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==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of May | + | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of May 28, 2017. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | ||
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#Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu PH, Hua B, Silberman RE, Springer M, Amon A, (2017) "Aneuploidy Causes Non-genetic Individuality." <i>Cell</i> <b>169</b>(2):229–242.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388408 28388408]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.021 10.1016/j.cell.2017.03.021]; GPMDB: [http://gpmdb.org/data/keyword/28388408 3]. | #Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu PH, Hua B, Silberman RE, Springer M, Amon A, (2017) "Aneuploidy Causes Non-genetic Individuality." <i>Cell</i> <b>169</b>(2):229–242.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388408 28388408]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.021 10.1016/j.cell.2017.03.021]; GPMDB: [http://gpmdb.org/data/keyword/28388408 3]. | ||
#Worst TS, von Hardenberg J, Gross JC, Erben P, Schnoelzer M, Hausser I, Bugert P, Michel MS, Boutros M, (2017) "A database-augmented, exosome-based mass spectrometry approach exemplarily identifies circulating claudin 3 as biomarker in prostate cancer." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28396511 28396511]; doi: [https://dx.doi.org/10.1074/mcp.M117.068577 10.1074/mcp.M117.068577]; GPMDB: [http://gpmdb.org/data/keyword/28396511 17]. | #Worst TS, von Hardenberg J, Gross JC, Erben P, Schnoelzer M, Hausser I, Bugert P, Michel MS, Boutros M, (2017) "A database-augmented, exosome-based mass spectrometry approach exemplarily identifies circulating claudin 3 as biomarker in prostate cancer." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28396511 28396511]; doi: [https://dx.doi.org/10.1074/mcp.M117.068577 10.1074/mcp.M117.068577]; GPMDB: [http://gpmdb.org/data/keyword/28396511 17]. | ||
- | #Rinschen MM, Grahammer F, Hoppe AK, Kohli P, Hagmann H, Kretz O, Bertsch S, Höhne M, Göbel H, Bartram MP, Gandhirajan RK, Krüger M, Brinkkoetter PT, Huber TB, Kann M, Wickström SA, Benzing T, Schermer B, (2017) "YAP-mediated mechanotransduction determines the podocyte's response to damage." <i>Sci Signal</i> <b>10</b>(474):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28400537 28400537]; doi: [https://dx.doi.org/10.1126/scisignal.aaf8165 10.1126/scisignal.aaf8165]; GPMDB: [http://gpmdb.org/data/keyword/28400537 | + | #Rinschen MM, Grahammer F, Hoppe AK, Kohli P, Hagmann H, Kretz O, Bertsch S, Höhne M, Göbel H, Bartram MP, Gandhirajan RK, Krüger M, Brinkkoetter PT, Huber TB, Kann M, Wickström SA, Benzing T, Schermer B, (2017) "YAP-mediated mechanotransduction determines the podocyte's response to damage." <i>Sci Signal</i> <b>10</b>(474):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28400537 28400537]; doi: [https://dx.doi.org/10.1126/scisignal.aaf8165 10.1126/scisignal.aaf8165]; GPMDB: [http://gpmdb.org/data/keyword/28400537 23]. |
#Müller MM, Lehmann R, Klassert TE, Reifenstein S, Conrad T, Moore C, Kuhn A, Behnert A, Guthke R, Driesch D, Slevogt H, (2017) "Global analysis of glycoproteins identifies markers of endotoxin tolerant monocytes and GPR84 as a modulator of TNFα expression." <i>Sci Rep</i> <b>7</b>(1):838; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28404994 28404994]; doi: [https://dx.doi.org/10.1038/s41598-017-00828-y 10.1038/s41598-017-00828-y]; GPMDB: [http://gpmdb.org/data/keyword/28404994 138]. | #Müller MM, Lehmann R, Klassert TE, Reifenstein S, Conrad T, Moore C, Kuhn A, Behnert A, Guthke R, Driesch D, Slevogt H, (2017) "Global analysis of glycoproteins identifies markers of endotoxin tolerant monocytes and GPR84 as a modulator of TNFα expression." <i>Sci Rep</i> <b>7</b>(1):838; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28404994 28404994]; doi: [https://dx.doi.org/10.1038/s41598-017-00828-y 10.1038/s41598-017-00828-y]; GPMDB: [http://gpmdb.org/data/keyword/28404994 138]. | ||
