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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 19, 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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#Sinha A, Huang V, Livingstone J, Wang J, Fox NS, Kurganovs N, Ignatchenko V, Fritsch K, Donmez N, Heisler LE, Shiah YJ, Yao CQ, Alfaro JA, Volik S, Lapuk A, Fraser M, Kron K, Murison A, Lupien M, Sahinalp C, Collins CC, Tetu B, Masoomian M, Berman DM, van der Kwast T, Bristow RG, Kislinger T, Boutros PC, (2019) "The Proteogenomic Landscape of Curable Prostate Cancer." <i>Cancer Cell</i> <b>35</b>(3):414–427.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30889379 30889379]; doi: [https://dx.doi.org/10.1016/j.ccell.2019.02.005 10.1016/j.ccell.2019.02.005]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30889379 108]. | #Sinha A, Huang V, Livingstone J, Wang J, Fox NS, Kurganovs N, Ignatchenko V, Fritsch K, Donmez N, Heisler LE, Shiah YJ, Yao CQ, Alfaro JA, Volik S, Lapuk A, Fraser M, Kron K, Murison A, Lupien M, Sahinalp C, Collins CC, Tetu B, Masoomian M, Berman DM, van der Kwast T, Bristow RG, Kislinger T, Boutros PC, (2019) "The Proteogenomic Landscape of Curable Prostate Cancer." <i>Cancer Cell</i> <b>35</b>(3):414–427.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30889379 30889379]; doi: [https://dx.doi.org/10.1016/j.ccell.2019.02.005 10.1016/j.ccell.2019.02.005]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30889379 108]. | ||
#Xu B, Zheng C, Chen X, Zhang Z, Liu J, Spencer P, Yang X, (2019) "Dysregulation of Myosin Complex and Striated Muscle Contraction Pathway in the Brain of ALS-SOD1 mouse model." <i>ACS Chem Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30889949 30889949]; doi: [https://dx.doi.org/10.1021/acschemneuro.8b00704 10.1021/acschemneuro.8b00704]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30889949 1]. | #Xu B, Zheng C, Chen X, Zhang Z, Liu J, Spencer P, Yang X, (2019) "Dysregulation of Myosin Complex and Striated Muscle Contraction Pathway in the Brain of ALS-SOD1 mouse model." <i>ACS Chem Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30889949 30889949]; doi: [https://dx.doi.org/10.1021/acschemneuro.8b00704 10.1021/acschemneuro.8b00704]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30889949 1]. | ||
+ | #Schmitt M, Sinnberg T, Nalpas NC, Maass A, Schittek B, Macek B, (2019) "Quantitative proteomics links the intermediate filament nestin to resistance to targeted BRAF inhibition in melanoma cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30890564 30890564]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001302 10.1074/mcp.RA119.001302]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30890564 48]. | ||
#Borgermann N, Ackermann L, Schwertman P, Hendriks IA, Thijssen K, Liu JC, Lans H, Nielsen ML, Mailand N, (2019) "SUMOylation promotes protective responses to DNA-protein crosslinks." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30914427 30914427]; doi: [https://dx.doi.org/10.15252/embj.2019101496 10.15252/embj.2019101496]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30914427 52]. | #Borgermann N, Ackermann L, Schwertman P, Hendriks IA, Thijssen K, Liu JC, Lans H, Nielsen ML, Mailand N, (2019) "SUMOylation promotes protective responses to DNA-protein crosslinks." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30914427 30914427]; doi: [https://dx.doi.org/10.15252/embj.2019101496 10.15252/embj.2019101496]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30914427 52]. | ||
#Betancourt LH, Pawłowski K, Eriksson J, Szasz AM, Mitra S, Pla I, Welinder C, Ekedahl H, Broberg P, Appelqvist R, Yakovleva M, Sugihara Y, Miharada K, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Wieslander E, Horvatovich P, Malm J, Jönsson G, Marko-Varga G, (2019) "Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data." <i>Sci Rep</i> <b>9</b>(1):5154; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30914758 30914758]; doi: [https://dx.doi.org/10.1038/s41598-019-41625-z 10.1038/s41598-019-41625-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30914758 111]. | #Betancourt LH, Pawłowski K, Eriksson J, Szasz AM, Mitra S, Pla I, Welinder C, Ekedahl H, Broberg P, Appelqvist R, Yakovleva M, Sugihara Y, Miharada K, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Wieslander E, Horvatovich P, Malm J, Jönsson G, Marko-Varga G, (2019) "Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data." <i>Sci Rep</i> <b>9</b>(1):5154; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30914758 30914758]; doi: [https://dx.doi.org/10.1038/s41598-019-41625-z 10.1038/s41598-019-41625-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30914758 111]. | ||
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#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]. | #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]. | #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]. | ||
+ | #Chen F, Welker F, Shen CC, Bailey SE, Bergmann I, Davis S, Xia H, Wang H, Fischer R, Freidline SE, Yu TL, Skinner MM, Stelzer S, Dong G, Fu Q, Dong G, Wang J, Zhang D, Hublin JJ, (2019) "A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau." <i>Nature</i> <b>569</b>(7756):409–412; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31043746 31043746]; doi: [https://dx.doi.org/10.1038/s41586-019-1139-x 10.1038/s41586-019-1139-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31043746 8]. | ||
+ | #Dybas JM, O'Leary CE, Ding H, Spruce LA, Seeholzer SH, Oliver PM, (2019) "Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4<sup>+</sup> T cells." <i>Nat Immunol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31061531 31061531]; doi: [https://dx.doi.org/10.1038/s41590-019-0381-6 10.1038/s41590-019-0381-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31061531 118]. |
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 19, 2019.