472.CAN-17-1745]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29789417 530]. | #Löffler MW, Kowalewski DJ, Backert L, Bernhardt J, Adam P, Schuster H, Dengler F, Backes D, Kopp HG, Beckert S, Wagner S, Königsrainer I, Kohlbacher O, Kanz L, Königsrainer A, Rammensee HG, Stevanovic S, Haen SP, (2018) "Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation." <i>Cancer Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29789417 29789417]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-17-1745 10.1158/0008-5472.CAN-17-1745]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29789417 530]. | ||
#Souquet B, Freed E, Berto A, Andric V, Audugé N, Reina-San-Martin B, Lacy E, Doye V, (2018) "Nup133 Is Required for Proper Nuclear Pore Basket Assembly and Dynamics in Embryonic Stem Cells." <i>Cell Rep</i> <b>23</b>(8):2443–2454; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29791854 29791854]; doi: [https://dx.doi.org/10.1016/j.celrep.2018.04.070 10.1016/j.celrep.2018.04.070]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29791854 18]. | #Souquet B, Freed E, Berto A, Andric V, Audugé N, Reina-San-Martin B, Lacy E, Doye V, (2018) "Nup133 Is Required for Proper Nuclear Pore Basket Assembly and Dynamics in Embryonic Stem Cells." <i>Cell Rep</i> <b>23</b>(8):2443–2454; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29791854 29791854]; doi: [https://dx.doi.org/10.1016/j.celrep.2018.04.070 10.1016/j.celrep.2018.04.070]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29791854 18]. | ||
+ | #Nieto R LM, Mehaffy C, Islam MN, Fitzgerald B, Belisle J, Prenni J, Dobos KM, (2018) "Biochemical characterization of isoniazid resistant <i>Mycobacterium tuberculosis</i>: can the analysis of clonal strains reveal novel targetable pathways?" <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29844232 29844232]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000821 10.1074/mcp.RA118.000821]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29844232 88]. | ||
#Muller L, Fornecker L, Chion M, Van Dorsselaer A, Cianférani S, Rabilloud T, Carapito C, (2018) "Extended investigation of tube-gel sample preparation: a versatile and simple choice for high throughput quantitative proteomics." <i>Sci Rep</i> <b>8</b>(1):8260; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29844437 29844437]; doi: [https://dx.doi.org/10.1038/s41598-018-26600-4 10.1038/s41598-018-26600-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29844437 40]. | #Muller L, Fornecker L, Chion M, Van Dorsselaer A, Cianférani S, Rabilloud T, Carapito C, (2018) "Extended investigation of tube-gel sample preparation: a versatile and simple choice for high throughput quantitative proteomics." <i>Sci Rep</i> <b>8</b>(1):8260; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29844437 29844437]; doi: [https://dx.doi.org/10.1038/s41598-018-26600-4 10.1038/s41598-018-26600-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29844437 40]. | ||
#Mohammad I, Nousiainen K, Bhosale SD, Starskaia I, Moulder R, Rokka A, Cheng F, Mohanasundaram P, Eriksson JE, Goodlett DR, Lähdesmäki H, Chen Z, (2018) "Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells." <i>PLoS Biol</i> <b>16</b>(5):e2004194; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29851958 29851958]; doi: [https://dx.doi.org/10.1371/journal.pbio.2004194 10.1371/journal.pbio.2004194]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29851958 45]. | #Mohammad I, Nousiainen K, Bhosale SD, Starskaia I, Moulder R, Rokka A, Cheng F, Mohanasundaram P, Eriksson JE, Goodlett DR, Lähdesmäki H, Chen Z, (2018) "Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells." <i>PLoS Biol</i> <b>16</b>(5):e2004194; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29851958 29851958]; doi: [https://dx.doi.org/10.1371/journal.pbio.2004194 10.1371/journal.pbio.2004194]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29851958 45]. | ||