#Wang M, Guo Y, Wang M, Zhou T, Xue Y, Du G, Wei X, Wang J, Qi L, Zhang H, Li L, Ye L, Guo X, Wu X, (2017) "The GDNF-responsive Phosphoprotein Landscape Identifies Raptor Phosphorylation Required for Spermatogonial Progenitor Cell Proliferation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28408662 28408662]; doi: [https://dx.doi.org/10.1074/mcp.M116.065797 10.1074/mcp.M116.065797]; GPMDB: [http://gpmdb.org/data/keyword/28408662 21]. | #Wang M, Guo Y, Wang M, Zhou T, Xue Y, Du G, Wei X, Wang J, Qi L, Zhang H, Li L, Ye L, Guo X, Wu X, (2017) "The GDNF-responsive Phosphoprotein Landscape Identifies Raptor Phosphorylation Required for Spermatogonial Progenitor Cell Proliferation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28408662 28408662]; doi: [https://dx.doi.org/10.1074/mcp.M116.065797 10.1074/mcp.M116.065797]; GPMDB: [http://gpmdb.org/data/keyword/28408662 21]. | ||
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#Nguyen EV, Huhtinen K, Goo YA, Kaipio K, Andersson N, Rantanen V, Hynninen J, Lahesmaa R, Carpen O, Goodlett DR, (2017) "Hyper-phosphorylation of Sequestosome-1 distinguishes resistance to cisplatin in patient derived high grade serous ovarian cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28455291 28455291]; doi: [https://dx.doi.org/10.1074/mcp.M116.058321 10.1074/mcp.M116.058321]; GPMDB: [http://gpmdb.org/data/keyword/28455291 60]. | #Nguyen EV, Huhtinen K, Goo YA, Kaipio K, Andersson N, Rantanen V, Hynninen J, Lahesmaa R, Carpen O, Goodlett DR, (2017) "Hyper-phosphorylation of Sequestosome-1 distinguishes resistance to cisplatin in patient derived high grade serous ovarian cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28455291 28455291]; doi: [https://dx.doi.org/10.1074/mcp.M116.058321 10.1074/mcp.M116.058321]; GPMDB: [http://gpmdb.org/data/keyword/28455291 60]. | ||
#van Aalderen MC, van den Biggelaar M, Remmerswaal EBM, van Alphen FPJ, Meijer AB, Ten Berge IJM, van Lier RAW, (2017) "Label-free Analysis of CD8<sup>+</sup> T Cell Subset Proteomes Supports a Progressive Differentiation Model of Human-Virus-Specific T Cells." <i>Cell Rep</i> <b>19</b>(5):1068–1079; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28467900 28467900]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.04.014 10.1016/j.celrep.2017.04.014]; GPMDB: [http://gpmdb.org/data/keyword/28467900 84]. | #van Aalderen MC, van den Biggelaar M, Remmerswaal EBM, van Alphen FPJ, Meijer AB, Ten Berge IJM, van Lier RAW, (2017) "Label-free Analysis of CD8<sup>+</sup> T Cell Subset Proteomes Supports a Progressive Differentiation Model of Human-Virus-Specific T Cells." <i>Cell Rep</i> <b>19</b>(5):1068–1079; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28467900 28467900]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.04.014 10.1016/j.celrep.2017.04.014]; GPMDB: [http://gpmdb.org/data/keyword/28467900 84]. | ||
+ | #Ozdian T, Holub D, Maceckova Z, Varanasi L, Rylova G, Rehulka J, Vaclavkova J, Slavik H, Moudry P, Znojek P, Stankova J, de Sanctis JB, Hajduch M, Dzubak P, (2017) "Proteomic profiling reveals DNA damage, nucleolar and ribosomal stress are the main responses to oxaliplatin treatment in cancer cells." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28478306 28478306]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.05.005 10.1016/j.jprot.2017.05.005]; GPMDB: [http://gpmdb.org/data/keyword/28478306 60]. | ||
+ | #Murr A, Pink C, Hammer E, Michalik S, Dhople VM, Holtfreter B, Völker U, Kocher T, Gesell Salazar M, (2017) "Cross-Sectional Association of Salivary Proteins with Age, Sex, Body Mass Index, Smoking, and Education." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28481548 28481548]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00133 10.1021/acs.jproteome.7b00133]; GPMDB: [http://gpmdb.org/data/keyword/28481548 209]. | ||
+ | #Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ, (2017) "Common genetic variation drives molecular heterogeneity in human iPSCs." <i>Nature</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28489815 28489815]; doi: [https://dx.doi.org/10.1038/nature22403 10.1038/nature22403]; GPMDB: [http://gpmdb.org/data/keyword/28489815 47]. |
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.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of May 28, 2017.