Line 27: | Line 27: | ||
==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 August 18, 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]. | ||
Line 585: | Line 585: | ||
#Bland C, Bellanger L, Armengaud J, (2014) "Magnetic immunoaffinity enrichment for selective capture and MS/MS analysis of N-terminal-TMPP-labeled peptides." <i>J Proteome Res</i> <b>13</b>(2):668–80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24313271 24313271]; doi: [https://dx.doi.org/10.1021/pr400774z 10.1021/pr400774z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24313271 9]. | #Bland C, Bellanger L, Armengaud J, (2014) "Magnetic immunoaffinity enrichment for selective capture and MS/MS analysis of N-terminal-TMPP-labeled peptides." <i>J Proteome Res</i> <b>13</b>(2):668–80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24313271 24313271]; doi: [https://dx.doi.org/10.1021/pr400774z 10.1021/pr400774z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24313271 9]. | ||
#Tsai CF, Hsu CC, Hung JN, Wang YT, Choong WK, Zeng MY, Lin PY, Hong RW, Sung TY, Chen YJ, (2014) "Sequential phosphoproteomic enrichment through complementary metal-directed immobilized metal ion affinity chromatography." <i>Anal Chem</i> <b>86</b>(1):685–93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24313913 24313913]; doi: [https://dx.doi.org/10.1021/ac4031175 10.1021/ac4031175]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24313913 27]. | #Tsai CF, Hsu CC, Hung JN, Wang YT, Choong WK, Zeng MY, Lin PY, Hong RW, Sung TY, Chen YJ, (2014) "Sequential phosphoproteomic enrichment through complementary metal-directed immobilized metal ion affinity chromatography." <i>Anal Chem</i> <b>86</b>(1):685–93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24313913 24313913]; doi: [https://dx.doi.org/10.1021/ac4031175 10.1021/ac4031175]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24313913 27]. | ||
+ | #Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG, (2014) "Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins." <i>Nat Methods</i> <b>11</b>(2):149–55; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24317253 24317253]; doi: [https://dx.doi.org/10.1038/nmeth.2763 10.1038/nmeth.2763]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24317253 221]. | ||
#Kao L, Wang YT, Chen YC, Tseng SF, Jhang JC, Chen YJ, Teng SC, (2014) "Global analysis of cdc14 dephosphorylation sites reveals essential regulatory role in mitosis and cytokinesis." <i>Mol Cell Proteomics</i> <b>13</b>(2):594–605; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24319056 24319056]; doi: [https://dx.doi.org/10.1074/mcp.M113.032680 10.1074/mcp.M113.032680]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24319056 9]. | #Kao L, Wang YT, Chen YC, Tseng SF, Jhang JC, Chen YJ, Teng SC, (2014) "Global analysis of cdc14 dephosphorylation sites reveals essential regulatory role in mitosis and cytokinesis." <i>Mol Cell Proteomics</i> <b>13</b>(2):594–605; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24319056 24319056]; doi: [https://dx.doi.org/10.1074/mcp.M113.032680 10.1074/mcp.M113.032680]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24319056 9]. | ||
#Beck F, Geiger J, Gambaryan S, Veit J, Vaudel M, Nollau P, Kohlbacher O, Martens L, Walter U, Sickmann A, Zahedi RP, (2014) "Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways." <i>Blood</i> <b>123</b>(5):e1–e10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24324209 24324209]; doi: [https://dx.doi.org/10.1182/blood-2013-07-512384 10.1182/blood-2013-07-512384]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24324209 19]. | #Beck F, Geiger J, Gambaryan S, Veit J, Vaudel M, Nollau P, Kohlbacher O, Martens L, Walter U, Sickmann A, Zahedi RP, (2014) "Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways." <i>Blood</i> <b>123</b>(5):e1–e10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24324209 24324209]; doi: [https://dx.doi.org/10.1182/blood-2013-07-512384 10.1182/blood-2013-07-512384]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24324209 19]. | ||
Line 1,936: | Line 1,937: | ||
#Simunovic F, Winninger O, Strassburg S, Koch HG, Finkenzeller G, Stark GB, Lampert FM, (2019) "Increased differentiation and production of extracellular matrix components of primary human osteoblasts after cocultivation with endothelial cells: A quantitative proteomics approach." <i>J Cell Biochem</i> <b>120</b>(1):396–404; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30126049 30126049]; doi: [https://dx.doi.org/10.1002/jcb.27394 10.1002/jcb.27394]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30126049 20]. | #Simunovic F, Winninger O, Strassburg S, Koch HG, Finkenzeller G, Stark GB, Lampert FM, (2019) "Increased differentiation and production of extracellular matrix components of primary human osteoblasts after cocultivation with endothelial cells: A quantitative proteomics approach." <i>J Cell Biochem</i> <b>120</b>(1):396–404; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30126049 30126049]; doi: [https://dx.doi.org/10.1002/jcb.27394 10.1002/jcb.27394]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30126049 20]. | ||
