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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 October 13, 2019. |
#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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#He PH, Dong WX, Chu XL, Feng MG, Ying SH, (2016) "The cellular proteome is affected by a gelsolin (BbGEL1) during morphological transitions in aerobic surface versus liquid growth in the entomopathogenic fungus Beauveria bassiana." <i>Environ Microbiol</i> <b>18</b>(11):4153–4169; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554994 27554994]; doi: [https://dx.doi.org/10.1111/1462-2920.13500 10.1111/1462-2920.13500]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27554994 34]. | #He PH, Dong WX, Chu XL, Feng MG, Ying SH, (2016) "The cellular proteome is affected by a gelsolin (BbGEL1) during morphological transitions in aerobic surface versus liquid growth in the entomopathogenic fungus Beauveria bassiana." <i>Environ Microbiol</i> <b>18</b>(11):4153–4169; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554994 27554994]; doi: [https://dx.doi.org/10.1111/1462-2920.13500 10.1111/1462-2920.13500]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27554994 34]. | ||
#Viktorovskaya OV, Greco TM, Cristea IM, Thompson SR, (2016) "Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements." <i>PLoS Negl Trop Dis</i> <b>10</b>(8):e0004921; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27556644 27556644]; doi: [https://dx.doi.org/10.1371/journal.pntd.0004921 10.1371/journal.pntd.0004921]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27556644 7]. | #Viktorovskaya OV, Greco TM, Cristea IM, Thompson SR, (2016) "Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements." <i>PLoS Negl Trop Dis</i> <b>10</b>(8):e0004921; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27556644 27556644]; doi: [https://dx.doi.org/10.1371/journal.pntd.0004921 10.1371/journal.pntd.0004921]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27556644 7]. | ||
- | #Cassidy L, Prasse D, Linke D, Schmitz RA, Tholey A, (2016) "Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei." <i>J Proteome Res</i> <b>15</b>(10):3773–3783; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27557128 27557128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00569 10.1021/acs.jproteome.6b00569]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27557128 | + | #Cassidy L, Prasse D, Linke D, Schmitz RA, Tholey A, (2016) "Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei." <i>J Proteome Res</i> <b>15</b>(10):3773–3783; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27557128 27557128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00569 10.1021/acs.jproteome.6b00569]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27557128 12]. |
#Häupl B, Ihling CH, Sinz A, (2016) "Protein Interaction Network of Human Protein Kinase D2 Revealed by Chemical Cross-Linking/Mass Spectrometry." <i>J Proteome Res</i> <b>15</b>(10):3686–3699; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27559607 27559607]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00513 10.1021/acs.jproteome.6b00513]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27559607 81]. | #Häupl B, Ihling CH, Sinz A, (2016) "Protein Interaction Network of Human Protein Kinase D2 Revealed by Chemical Cross-Linking/Mass Spectrometry." <i>J Proteome Res</i> <b>15</b>(10):3686–3699; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27559607 27559607]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00513 10.1021/acs.jproteome.6b00513]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27559607 81]. | ||
#Jiang Y, Lee J, Lee JH, Lee JW, Kim JH, Choi WH, Yoo YD, Cha-Molstad H, Kim BY, Kwon YT, Noh SA, Kim KP, Lee MJ, (2016) "The arginylation branch of the N-end rule pathway positively regulates cellular autophagic flux and clearance of proteotoxic proteins." <i>Autophagy</i> <b>12</b>(11):2197–2212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27560450 27560450]; doi: [https://dx.doi.org/10.1080/15548627.2016.1222991 10.1080/15548627.2016.1222991]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27560450 2]. | #Jiang Y, Lee J, Lee JH, Lee JW, Kim JH, Choi WH, Yoo YD, Cha-Molstad H, Kim BY, Kwon YT, Noh SA, Kim KP, Lee MJ, (2016) "The arginylation branch of the N-end rule pathway positively regulates cellular autophagic flux and clearance of proteotoxic proteins." <i>Autophagy</i> <b>12</b>(11):2197–2212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27560450 27560450]; doi: [https://dx.doi.org/10.1080/15548627.2016.1222991 10.1080/15548627.2016.1222991]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27560450 2]. | ||
