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#Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA, (2013) "Integrated proteomic analysis of post-translational modifications by serial enrichment." <i>Nat Methods</i> <b>10</b>(7):634–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23749302 23749302]; doi: [https://dx.doi.org/10.1038/nmeth.2518 10.1038/nmeth.2518]; GPMDB: [http://gpmdb.org/data/keyword/23749302 231]. | #Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA, (2013) "Integrated proteomic analysis of post-translational modifications by serial enrichment." <i>Nat Methods</i> <b>10</b>(7):634–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23749302 23749302]; doi: [https://dx.doi.org/10.1038/nmeth.2518 10.1038/nmeth.2518]; GPMDB: [http://gpmdb.org/data/keyword/23749302 231]. | ||
#Joshi P, Greco TM, Guise AJ, Luo Y, Yu F, Nesvizhskii AI, Cristea IM, (2013) "The functional interactome landscape of the human histone deacetylase family." <i>Mol Syst Biol</i> <b>9</b>:672; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23752268 23752268]; doi: [https://dx.doi.org/10.1038/msb.2013.26 10.1038/msb.2013.26]; GPMDB: [http://gpmdb.org/data/keyword/23752268 75]. | #Joshi P, Greco TM, Guise AJ, Luo Y, Yu F, Nesvizhskii AI, Cristea IM, (2013) "The functional interactome landscape of the human histone deacetylase family." <i>Mol Syst Biol</i> <b>9</b>:672; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23752268 23752268]; doi: [https://dx.doi.org/10.1038/msb.2013.26 10.1038/msb.2013.26]; GPMDB: [http://gpmdb.org/data/keyword/23752268 75]. | ||
+ | #Wierer M, Verde G, Pisano P, Molina H, Font-Mateu J, Di Croce L, Beato M, (2013) "PLK1 signaling in breast cancer cells cooperates with estrogen receptor-dependent gene transcription." <i>Cell Rep</i> <b>3</b>(6):2021–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23770244 23770244]; doi: [https://dx.doi.org/10.1016/j.celrep.2013.05.024 10.1016/j.celrep.2013.05.024]; GPMDB: [http://gpmdb.org/data/keyword/23770244 7]. | ||
#Takahashi Y, Ebisu Y, Kinoshita T, Doi M, Okuma E, Murata Y, Shimazaki K, (2013) "bHLH transcription factors that facilitate K⁺ uptake during stomatal opening are repressed by abscisic acid through phosphorylation." <i>Sci Signal</i> <b>6</b>(280):ra48; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23779086 23779086]; doi: [https://dx.doi.org/10.1126/scisignal.2003760 10.1126/scisignal.2003760]; GPMDB: [http://gpmdb.org/data/keyword/23779086 2]. | #Takahashi Y, Ebisu Y, Kinoshita T, Doi M, Okuma E, Murata Y, Shimazaki K, (2013) "bHLH transcription factors that facilitate K⁺ uptake during stomatal opening are repressed by abscisic acid through phosphorylation." <i>Sci Signal</i> <b>6</b>(280):ra48; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23779086 23779086]; doi: [https://dx.doi.org/10.1126/scisignal.2003760 10.1126/scisignal.2003760]; GPMDB: [http://gpmdb.org/data/keyword/23779086 2]. | ||
#Freund DM, Prenni JE, Curthoys NP, (2013) "Proteomic profiling of the mitochondrial inner membrane of rat renal proximal convoluted tubules." <i>Proteomics</i> <b>13</b>(16):2495–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23780708 23780708]; doi: [https://dx.doi.org/10.1002/pmic.201200558 10.1002/pmic.201200558]; GPMDB: [http://gpmdb.org/data/keyword/23780708 10]. | #Freund DM, Prenni JE, Curthoys NP, (2013) "Proteomic profiling of the mitochondrial inner membrane of rat renal proximal convoluted tubules." <i>Proteomics</i> <b>13</b>(16):2495–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23780708 23780708]; doi: [https://dx.doi.org/10.1002/pmic.201200558 10.1002/pmic.201200558]; GPMDB: [http://gpmdb.org/data/keyword/23780708 10]. | ||