#Marín E, Haesaert A, Padilla L, Adán J, Hernáez ML, Monteoliva L, Gil C, (2018) "Unraveling <i>Gardnerella vaginalis</i> Surface Proteins Using Cell Shaving Proteomics." <i>Front Microbiol</i> <b>9</b>:975; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29867878 29867878]; doi: [https://dx.doi.org/10.3389/fmicb.2018.00975 10.3389/fmicb.2018.00975]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29867878 3]. | #Marín E, Haesaert A, Padilla L, Adán J, Hernáez ML, Monteoliva L, Gil C, (2018) "Unraveling <i>Gardnerella vaginalis</i> Surface Proteins Using Cell Shaving Proteomics." <i>Front Microbiol</i> <b>9</b>:975; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29867878 29867878]; doi: [https://dx.doi.org/10.3389/fmicb.2018.00975 10.3389/fmicb.2018.00975]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29867878 3]. | ||
#Portela M, Yang L, Paul S, Li X, Veraksa A, Parsons LM, Richardson HE, (2018) "Lgl reduces endosomal vesicle acidification and Notch signaling by promoting the interaction between Vap33 and the V-ATPase complex." <i>Sci Signal</i> <b>11</b>(533):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29871910 29871910]; doi: [https://dx.doi.org/10.1126/scisignal.aar1976 10.1126/scisignal.aar1976]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29871910 11]. | #Portela M, Yang L, Paul S, Li X, Veraksa A, Parsons LM, Richardson HE, (2018) "Lgl reduces endosomal vesicle acidification and Notch signaling by promoting the interaction between Vap33 and the V-ATPase complex." <i>Sci Signal</i> <b>11</b>(533):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29871910 29871910]; doi: [https://dx.doi.org/10.1126/scisignal.aar1976 10.1126/scisignal.aar1976]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29871910 11]. | ||
+ | #Serandour AA, Mohammed H, Miremadi A, Mulder KW, Carroll JS, (2018) "TRPS1 regulates oestrogen receptor binding and histone acetylation at enhancers." <i>Oncogene</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29895970 29895970]; doi: [https://dx.doi.org/10.1038/s41388-018-0312-2 10.1038/s41388-018-0312-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29895970 7]. | ||
#Madeira JP, Alpha-Bazin B, Armengaud J, Duport C, (2018) "Time-course proteomics dataset to monitor protein-bound methionine oxidation <i>in Bacillus cereus</i> ATCC 14579." <i>Data Brief</i> <b>18</b>:394–398; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29896523 29896523]; doi: [https://dx.doi.org/10.1016/j.dib.2018.03.030 10.1016/j.dib.2018.03.030]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29896523 18]. | #Madeira JP, Alpha-Bazin B, Armengaud J, Duport C, (2018) "Time-course proteomics dataset to monitor protein-bound methionine oxidation <i>in Bacillus cereus</i> ATCC 14579." <i>Data Brief</i> <b>18</b>:394–398; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29896523 29896523]; doi: [https://dx.doi.org/10.1016/j.dib.2018.03.030 10.1016/j.dib.2018.03.030]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29896523 18]. | ||
+ | #He C, Jia C, Zhang Y, Xu P, (2018) "Enrichment-Based Proteogenomics Identifies Microproteins, Missing Proteins, and Novel smORFs in Saccharomyces cerevisiae." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29897761 29897761]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00032 10.1021/acs.jproteome.8b00032]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29897761 20]. | ||
#Adav SS, Wei J, Terence Y, Ang BC, Yip LW, Sze SK, (2018) "Proteomic Analysis of Aqueous Humor from Primary Open Angle Glaucoma Patients on Drug Treatment Revealed Altered Complement Activation Cascade." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29901396 29901396]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00244 10.1021/acs.jproteome.8b00244]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29901396 80]. | #Adav SS, Wei J, Terence Y, Ang BC, Yip LW, Sze SK, (2018) "Proteomic Analysis of Aqueous Humor from Primary Open Angle Glaucoma Patients on Drug Treatment Revealed Altered Complement Activation Cascade." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29901396 29901396]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00244 10.1021/acs.jproteome.8b00244]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29901396 80]. | ||