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#Wildburger NC, Esparza TJ, LeDuc RD, Fellers RT, Thomas PM, Cairns NJ, Kelleher NL, Bateman RJ, Brody DL, (2017) "Diversity of Amyloid-beta Proteoforms in the Alzheimer's Disease Brain." <i>Sci Rep</i> <b>7</b>(1):9520; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28842697 28842697]; doi: [https://dx.doi.org/10.1038/s41598-017-10422-x 10.1038/s41598-017-10422-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28842697 22]. | #Wildburger NC, Esparza TJ, LeDuc RD, Fellers RT, Thomas PM, Cairns NJ, Kelleher NL, Bateman RJ, Brody DL, (2017) "Diversity of Amyloid-beta Proteoforms in the Alzheimer's Disease Brain." <i>Sci Rep</i> <b>7</b>(1):9520; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28842697 28842697]; doi: [https://dx.doi.org/10.1038/s41598-017-10422-x 10.1038/s41598-017-10422-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28842697 22]. | ||
#Andersen PR, Tirian L, Vunjak M, Brennecke J, (2017) "A heterochromatin-dependent transcription machinery drives piRNA expression." <i>Nature</i> <b>549</b>(7670):54–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28847004 28847004]; doi: [https://dx.doi.org/10.1038/nature23482 10.1038/nature23482]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28847004 46]. | #Andersen PR, Tirian L, Vunjak M, Brennecke J, (2017) "A heterochromatin-dependent transcription machinery drives piRNA expression." <i>Nature</i> <b>549</b>(7670):54–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28847004 28847004]; doi: [https://dx.doi.org/10.1038/nature23482 10.1038/nature23482]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28847004 46]. | ||
+ | #Guo J, Wang P, Cheng Q, Sun L, Wang H, Wang Y, Kao L, Li Y, Qiu T, Yang W, Shen H, (2017) "Proteomic analysis reveals strong mitochondrial involvement in cytoplasmic male sterility of pepper (Capsicum annuum L.)." <i>J Proteomics</i> <b>168</b>:15–27; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28847649 28847649]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.08.013 10.1016/j.jprot.2017.08.013]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28847649 6]. | ||
#Mohl BP, Emmott E, Roy P, (2017) "Phosphoproteomic analysis reveals the importance of kinase regulation during orbivirus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28851738 28851738]; doi: [https://dx.doi.org/10.1074/mcp.M117.067355 10.1074/mcp.M117.067355]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28851738 6]. | #Mohl BP, Emmott E, Roy P, (2017) "Phosphoproteomic analysis reveals the importance of kinase regulation during orbivirus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28851738 28851738]; doi: [https://dx.doi.org/10.1074/mcp.M117.067355 10.1074/mcp.M117.067355]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28851738 6]. | ||
#Merkley ED, Sego LH, Lin A, Leiser OP, Kaiser BLD, Adkins JN, Keim PS, Wagner DM, Kreuzer HW, (2017) "Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague." <i>PLoS One</i> <b>12</b>(8):e0183478; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28854255 28854255]; doi: [https://dx.doi.org/10.1371/journal.pone.0183478 10.1371/journal.pone.0183478]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28854255 343]. | #Merkley ED, Sego LH, Lin A, Leiser OP, Kaiser BLD, Adkins JN, Keim PS, Wagner DM, Kreuzer HW, (2017) "Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague." <i>PLoS One</i> <b>12</b>(8):e0183478; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28854255 28854255]; doi: [https://dx.doi.org/10.1371/journal.pone.0183478 10.1371/journal.pone.0183478]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28854255 343]. | ||
