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 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 12, 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 1,997: | Line 1,997: | ||
#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]. | ||
- | #Brummer T, Müller SA, Pan-Montojo F, Yoshida F, Fellgiebel A, Tomita T, Endres K, Lichtenthaler SF, (2019) "NrCAM is a marker for substrate-selective activation of ADAM10 in Alzheimer's disease." <i>EMBO Mol Med</i> <b>11</b>(4):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30833305 30833305]; doi: [https://dx.doi.org/10.15252/emmm.201809695 10.15252/emmm.201809695]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30833305 | + | #Brummer T, Müller SA, Pan-Montojo F, Yoshida F, Fellgiebel A, Tomita T, Endres K, Lichtenthaler SF, (2019) "NrCAM is a marker for substrate-selective activation of ADAM10 in Alzheimer's disease." <i>EMBO Mol Med</i> <b>11</b>(4):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30833305 30833305]; doi: [https://dx.doi.org/10.15252/emmm.201809695 10.15252/emmm.201809695]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30833305 72]. |
#Hansen BK, Gupta R, Baldus L, Lyon D, Narita T, Lammers M, Choudhary C, Weinert BT, (2019) "Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation." <i>Nat Commun</i> <b>10</b>(1):1055; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30837475 30837475]; doi: [https://dx.doi.org/10.1038/s41467-019-09024-0 10.1038/s41467-019-09024-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30837475 123]. | #Hansen BK, Gupta R, Baldus L, Lyon D, Narita T, Lammers M, Choudhary C, Weinert BT, (2019) "Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation." <i>Nat Commun</i> <b>10</b>(1):1055; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30837475 30837475]; doi: [https://dx.doi.org/10.1038/s41467-019-09024-0 10.1038/s41467-019-09024-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30837475 123]. | ||
#Marei WFA, Van Raemdonck G, Baggerman G, Bols PEJ, Leroy JLMR, (2019) "Proteomic changes in oocytes after in vitro maturation in lipotoxic conditions are different from those in cumulus cells." <i>Sci Rep</i> <b>9</b>(1):3673; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30842615 30842615]; doi: [https://dx.doi.org/10.1038/s41598-019-40122-7 10.1038/s41598-019-40122-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30842615 2]. | #Marei WFA, Van Raemdonck G, Baggerman G, Bols PEJ, Leroy JLMR, (2019) "Proteomic changes in oocytes after in vitro maturation in lipotoxic conditions are different from those in cumulus cells." <i>Sci Rep</i> <b>9</b>(1):3673; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30842615 30842615]; doi: [https://dx.doi.org/10.1038/s41598-019-40122-7 10.1038/s41598-019-40122-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30842615 2]. | ||
Line 2,019: | Line 2,019: | ||
#Na CH, Sharma N, Madugundu AK, Chen R, Atalar Aksit M, Rosson GD, Cutting GR, Pandey A, (2019) "Integrated transcriptomic and proteomic analysis of human eccrine sweat glands identifies missing and novel proteins." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30979791 30979791]; doi: [https://dx.doi.org/10.1074/mcp.RA118.001101 10.1074/mcp.RA118.001101]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30979791 3]. | #Na CH, Sharma N, Madugundu AK, Chen R, Atalar Aksit M, Rosson GD, Cutting GR, Pandey A, (2019) "Integrated transcriptomic and proteomic analysis of human eccrine sweat glands identifies missing and novel proteins." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30979791 30979791]; doi: [https://dx.doi.org/10.1074/mcp.RA118.001101 10.1074/mcp.RA118.001101]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30979791 3]. | ||
#Guergues J, Zhang P, Liu B, Stevens SM Jr, (2019) "Improved Methodology for Sensitive and Rapid Quantitative Proteomic Analysis of Adult-Derived Mouse Microglia: Application to a Novel In Vitro Mouse Microglial Cell Model." <i>Proteomics</i> <b></b>:e1800469; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30980500 30980500]; doi: [https://dx.doi.org/10.1002/pmic.201800469 10.1002/pmic.201800469]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30980500 6]. | #Guergues J, Zhang P, Liu B, Stevens SM Jr, (2019) "Improved Methodology for Sensitive and Rapid Quantitative Proteomic Analysis of Adult-Derived Mouse Microglia: Application to a Novel In Vitro Mouse Microglial Cell Model." <i>Proteomics</i> <b></b>:e1800469; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30980500 30980500]; doi: [https://dx.doi.org/10.1002/pmic.201800469 10.1002/pmic.201800469]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30980500 6]. | ||
- | #Zhou B, Yan Y, Wang Y, You S, Freeman MR, Yang W, (2019) "Quantitative proteomic analysis of prostate tissue specimens identifies deregulated protein complexes in primary prostate cancer." <i>Clin Proteomics</i> <b>16</b>:15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31011308 31011308]; doi: [https://dx.doi.org/10.1186/s12014-019-9236-2 10.1186/s12014-019-9236-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31011308 1]. | + | #Zhou B, Yan Y, Wang Y, You S, Freeman MR, Yang W, (2019) "Quantitative proteomic analysis of prostate tissue specimens identifies deregulated protein complexes in primary prostate cancer." <i>Clin Proteomics</i> <b>16</b>:15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31011308 31011308]; doi: [https://dx.doi.org/10.1186/s12014-019-9236-2 10.1186/s12014-019-9236-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31011308 2]. |
+ | #Trzeciecka A, Bhattacharya SK, (2019) "Dataset of growth cone-enriched lipidome and proteome of embryonic to early postnatal mouse brain." <i>Data Brief</i> <b>24</b>:103865; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31016214 31016214]; doi: [https://dx.doi.org/10.1016/j.dib.2019.103865 10.1016/j.dib.2019.103865]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31016214 60]. | ||
+ | #Löffler MW, Mohr C, Bichmann L, Freudenmann LK, Walzer M, Schroeder CM, Trautwein N, Hilke FJ, Zinser RS, Mühlenbruch L, Kowalewski DJ, Schuster H, Sturm M, Matthes J, Riess O, Czemmel S, Nahnsen S, Königsrainer I, Thiel K, Nadalin S, Beckert S, Bösmüller H, Fend F, Velic A, Maček B, Haen SP, Buonaguro L, Kohlbacher O, Stevanović S, Königsrainer A, HEPAVAC Consortium., Rammensee HG, (2019) "Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma." <i>Genome Med</i> <b>11</b>(1):28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31039795 31039795]; doi: [https://dx.doi.org/10.1186/s13073-019-0636-8 10.1186/s13073-019-0636-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31039795 178]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of May 12, 2019.