#Shen ZQ, Shi B, Wang TR, Jiao J, Shang X, Wu QJ, Zhou YM, Cao TF, Du Q, Wang XX, Li D, (2018) "Characterization of the Sperm Proteome and Reproductive Outcomes with <i>in Vitro</i> Fertilization after a Reduction in Male Ejaculatory Abstinence Period." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30126978 30126978]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000541 10.1074/mcp.RA117.000541]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30126978 18]. | #Shen ZQ, Shi B, Wang TR, Jiao J, Shang X, Wu QJ, Zhou YM, Cao TF, Du Q, Wang XX, Li D, (2018) "Characterization of the Sperm Proteome and Reproductive Outcomes with <i>in Vitro</i> Fertilization after a Reduction in Male Ejaculatory Abstinence Period." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30126978 30126978]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000541 10.1074/mcp.RA117.000541]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30126978 18]. | ||
+ | #Locatelli G, Theodorou D, Kendirli A, Jordão MJC, Staszewski O, Phulphagar K, Cantuti-Castelvetri L, Dagkalis A, Bessis A, Simons M, Meissner F, Prinz M, Kerschensteiner M, (2018) "Mononuclear phagocytes locally specify and adapt their phenotype in a multiple sclerosis model." <i>Nat Neurosci</i> <b>21</b>(9):1196–1208; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30127427 30127427]; doi: [https://dx.doi.org/10.1038/s41593-018-0212-3 10.1038/s41593-018-0212-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30127427 78]. | ||
#DeLeon-Pennell KY, Mouton AJ, Ero OK, Ma Y, Padmanabhan Iyer R, Flynn ER, Espinoza I, Musani SK, Vasan RS, Hall ME, Fox ER, Lindsey ML, (2018) "LXR/RXR signaling and neutrophil phenotype following myocardial infarction classify sex differences in remodeling." <i>Basic Res Cardiol</i> <b>113</b>(5):40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30132266 30132266]; doi: [https://dx.doi.org/10.1007/s00395-018-0699-5 10.1007/s00395-018-0699-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30132266 120]. | #DeLeon-Pennell KY, Mouton AJ, Ero OK, Ma Y, Padmanabhan Iyer R, Flynn ER, Espinoza I, Musani SK, Vasan RS, Hall ME, Fox ER, Lindsey ML, (2018) "LXR/RXR signaling and neutrophil phenotype following myocardial infarction classify sex differences in remodeling." <i>Basic Res Cardiol</i> <b>113</b>(5):40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30132266 30132266]; doi: [https://dx.doi.org/10.1007/s00395-018-0699-5 10.1007/s00395-018-0699-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30132266 120]. | ||
#Weßbecher IM, Hinrichsen I, Funke S, Oellerich T, Plotz G, Zeuzem S, Grus FH, Biondi RM, Brieger A, (2018) "DNA mismatch repair activity of MutLα is regulated by CK2-dependent phosphorylation of MLH1 (S477)." <i>Mol Carcinog</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30136313 30136313]; doi: [https://dx.doi.org/10.1002/mc.22892 10.1002/mc.22892]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30136313 2]. | #Weßbecher IM, Hinrichsen I, Funke S, Oellerich T, Plotz G, Zeuzem S, Grus FH, Biondi RM, Brieger A, (2018) "DNA mismatch repair activity of MutLα is regulated by CK2-dependent phosphorylation of MLH1 (S477)." <i>Mol Carcinog</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30136313 30136313]; doi: [https://dx.doi.org/10.1002/mc.22892 10.1002/mc.22892]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30136313 2]. | ||
+ | #Bruning U, Morales-Rodriguez F, Kalucka J, Goveia J, Taverna F, Queiroz KCS, Dubois C, Cantelmo AR, Chen R, Loroch S, Timmerman E, Caixeta V, Bloch K, Conradi LC, Treps L, Staes A, Gevaert K, Tee A, Dewerchin M, Semenkovich CF, Impens F, Schilling B, Verdin E, Swinnen JV, Meier JL, Kulkarni RA, Sickmann A, Ghesquière B, Schoonjans L, Li X, Mazzone M, Carmeliet P, (2018) "Impairment of Angiogenesis by Fatty Acid Synthase Inhibition Involves mTOR Malonylation." <i>Cell Metab</i> <b>28</b>(6):866–880.e15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30146486 30146486]; doi: [https://dx.doi.org/10.1016/j.cmet.2018.07.019 10.1016/j.cmet.2018.07.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30146486 2]. | ||