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#Bonnet J, Garcia C, Leger T, Couquet MP, Vignoles P, Gedeao V, Ndung'u J, Boudot C, Bisser S, Courtioux B, (2018) "Proteome characterization in various biological fluids of Trypanosoma brucei gambiense-infected subjects." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30414516 30414516]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.11.005 10.1016/j.jprot.2018.11.005]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30414516 40]. | #Bonnet J, Garcia C, Leger T, Couquet MP, Vignoles P, Gedeao V, Ndung'u J, Boudot C, Bisser S, Courtioux B, (2018) "Proteome characterization in various biological fluids of Trypanosoma brucei gambiense-infected subjects." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30414516 30414516]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.11.005 10.1016/j.jprot.2018.11.005]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30414516 40]. | ||
#Gontan C, Mira-Bontenbal H, Magaraki A, Dupont C, Barakat TS, Rentmeester E, Demmers J, Gribnau J, (2018) "REX1 is the critical target of RNF12 in imprinted X chromosome inactivation in mice." <i>Nat Commun</i> <b>9</b>(1):4752; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30420655 30420655]; doi: [https://dx.doi.org/10.1038/s41467-018-07060-w 10.1038/s41467-018-07060-w]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30420655 120]. | #Gontan C, Mira-Bontenbal H, Magaraki A, Dupont C, Barakat TS, Rentmeester E, Demmers J, Gribnau J, (2018) "REX1 is the critical target of RNF12 in imprinted X chromosome inactivation in mice." <i>Nat Commun</i> <b>9</b>(1):4752; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30420655 30420655]; doi: [https://dx.doi.org/10.1038/s41467-018-07060-w 10.1038/s41467-018-07060-w]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30420655 120]. | ||
+ | #Gfeller D, Guillaume P, Michaux J, Pak HS, Daniel RT, Racle J, Coukos G, Bassani-Sternberg M, (2018) "The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands." <i>J Immunol</i> <b>201</b>(12):3705–3716; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30429286 30429286]; doi: [https://dx.doi.org/10.4049/jimmunol.1800914 10.4049/jimmunol.1800914]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30429286 11]. | ||
#Bigenzahn JW, Collu GM, Kartnig F, Pieraks M, Vladimer GI, Heinz LX, Sedlyarov V, Schischlik F, Fauster A, Rebsamen M, Parapatics K, Blomen VA, Müller AC, Winter GE, Kralovics R, Brummelkamp TR, Mlodzik M, Superti-Furga G, (2018) "LZTR1 is a regulator of RAS ubiquitination and signaling." <i>Science</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30442766 30442766]; doi: [https://dx.doi.org/10.1126/science.aap8210 10.1126/science.aap8210]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30442766 20]. | #Bigenzahn JW, Collu GM, Kartnig F, Pieraks M, Vladimer GI, Heinz LX, Sedlyarov V, Schischlik F, Fauster A, Rebsamen M, Parapatics K, Blomen VA, Müller AC, Winter GE, Kralovics R, Brummelkamp TR, Mlodzik M, Superti-Furga G, (2018) "LZTR1 is a regulator of RAS ubiquitination and signaling." <i>Science</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30442766 30442766]; doi: [https://dx.doi.org/10.1126/science.aap8210 10.1126/science.aap8210]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30442766 20]. | ||
#Cominetti O, Núñez Galindo A, Corthésy J, Valsesia A, Irincheeva I, Kussmann M, Saris WHM, Astrup A, McPherson R, Harper ME, Dent R, Hager J, Dayon L, (2018) "Obesity shows preserved plasma proteome in large independent clinical cohorts." <i>Sci Rep</i> <b>8</b>(1):16981; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30451909 30451909]; doi: [https://dx.doi.org/10.1038/s41598-018-35321-7 10.1038/s41598-018-35321-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30451909 318]. | #Cominetti O, Núñez Galindo A, Corthésy J, Valsesia A, Irincheeva I, Kussmann M, Saris WHM, Astrup A, McPherson R, Harper ME, Dent R, Hager J, Dayon L, (2018) "Obesity shows preserved plasma proteome in large independent clinical cohorts." <i>Sci Rep</i> <b>8</b>(1):16981; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30451909 30451909]; doi: [https://dx.doi.org/10.1038/s41598-018-35321-7 10.1038/s41598-018-35321-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30451909 318]. | ||
