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==Data from publications== | ==Data from publications== | ||
- | The following is a 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 January | + | The following is a 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 January 17, 2016. |
#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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#Aeberhard L, Banhart S, Fischer M, Jehmlich N, Rose L, Koch S, Laue M, Renard BY, Schmidt F, Heuer D, (2015) "The Proteome of the Isolated Chlamydia trachomatis Containing Vacuole Reveals a Complex Trafficking Platform Enriched for Retromer Components." <i>PLoS Pathog</i> <b>11</b>(6):e1004883; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26042774 26042774]; doi: [https://dx.doi.org/10.1371/journal.ppat.1004883 10.1371/journal.ppat.1004883]; GPMDB: [http://gpmdb.org/data/keyword/26042774 24]. | #Aeberhard L, Banhart S, Fischer M, Jehmlich N, Rose L, Koch S, Laue M, Renard BY, Schmidt F, Heuer D, (2015) "The Proteome of the Isolated Chlamydia trachomatis Containing Vacuole Reveals a Complex Trafficking Platform Enriched for Retromer Components." <i>PLoS Pathog</i> <b>11</b>(6):e1004883; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26042774 26042774]; doi: [https://dx.doi.org/10.1371/journal.ppat.1004883 10.1371/journal.ppat.1004883]; GPMDB: [http://gpmdb.org/data/keyword/26042774 24]. | ||
#Marie P, Labas V, Brionne A, Harichaux G, Hennequet-Antier C, Rodriguez-Navarro AB, Nys Y, Gautron J, (2015) "Quantitative proteomics provides new insights into chicken eggshell matrix protein functions during the primary events of mineralisation and the active calcification phase." <i>J Proteomics</i> <b>126</b>:140–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26049031 26049031]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.05.034 10.1016/j.jprot.2015.05.034]; GPMDB: [http://gpmdb.org/data/keyword/26049031 180]. | #Marie P, Labas V, Brionne A, Harichaux G, Hennequet-Antier C, Rodriguez-Navarro AB, Nys Y, Gautron J, (2015) "Quantitative proteomics provides new insights into chicken eggshell matrix protein functions during the primary events of mineralisation and the active calcification phase." <i>J Proteomics</i> <b>126</b>:140–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26049031 26049031]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.05.034 10.1016/j.jprot.2015.05.034]; GPMDB: [http://gpmdb.org/data/keyword/26049031 180]. | ||
- | #Higgins R, Gendron JM, Rising L, Mak R, Webb K, Kaiser SE, Zuzow N, Riviere P, Yang B, Fenech E, Tang X, Lindsay SA, Christianson JC, Hampton RY, Wasserman SA, Bennett EJ, (2015) "The Unfolded Protein Response Triggers Site-Specific Regulatory Ubiquitylation of 40S Ribosomal Proteins." <i>Mol Cell</i> <b>59</b>(1):35–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26051182 26051182]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.04.026 10.1016/j.molcel.2015.04.026]; GPMDB: [http://gpmdb.org/data/keyword/26051182 | + | #Higgins R, Gendron JM, Rising L, Mak R, Webb K, Kaiser SE, Zuzow N, Riviere P, Yang B, Fenech E, Tang X, Lindsay SA, Christianson JC, Hampton RY, Wasserman SA, Bennett EJ, (2015) "The Unfolded Protein Response Triggers Site-Specific Regulatory Ubiquitylation of 40S Ribosomal Proteins." <i>Mol Cell</i> <b>59</b>(1):35–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26051182 26051182]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.04.026 10.1016/j.molcel.2015.04.026]; GPMDB: [http://gpmdb.org/data/keyword/26051182 54]. |
#McCloy RA, Parker BL, Rogers S, Chaudhuri R, Gayevskiy V, Hoffman NJ, Ali N, Watkins DN, Daly RJ, James DE, Lorca T, Castro A, Burgess A, (2015) "Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs." <i>Mol Cell Proteomics</i> <b>14</b>(8):2194–212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26055452 26055452]; doi: [https://dx.doi.org/10.1074/mcp.M114.046938 10.1074/mcp.M114.046938]; GPMDB: [http://gpmdb.org/data/keyword/26055452 29]. | #McCloy RA, Parker BL, Rogers S, Chaudhuri R, Gayevskiy V, Hoffman NJ, Ali N, Watkins DN, Daly RJ, James DE, Lorca T, Castro A, Burgess A, (2015) "Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs." <i>Mol Cell Proteomics</i> <b>14</b>(8):2194–212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26055452 26055452]; doi: [https://dx.doi.org/10.1074/mcp.M114.046938 10.1074/mcp.M114.046938]; GPMDB: [http://gpmdb.org/data/keyword/26055452 29]. | ||
#Mulvey CM, Schröter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LT, Niakan KK, Martinez-Arias A, Lilley KS, (2015) "Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells." <i>Stem Cells</i> <b>33</b>(9):2712–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26059426 26059426]; doi: [https://dx.doi.org/10.1002/stem.2067 10.1002/stem.2067]; GPMDB: [http://gpmdb.org/data/keyword/26059426 7]. | #Mulvey CM, Schröter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LT, Niakan KK, Martinez-Arias A, Lilley KS, (2015) "Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells." <i>Stem Cells</i> <b>33</b>(9):2712–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26059426 26059426]; doi: [https://dx.doi.org/10.1002/stem.2067 10.1002/stem.2067]; GPMDB: [http://gpmdb.org/data/keyword/26059426 7]. |
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 pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a 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 January 17, 2016.