#Varland S, Aksnes H, Kryuchkov F, Impens F, Van Haver D, Jonckheere V, Ziegler M, Gevaert K, Van Damme P, Arnesen T, (2018) "N-terminal acetylation levels are maintained during acetyl-CoA deficiency in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30150368 30150368]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000982 10.1074/mcp.RA118.000982]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30150368 17]. | #Varland S, Aksnes H, Kryuchkov F, Impens F, Van Haver D, Jonckheere V, Ziegler M, Gevaert K, Van Damme P, Arnesen T, (2018) "N-terminal acetylation levels are maintained during acetyl-CoA deficiency in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30150368 30150368]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000982 10.1074/mcp.RA118.000982]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30150368 17]. | ||
#Béguin EP, van den Eshof BL, Hoogendijk AJ, Nota B, Mertens K, Meijer AB, van den Biggelaar M, (2018) "Integrated proteomic analysis of tumor necrosis factor α and interleukin 1β-induced endothelial inflammation." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30153514 30153514]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.08.011 10.1016/j.jprot.2018.08.011]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30153514 51]. | #Béguin EP, van den Eshof BL, Hoogendijk AJ, Nota B, Mertens K, Meijer AB, van den Biggelaar M, (2018) "Integrated proteomic analysis of tumor necrosis factor α and interleukin 1β-induced endothelial inflammation." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30153514 30153514]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.08.011 10.1016/j.jprot.2018.08.011]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30153514 51]. | ||
+ | #Yanovich G, Agmon H, Harel M, Sonnenblick A, Peretz T, Geiger T, (2018) "Clinical Proteomics of Breast Cancer Reveals a Novel Layer of Breast Cancer Classification." <i>Cancer Res</i> <b>78</b>(20):6001–6010; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30154156 30154156]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-18-1079 10.1158/0008-5472.CAN-18-1079]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30154156 19]. | ||
#Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | #Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | ||
#Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | #Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | ||
Line 2,043: | Line 2,047: | ||
#Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK, (2019) "Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming." <i>Cell Syst</i> <b>8</b>(5):412–426.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078528 31078528]; doi: [https://dx.doi.org/10.1016/j.cels.2019.03.009 10.1016/j.cels.2019.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078528 24]. | #Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK, (2019) "Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming." <i>Cell Syst</i> <b>8</b>(5):412–426.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078528 31078528]; doi: [https://dx.doi.org/10.1016/j.cels.2019.03.009 10.1016/j.cels.2019.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078528 24]. | ||
#Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanovic S, Gygi SP, Gujar S, (2019) "Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy." <i>J Proteome Res</i> <b>18</b>(6):2666–2675; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31095916 31095916]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00173 10.1021/acs.jproteome.9b00173]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31095916 11]. | #Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanovic S, Gygi SP, Gujar S, (2019) "Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy." <i>J Proteome Res</i> <b>18</b>(6):2666–2675; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31095916 31095916]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00173 10.1021/acs.jproteome.9b00173]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31095916 11]. | ||
+ | #Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T, (2019) "Proteomic and Metabolomic Profiling of <i>Deinococcus radiodurans</i> Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions." <i>Front Microbiol</i> <b>10</b>:909; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31110498 31110498]; doi: [https://dx.doi.org/10.3389/fmicb.2019.00909 10.3389/fmicb.2019.00909]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31110498 17]. | ||
#Chu F, Mason KE, Anex DS, Jones AD, Hart BR, (2019) "Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification." <i>Sci Rep</i> <b>9</b>(1):7641; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31113963 31113963]; doi: [https://dx.doi.org/10.1038/s41598-019-44007-7 10.1038/s41598-019-44007-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31113963 36]. | #Chu F, Mason KE, Anex DS, Jones AD, Hart BR, (2019) "Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification." <i>Sci Rep</i> <b>9</b>(1):7641; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31113963 31113963]; doi: [https://dx.doi.org/10.1038/s41598-019-44007-7 10.1038/s41598-019-44007-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31113963 36]. | ||