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#Pfaff F, Hägglund S, Zoli M, Blaise-Boisseau S, Laloy E, Koethe S, Zühlke D, Riedel K, Zientara S, Bakkali-Kassimi L, Valarcher JF, Höper D, Beer M, Eschbaumer M, (2019) "Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus." <i>Viruses</i> <b>11</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30642035 30642035]; doi: [https://dx.doi.org/10.3390/v11010053 10.3390/v11010053]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30642035 110]. | #Pfaff F, Hägglund S, Zoli M, Blaise-Boisseau S, Laloy E, Koethe S, Zühlke D, Riedel K, Zientara S, Bakkali-Kassimi L, Valarcher JF, Höper D, Beer M, Eschbaumer M, (2019) "Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus." <i>Viruses</i> <b>11</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30642035 30642035]; doi: [https://dx.doi.org/10.3390/v11010053 10.3390/v11010053]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30642035 110]. | ||
#Kosack L, Wingelhofer B, Popa A, Orlova A, Agerer B, Vilagos B, Majek P, Parapatics K, Lercher A, Ringler A, Klughammer J, Smyth M, Khamina K, Baazim H, de Araujo ED, Rosa DA, Park J, Tin G, Ahmar S, Gunning PT, Bock C, Siddle HV, Woods GM, Kubicek S, Murchison EP, Bennett KL, Moriggl R, Bergthaler A, (2019) "The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease." <i>Cancer Cell</i> <b>35</b>(1):125–139.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30645971 30645971]; doi: [https://dx.doi.org/10.1016/j.ccell.2018.11.018 10.1016/j.ccell.2018.11.018]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30645971 20]. | #Kosack L, Wingelhofer B, Popa A, Orlova A, Agerer B, Vilagos B, Majek P, Parapatics K, Lercher A, Ringler A, Klughammer J, Smyth M, Khamina K, Baazim H, de Araujo ED, Rosa DA, Park J, Tin G, Ahmar S, Gunning PT, Bock C, Siddle HV, Woods GM, Kubicek S, Murchison EP, Bennett KL, Moriggl R, Bergthaler A, (2019) "The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease." <i>Cancer Cell</i> <b>35</b>(1):125–139.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30645971 30645971]; doi: [https://dx.doi.org/10.1016/j.ccell.2018.11.018 10.1016/j.ccell.2018.11.018]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30645971 20]. | ||
+ | #Liu Z, Lv J, Zhang Z, Li H, Yang B, Chen W, Dai X, Li X, Yang S, Liu L, Ou L, Ma Y, Zou X, (2019) "Integrative Transcriptome and Proteome Analysis Identifies Major Metabolic Pathways Involved in Pepper Fruit Development." <i>J Proteome Res</i> <b>18</b>(3):982–994; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30650966 30650966]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00673 10.1021/acs.jproteome.8b00673]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30650966 24]. | ||
#van Oorschot R, Hansen M, Koornneef JM, Marneth AE, Bergevoet SM, van Bergen MGJM, van Alphen FPJ, van der Zwaan C, Martens JHA, Vermeulen M, Jansen PWTC, Baltissen MPA, Laros-van Gorkom BAP, Janssen H, Jansen JH, von Lindern M, Meijer AB, van den Akker E, van der Reijden BA, (2019) "Molecular mechanisms of bleeding disorder-associated GFI1BQ287* mutation and its affected pathways in megakaryocytes and platelets." <i>Haematologica</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30655368 30655368]; doi: [https://dx.doi.org/10.3324/haematol.2018.194555 10.3324/haematol.2018.194555]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30655368 63]. | #van Oorschot R, Hansen M, Koornneef JM, Marneth AE, Bergevoet SM, van Bergen MGJM, van Alphen FPJ, van der Zwaan C, Martens JHA, Vermeulen M, Jansen PWTC, Baltissen MPA, Laros-van Gorkom BAP, Janssen H, Jansen JH, von Lindern M, Meijer AB, van den Akker E, van der Reijden BA, (2019) "Molecular mechanisms of bleeding disorder-associated GFI1BQ287* mutation and its affected pathways in megakaryocytes and platelets." <i>Haematologica</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30655368 30655368]; doi: [https://dx.doi.org/10.3324/haematol.2018.194555 10.3324/haematol.2018.194555]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30655368 63]. | ||
#Tsukada T, Isowa Y, Kito K, Yoshida S, Toneri S, Horiguchi K, Fujiwara K, Yashiro T, Kato T, Kato Y, (2019) "Identification of TGFβ-induced proteins in non-endocrine mouse pituitary cell line TtT/GF by SILAC-assisted quantitative mass spectrometry." <i>Cell Tissue Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30666536 30666536]; doi: [https://dx.doi.org/10.1007/s00441-018-02989-2 10.1007/s00441-018-02989-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30666536 11]. | #Tsukada T, Isowa Y, Kito K, Yoshida S, Toneri S, Horiguchi K, Fujiwara K, Yashiro T, Kato T, Kato Y, (2019) "Identification of TGFβ-induced proteins in non-endocrine mouse pituitary cell line TtT/GF by SILAC-assisted quantitative mass spectrometry." <i>Cell Tissue Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30666536 30666536]; doi: [https://dx.doi.org/10.1007/s00441-018-02989-2 10.1007/s00441-018-02989-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30666536 11]. | ||