- | #Steenbeek SC, Pham TV, de Ligt J, Zomer A, Knol JC, Piersma SR, Schelfhorst T, Huisjes R, Schiffelers RM, Cuppen E, Jimenez CR, van Rheenen J, (2018) "Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29907695 29907695]; doi: [https://dx.doi.org/10.15252/embj.201798357 10.15252/embj.201798357]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29907695 | + | #Steenbeek SC, Pham TV, de Ligt J, Zomer A, Knol JC, Piersma SR, Schelfhorst T, Huisjes R, Schiffelers RM, Cuppen E, Jimenez CR, van Rheenen J, (2018) "Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29907695 29907695]; doi: [https://dx.doi.org/10.15252/embj.201798357 10.15252/embj.201798357]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29907695 67]. |
+ | #Huang H, Scheffler TL, Gerrard DE, Larsen MR, Lametsch R, (2018) "Quantitative Proteomics and Phosphoproteomics Analysis Revealed Different Regulatory Mechanisms of Halothane and Rendement Napole Genes in Porcine Muscle Metabolism." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29916714 29916714]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00294 10.1021/acs.jproteome.8b00294]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29916714 6]. | ||
+ | #Rapino F, Delaunay S, Rambow F, Zhou Z, Tharun L, De Tullio P, Sin O, Shostak K, Schmitz S, Piepers J, Ghesquière B, Karim L, Charloteaux B, Jamart D, Florin A, Lambert C, Rorive A, Jerusalem G, Leucci E, Dewaele M, Vooijs M, Leidel SA, Georges M, Voz M, Peers B, Büttner R, Marine JC, Chariot A, Close P, (2018) "Codon-specific translation reprogramming promotes resistance to targeted therapy." <i>Nature</i> <b>558</b>(7711):605–609; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29925953 29925953]; doi: [https://dx.doi.org/10.1038/s41586-018-0243-7 10.1038/s41586-018-0243-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29925953 40]. | ||
+ | #Kim DS, Anantharam P, Hoffmann A, Meade ML, Grobe N, Gearhart JM, Whitley EM, Mahama B, Rumbeiha WK, (2018) "Broad spectrum proteomics analysis of the inferior colliculus following acute hydrogen sulfide exposure." <i>Toxicol Appl Pharmacol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29932956 29932956]; doi: [https://dx.doi.org/10.1016/j.taap.2018.06.001 10.1016/j.taap.2018.06.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29932956 6]. | ||
+ | #Drulis-Fajdasz D, Rakus D, Wiśniewski JR, McCubrey JA, Gizak A, (2018) "Systematic analysis of GSK-3 signaling pathways in aging of cerebral tissue." <i>Adv Biol Regul</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29958836 29958836]; doi: [https://dx.doi.org/10.1016/j.jbior.2018.06.001 10.1016/j.jbior.2018.06.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29958836 72]. | ||
+ | #Pietras Z, Wojcik MA, Borowski LS, Szewczyk M, Kulinski TM, Cysewski D, Stepien PP, Dziembowski A, Szczesny RJ, (2018) "Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria." <i>Nat Commun</i> <b>9</b>(1):2558; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29967381 29967381]; doi: [https://dx.doi.org/10.1038/s41467-018-05007-9 10.1038/s41467-018-05007-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29967381 18]. | ||
+ | #Akimov V, Barrio-Hernandez I, Hansen SVF, Hallenborg P, Pedersen AK, Bekker-Jensen DB, Puglia M, Christensen SDK, Vanselow JT, Nielsen MM, Kratchmarova I, Kelstrup CD, Olsen JV, Blagoev B, (2018) "UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites." <i>Nat Struct Mol Biol</i> <b>25</b>(7):631–640; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29967540 29967540]; doi: [https://dx.doi.org/10.1038/s41594-018-0084-y 10.1038/s41594-018-0084-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29967540 136]. | ||
+ | #Sureka R, Wadhwa R, Thakur SS, Pathak RU, Mishra RK, (2018) "Comparison of Nuclear Matrix and Mitotic Chromosome Scaffold proteins in Drosophila S2 cells - Transmission of hallmarks of nuclear organization through mitosis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29991507 29991507]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000591 10.1074/mcp.RA118.000591]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29991507 6]. |
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 July 22, 2018.