#Sap KA, Guler AT, Bezstarosti K, Bury AE, Juenemann K, Demmers J, Reits E, (2019) "Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31138642 31138642]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001486 10.1074/mcp.RA119.001486]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31138642 64]. | #Sap KA, Guler AT, Bezstarosti K, Bury AE, Juenemann K, Demmers J, Reits E, (2019) "Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31138642 31138642]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001486 10.1074/mcp.RA119.001486]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31138642 64]. | ||
Line 2,048: | Line 2,053: | ||
#Wang Y, Tatham MH, Schmidt-Heck W, Swann C, Singh-Dolt K, Meseguer-Ripolles J, Lucendo-Villarin B, Kunath T, Rudd TR, Smith AJH, Hengstler JG, Godoy P, Hay RT, Hay DC, (2019) "Multiomics Analyses of HNF4α Protein Domain Function during Human Pluripotent Stem Cell Differentiation." <i>iScience</i> <b>16</b>:206–217; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31185456 31185456]; doi: [https://dx.doi.org/10.1016/j.isci.2019.05.028 10.1016/j.isci.2019.05.028]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31185456 96]. | #Wang Y, Tatham MH, Schmidt-Heck W, Swann C, Singh-Dolt K, Meseguer-Ripolles J, Lucendo-Villarin B, Kunath T, Rudd TR, Smith AJH, Hengstler JG, Godoy P, Hay RT, Hay DC, (2019) "Multiomics Analyses of HNF4α Protein Domain Function during Human Pluripotent Stem Cell Differentiation." <i>iScience</i> <b>16</b>:206–217; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31185456 31185456]; doi: [https://dx.doi.org/10.1016/j.isci.2019.05.028 10.1016/j.isci.2019.05.028]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31185456 96]. | ||
#Ma F, Tremmel DM, Li Z, Lietz CB, Sackett SD, Odorico JS, Li L, (2019) "In-depth quantification of extracellular matrix proteins from human pancreas." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31200599 31200599]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00241 10.1021/acs.jproteome.9b00241]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31200599 30]. | #Ma F, Tremmel DM, Li Z, Lietz CB, Sackett SD, Odorico JS, Li L, (2019) "In-depth quantification of extracellular matrix proteins from human pancreas." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31200599 31200599]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00241 10.1021/acs.jproteome.9b00241]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31200599 30]. | ||
- | #Mendonça CF, Kuras M, Nogueira FCS, Plá I, Hortobágyi T, Csiba L, Palkovits M, Renner É, Döme P, Marko-Varga G, Domont GB, Rezeli M, (2019) "Proteomic signatures of brain regions affected by tau pathology in early and late stages of Alzheimer's disease." <i>Neurobiol Dis</i> <b>130</b>:104509; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31207390 31207390]; doi: [https://dx.doi.org/10.1016/j.nbd.2019.104509 10.1016/j.nbd.2019.104509]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31207390 | + | #Mendonça CF, Kuras M, Nogueira FCS, Plá I, Hortobágyi T, Csiba L, Palkovits M, Renner É, Döme P, Marko-Varga G, Domont GB, Rezeli M, (2019) "Proteomic signatures of brain regions affected by tau pathology in early and late stages of Alzheimer's disease." <i>Neurobiol Dis</i> <b>130</b>:104509; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31207390 31207390]; doi: [https://dx.doi.org/10.1016/j.nbd.2019.104509 10.1016/j.nbd.2019.104509]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31207390 367]. |
#Abdelhamed S, Butler JT, Doron B, Halse A, Nemecek E, Wilmarth PA, Marks DL, Chang BH, Horton T, Kurre P, (2019) "Extracellular vesicles impose quiescence on residual hematopoietic stem cells in the leukemic niche." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31208969 31208969]; doi: [https://dx.doi.org/10.15252/embr.201847546 10.15252/embr.201847546]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31208969 26]. | #Abdelhamed S, Butler JT, Doron B, Halse A, Nemecek E, Wilmarth PA, Marks DL, Chang BH, Horton T, Kurre P, (2019) "Extracellular vesicles impose quiescence on residual hematopoietic stem cells in the leukemic niche." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31208969 31208969]; doi: [https://dx.doi.org/10.15252/embr.201847546 10.15252/embr.201847546]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31208969 26]. | ||
+ | #Panhale A, Richter FM, Ramírez F, Shvedunova M, Manke T, Mittler G, Akhtar A, (2019) "CAPRI enables comparison of evolutionarily conserved RNA interacting regions." <i>Nat Commun</i> <b>10</b>(1):2682; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31213602 31213602]; doi: [https://dx.doi.org/10.1038/s41467-019-10585-3 10.1038/s41467-019-10585-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31213602 175]. | ||