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#Pauwels AM, Härtlova A, Peltier J, Driege Y, Baudelet G, Brodin P, Trost M, Beyaert R, Hoffmann E, (2019) "Spatiotemporal changes of the phagosomal proteome in dendritic cells in response to LPS stimulation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30808727 30808727]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001316 10.1074/mcp.RA119.001316]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30808727 20]. | #Pauwels AM, Härtlova A, Peltier J, Driege Y, Baudelet G, Brodin P, Trost M, Beyaert R, Hoffmann E, (2019) "Spatiotemporal changes of the phagosomal proteome in dendritic cells in response to LPS stimulation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30808727 30808727]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001316 10.1074/mcp.RA119.001316]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30808727 20]. | ||
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+ | #Yang W, Zhao X, Tao Y, Wu Y, He F, Tang L, (2019) "Proteomic analysis reveals a protective role of specific macrophage subsets in liver repair." <i>Sci Rep</i> <b>9</b>(1):2953; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30814596 30814596]; doi: [https://dx.doi.org/10.1038/s41598-019-39007-6 10.1038/s41598-019-39007-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30814596 40]. | ||
#Parker BL, Calkin AC, Seldin MM, Keating MF, Tarling EJ, Yang P, Moody SC, Liu Y, Zerenturk EJ, Needham EJ, Miller ML, Clifford BL, Morand P, Watt MJ, Meex RCR, Peng KY, Lee R, Jayawardana K, Pan C, Mellett NA, Weir JM, Lazarus R, Lusis AJ, Meikle PJ, James DE, de Aguiar Vallim TQ, Drew BG, (2019) "An integrative systems genetic analysis of mammalian lipid metabolism." <i>Nature</i> <b>567</b>(7747):187–193; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30814737 30814737]; doi: [https://dx.doi.org/10.1038/s41586-019-0984-y 10.1038/s41586-019-0984-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30814737 78]. | #Parker BL, Calkin AC, Seldin MM, Keating MF, Tarling EJ, Yang P, Moody SC, Liu Y, Zerenturk EJ, Needham EJ, Miller ML, Clifford BL, Morand P, Watt MJ, Meex RCR, Peng KY, Lee R, Jayawardana K, Pan C, Mellett NA, Weir JM, Lazarus R, Lusis AJ, Meikle PJ, James DE, de Aguiar Vallim TQ, Drew BG, (2019) "An integrative systems genetic analysis of mammalian lipid metabolism." <i>Nature</i> <b>567</b>(7747):187–193; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30814737 30814737]; doi: [https://dx.doi.org/10.1038/s41586-019-0984-y 10.1038/s41586-019-0984-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30814737 78]. | ||
#Jiang Y, Sun A, Zhao Y, Ying W, Sun H, Yang X, Xing B, Sun W, Ren L, Hu B, Li C, Zhang L, Qin G, Zhang M, Chen N, Zhang M, Huang Y, Zhou J, Zhao Y, Liu M, Zhu X, Qiu Y, Sun Y, Huang C, Yan M, Wang M, Liu W, Tian F, Xu H, Zhou J, Wu Z, Shi T, Zhu W, Qin J, Xie L, Fan J, Qian X, He F, Chinese Human Proteome Project (CNHPP) Consortium., (2019) "Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma." <i>Nature</i> <b>567</b>(7747):257–261; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30814741 30814741]; doi: [https://dx.doi.org/10.1038/s41586-019-0987-8 10.1038/s41586-019-0987-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30814741 688]. | #Jiang Y, Sun A, Zhao Y, Ying W, Sun H, Yang X, Xing B, Sun W, Ren L, Hu B, Li C, Zhang L, Qin G, Zhang M, Chen N, Zhang M, Huang Y, Zhou J, Zhao Y, Liu M, Zhu X, Qiu Y, Sun Y, Huang C, Yan M, Wang M, Liu W, Tian F, Xu H, Zhou J, Wu Z, Shi T, Zhu W, Qin J, Xie L, Fan J, Qian X, He F, Chinese Human Proteome Project (CNHPP) Consortium., (2019) "Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma." <i>Nature</i> <b>567</b>(7747):257–261; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30814741 30814741]; doi: [https://dx.doi.org/10.1038/s41586-019-0987-8 10.1038/s41586-019-0987-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30814741 688]. | ||
