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 5, 2018. |
#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 1,879: | Line 1,879: | ||
#Sureka R, Wadhwa R, Thakur SS, Pathak RU, Mishra RK, (2018) "Comparison of Nuclear Matrix and Mitotic Chromosome Scaffold proteins in Drosophila S2 cells - Transmission of hallmarks of nuclear organization through mitosis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29991507 29991507]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000591 10.1074/mcp.RA118.000591]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29991507 6]. | #Sureka R, Wadhwa R, Thakur SS, Pathak RU, Mishra RK, (2018) "Comparison of Nuclear Matrix and Mitotic Chromosome Scaffold proteins in Drosophila S2 cells - Transmission of hallmarks of nuclear organization through mitosis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29991507 29991507]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000591 10.1074/mcp.RA118.000591]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29991507 6]. | ||
#Kim D, Liu Y, Oberly S, Freire R, Smolka MB, (2018) "ATR-mediated proteome remodeling is a major determinant of homologous recombination capacity in cancer cells." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30010936 30010936]; doi: [https://dx.doi.org/10.1093/nar/gky625 10.1093/nar/gky625]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30010936 2]. | #Kim D, Liu Y, Oberly S, Freire R, Smolka MB, (2018) "ATR-mediated proteome remodeling is a major determinant of homologous recombination capacity in cancer cells." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30010936 30010936]; doi: [https://dx.doi.org/10.1093/nar/gky625 10.1093/nar/gky625]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30010936 2]. | ||
+ | #Dragoi D, Benesic A, Pichler G, Kulak NA, Bartsch HS, Gerbes AL, (2018) "Proteomics Analysis of Monocyte-Derived Hepatocyte-Like Cells Identifies Integrin Beta 3 as a Specific Biomarker for Drug-Induced Liver Injury by Diclofenac." <i>Front Pharmacol</i> <b>9</b>:699; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30022949 30022949]; doi: [https://dx.doi.org/10.3389/fphar.2018.00699 10.3389/fphar.2018.00699]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30022949 98]. | ||
+ | #Duda P, Wójcicka O, Wiśniewski JR, Rakus D, (2018) "Global quantitative TPA-based proteomics of mouse brain structures reveals significant alterations in expression of proteins involved in neuronal plasticity during aging." <i>Aging (Albany NY)</i> <b>10</b>(7):1682–1697; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30026405 30026405]; doi: [https://dx.doi.org/10.18632/aginh.101501 10.18632/aginh.101501]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30026405 59]. | ||
+ | #Evans J, Infusini G, McGovern J, Cuttle L, Webb A, Nebl T, Milla L, Kimble R, Kempf M, Andrews CJ, Leavesley D, Salamonsen LA, (2018) "Menstrual fluid factors facilitate tissue repair: identification and functional action in endometrial and skin repair." <i>FASEB J</i> <b></b>:fj201800086R; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30036086 30036086]; doi: [https://dx.doi.org/10.1096/fj.201800086R 10.1096/fj.201800086R]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30036086 46]. | ||
#Ghezraoui H, Oliveira C, Becker JR, Bilham K, Moralli D, Anzilotti C, Fischer R, Deobagkar-Lele M, Sanchiz-Calvo M, Fueyo-Marcos E, Bonham S, Kessler BM, Rottenberg S, Cornall RJ, Green CM, Chapman JR, (2018) "53BP1 cooperation with the REV7-shieldin complex underpins DNA structure-specific NHEJ." <i>Nature</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30046110 30046110]; doi: [https://dx.doi.org/10.1038/s41586-018-0362-1 10.1038/s41586-018-0362-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30046110 8]. | #Ghezraoui H, Oliveira C, Becker JR, Bilham K, Moralli D, Anzilotti C, Fischer R, Deobagkar-Lele M, Sanchiz-Calvo M, Fueyo-Marcos E, Bonham S, Kessler BM, Rottenberg S, Cornall RJ, Green CM, Chapman JR, (2018) "53BP1 cooperation with the REV7-shieldin complex underpins DNA structure-specific NHEJ." <i>Nature</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30046110 30046110]; doi: [https://dx.doi.org/10.1038/s41586-018-0362-1 10.1038/s41586-018-0362-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30046110 8]. | ||
+ | #Nilsen BW, Simon-Santamaria J, Örtengren U, Jensen E, Bruun JA, Michelsen VB, Sørensen KK, (2018) "Dose- and time-dependent effects of triethylene glycol dimethacrylate on the proteome of human THP-1 monocytes." <i>Eur J Oral Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30051916 30051916]; doi: [https://dx.doi.org/10.1111/eos.12559 10.1111/eos.12559]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30051916 72]. |
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 5, 2018.