#Schoor C, Brocke-Ahmadinejad N, Gieselmann V, Winter D, (2019) "Investigation of Oligodendrocyte Precursor Cell Differentiation by Quantitative Proteomics." <i>Proteomics</i> <b></b>:e1900057; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31216117 31216117]; doi: [https://dx.doi.org/10.1002/pmic.201900057 10.1002/pmic.201900057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31216117 5]. | #Schoor C, Brocke-Ahmadinejad N, Gieselmann V, Winter D, (2019) "Investigation of Oligodendrocyte Precursor Cell Differentiation by Quantitative Proteomics." <i>Proteomics</i> <b></b>:e1900057; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31216117 31216117]; doi: [https://dx.doi.org/10.1002/pmic.201900057 10.1002/pmic.201900057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31216117 5]. | ||
#Alriquet M, Martínez-Limón A, Hanspach G, Hengesbach M, Tartaglia GG, Calloni G, Vabulas RM, (2019) "Assembly of Proteins by Free RNA during the Early Phase of Proteostasis Stress." <i>J Proteome Res</i> <b>18</b>(7):2835–2847; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31244213 31244213]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00143 10.1021/acs.jproteome.9b00143]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31244213 12]. | #Alriquet M, Martínez-Limón A, Hanspach G, Hengesbach M, Tartaglia GG, Calloni G, Vabulas RM, (2019) "Assembly of Proteins by Free RNA during the Early Phase of Proteostasis Stress." <i>J Proteome Res</i> <b>18</b>(7):2835–2847; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31244213 31244213]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00143 10.1021/acs.jproteome.9b00143]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31244213 12]. | ||
+ | #Lignitto L, LeBoeuf SE, Homer H, Jiang S, Askenazi M, Karakousi TR, Pass HI, Bhutkar AJ, Tsirigos A, Ueberheide B, Sayin VI, Papagiannakopoulos T, Pagano M, (2019) "Nrf2 Activation Promotes Lung Cancer Metastasis by Inhibiting the Degradation of Bach1." <i>Cell</i> <b>178</b>(2):316–329.e18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31257023 31257023]; doi: [https://dx.doi.org/10.1016/j.cell.2019.06.003 10.1016/j.cell.2019.06.003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31257023 1]. | ||
+ | #Holthenrich A, Drexler HCA, Chehab T, Naß J, Gerke V, (2019) "Proximity proteomics of endothelial Weibel-Palade bodies identifies novel regulator of von-Willebrand factor secretion." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31262780 31262780]; doi: [https://dx.doi.org/10.1182/blood.2019000786 10.1182/blood.2019000786]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31262780 12]. | ||
+ | #Pierre N, Salée C, Massot C, Blétard N, Mazzucchelli G, Smargiasso N, Morsa D, Baiwir D, De Pauw E, Reenaers C, Van Kemseke C, Loly JP, Delvenne P, Meuwis MA, Louis E, (2019) "Proteomics highlights common and distinct pathophysiological processes associated to ileal and colonic ulcers in Crohn's disease." <i>J Crohns Colitis</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31282946 31282946]; doi: [https://dx.doi.org/10.1093/ecco-jcc/jjz130 10.1093/ecco-jcc/jjz130]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31282946 96]. | ||
+ | #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]. | ||
+ | #Christakopoulos C, Cehofski LJ, Christensen SR, Vorum H, Honoré B, (2019) "Proteomics reveals a set of highly enriched proteins in epiretinal membrane compared with inner limiting membrane." <i>Exp Eye Res</i> <b>186</b>:107722; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31302158 31302158]; doi: [https://dx.doi.org/10.1016/j.exer.2019.107722 10.1016/j.exer.2019.107722]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31302158 71]. | ||
+ | #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]. | ||
+ | #Patil S, Rajagopalan P, Patel K, Subbannayya T, Babu N, Mohan SV, Advani J, Sathe G, Bhandi S, Solanki HS, Sidransky D, Chatterjee A, Gowda H, Ferrari M, (2019) "Chronic shisha exposure alters phosphoproteome of oral keratinocytes." <i>J Cell Commun Signal</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31321732 31321732]; doi: [https://dx.doi.org/10.1007/s12079-019-00528-4 10.1007/s12079-019-00528-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31321732 6]. | ||
+ | #Buser DP, Ritz MF, Moes S, Tostado C, Frank S, Spiess M, Mariani L, Jenö P, Boulay JL, Hutter G, (2019) "Quantitative proteomics reveals reduction of endocytic machinery components in gliomas." <i>EBioMedicine</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31331834 31331834]; doi: [https://dx.doi.org/10.1016/j.ebiom.2019.07.039 10.1016/j.ebiom.2019.07.039]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31331834 50]. |
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 August 18, 2019.