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#Narayan R, Olsson N, Wagar LE, Medeiros BC, Meyer E, Czerwinski D, Khodadoust MS, Zhang L, Schultz L, Davis MM, Elias JE, Levy R, (2019) "Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin." <i>PLoS One</i> <b>14</b>(7):e0219547; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31291378 31291378]; doi: [https://dx.doi.org/10.1371/journal.pone.0219547 10.1371/journal.pone.0219547]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31291378 86]. | #Narayan R, Olsson N, Wagar LE, Medeiros BC, Meyer E, Czerwinski D, Khodadoust MS, Zhang L, Schultz L, Davis MM, Elias JE, Levy R, (2019) "Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin." <i>PLoS One</i> <b>14</b>(7):e0219547; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31291378 31291378]; doi: [https://dx.doi.org/10.1371/journal.pone.0219547 10.1371/journal.pone.0219547]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31291378 86]. | ||
#Gomig THB, Cavalli IJ, Souza RLR, Lucena ACR, Batista M, Machado KC, Marchini FK, Marchi FA, Lima RS, Urban CA, Cavalli LR, Ribeiro EMSF, (2019) "High-throughput mass spectrometry and bioinformatics analysis of breast cancer proteomic data." <i>Data Brief</i> <b>25</b>:104125; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31294064 31294064]; doi: [https://dx.doi.org/10.1016/j.dib.2019.104125 10.1016/j.dib.2019.104125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31294064 69]. | #Gomig THB, Cavalli IJ, Souza RLR, Lucena ACR, Batista M, Machado KC, Marchini FK, Marchi FA, Lima RS, Urban CA, Cavalli LR, Ribeiro EMSF, (2019) "High-throughput mass spectrometry and bioinformatics analysis of breast cancer proteomic data." <i>Data Brief</i> <b>25</b>:104125; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31294064 31294064]; doi: [https://dx.doi.org/10.1016/j.dib.2019.104125 10.1016/j.dib.2019.104125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31294064 69]. | ||
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#Kang T, Boland BB, Alarcon C, Grimsby JS, Rhodes CJ, Larsen MR, (2019) "Proteomic Analysis of Restored Insulin Production and Trafficking in Obese Diabetic Mouse Pancreatic Islets Following Euglycemia." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31317746 31317746]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00160 10.1021/acs.jproteome.9b00160]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31317746 66]. | #Kang T, Boland BB, Alarcon C, Grimsby JS, Rhodes CJ, Larsen MR, (2019) "Proteomic Analysis of Restored Insulin Production and Trafficking in Obese Diabetic Mouse Pancreatic Islets Following Euglycemia." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31317746 31317746]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00160 10.1021/acs.jproteome.9b00160]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31317746 66]. | ||
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+ | #Kawahara R, Recuero S, Nogueira FCS, Domont GB, Leite KRM, Srougi M, Thaysen-Andersen M, Palmisano G, (2019) "Tissue Proteome Signatures Associated with Five Grades of Prostate Cancer and Benign Prostatic Hyperplasia." <i>Proteomics</i> <b></b>:e1900174; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31576646 31576646]; doi: [https://dx.doi.org/10.1002/pmic.201900174 10.1002/pmic.201900174]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31576646 5]. | ||
+ | #Velásquez E, Martins de Souza D, Velásquez I, Carneiro GRA, Schmitt A, Falkai P, Domont GB, Nogueira FCS, (2019) "QUANTITATIVE SUBCELLULAR PROTEOMICS OF THE ORBITOFRONTAL CORTEX OF SCHIZOPHRENIA PATIENTS." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31581776 31581776]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00398 10.1021/acs.jproteome.9b00398]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31581776 46]. | ||
+ | #Lundby A, Franciosa G, Emdal KB, Refsgaard JC, Gnosa SP, Bekker-Jensen DB, Secher A, Maurya SR, Paul I, Mendez BL, Kelstrup CD, Francavilla C, Kveiborg M, Montoya G, Jensen LJ, Olsen JV, (2019) "Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites." <i>Cell</i> <b>179</b>(2):543–560.e26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31585087 31585087]; doi: [https://dx.doi.org/10.1016/j.cell.2019.09.008 10.1016/j.cell.2019.09.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31585087 255]. |
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.
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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 October 13, 2019.