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#Groessl M, Slany A, Bileck A, Gloessmann K, Kreutz D, Jaeger W, Pfeiler G, Gerner C, (2014) "Proteome profiling of breast cancer biopsies reveals a wound healing signature of cancer-associated fibroblasts." <i>J Proteome Res</i> <b>13</b>(11):4773–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25238572 25238572]; doi: [https://dx.doi.org/10.1021/pr500727h 10.1021/pr500727h]; GPMDB: [http://gpmdb.org/data/keyword/25238572 281]. | #Groessl M, Slany A, Bileck A, Gloessmann K, Kreutz D, Jaeger W, Pfeiler G, Gerner C, (2014) "Proteome profiling of breast cancer biopsies reveals a wound healing signature of cancer-associated fibroblasts." <i>J Proteome Res</i> <b>13</b>(11):4773–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25238572 25238572]; doi: [https://dx.doi.org/10.1021/pr500727h 10.1021/pr500727h]; GPMDB: [http://gpmdb.org/data/keyword/25238572 281]. | ||
#Song Z, Chen L, Wang J, Lu Y, Jiang W, Zhang W, (2014) "A transcriptional regulator Sll0794 regulates tolerance to biofuel ethanol in photosynthetic Synechocystis sp. PCC 6803." <i>Mol Cell Proteomics</i> <b>13</b>(12):3519–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25239498 25239498]; doi: [https://dx.doi.org/10.1074/mcp.M113.035675 10.1074/mcp.M113.035675]; GPMDB: [http://gpmdb.org/data/keyword/25239498 21]. | #Song Z, Chen L, Wang J, Lu Y, Jiang W, Zhang W, (2014) "A transcriptional regulator Sll0794 regulates tolerance to biofuel ethanol in photosynthetic Synechocystis sp. PCC 6803." <i>Mol Cell Proteomics</i> <b>13</b>(12):3519–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25239498 25239498]; doi: [https://dx.doi.org/10.1074/mcp.M113.035675 10.1074/mcp.M113.035675]; GPMDB: [http://gpmdb.org/data/keyword/25239498 21]. | ||
+ | #Schwenk J, Baehrens D, Haupt A, Bildl W, Boudkkazi S, Roeper J, Fakler B, Schulte U, (2014) "Regional diversity and developmental dynamics of the AMPA-receptor proteome in the mammalian brain." <i>Neuron</i> <b>84</b>(1):41–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25242221 25242221]; doi: [https://dx.doi.org/10.1016/j.neuron.2014.08.044 10.1016/j.neuron.2014.08.044]; GPMDB: [http://gpmdb.org/data/keyword/25242221 95]. | ||
#Wu X, Renuse S, Sahasrabuddhe NA, Zahari MS, Chaerkady R, Kim MS, Nirujogi RS, Mohseni M, Kumar P, Raju R, Zhong J, Yang J, Neiswinger J, Jeong JS, Newman R, Powers MA, Somani BL, Gabrielson E, Sukumar S, Stearns V, Qian J, Zhu H, Vogelstein B, Park BH, Pandey A, (2014) "Activation of diverse signalling pathways by oncogenic PIK3CA mutations." <i>Nat Commun</i> <b>5</b>:4961; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25247763 25247763]; doi: [https://dx.doi.org/10.1038/ncomms5961 10.1038/ncomms5961]; GPMDB: [http://gpmdb.org/data/keyword/25247763 91]. | #Wu X, Renuse S, Sahasrabuddhe NA, Zahari MS, Chaerkady R, Kim MS, Nirujogi RS, Mohseni M, Kumar P, Raju R, Zhong J, Yang J, Neiswinger J, Jeong JS, Newman R, Powers MA, Somani BL, Gabrielson E, Sukumar S, Stearns V, Qian J, Zhu H, Vogelstein B, Park BH, Pandey A, (2014) "Activation of diverse signalling pathways by oncogenic PIK3CA mutations." <i>Nat Commun</i> <b>5</b>:4961; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25247763 25247763]; doi: [https://dx.doi.org/10.1038/ncomms5961 10.1038/ncomms5961]; GPMDB: [http://gpmdb.org/data/keyword/25247763 91]. | ||
#van der Lelij P, Stocsits RR, Ladurner R, Petzold G, Kreidl E, Koch B, Schmitz J, Neumann B, Ellenberg J, Peters JM, (2014) "SNW1 enables sister chromatid cohesion by mediating the splicing of sororin and APC2 pre-mRNAs." <i>EMBO J</i> <b>33</b>(22):2643–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25257309 25257309]; doi: [https://dx.doi.org/10.15252/embj.201488202 10.15252/embj.201488202]; GPMDB: [http://gpmdb.org/data/keyword/25257309 2]. | #van der Lelij P, Stocsits RR, Ladurner R, Petzold G, Kreidl E, Koch B, Schmitz J, Neumann B, Ellenberg J, Peters JM, (2014) "SNW1 enables sister chromatid cohesion by mediating the splicing of sororin and APC2 pre-mRNAs." <i>EMBO J</i> <b>33</b>(22):2643–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25257309 25257309]; doi: [https://dx.doi.org/10.15252/embj.201488202 10.15252/embj.201488202]; GPMDB: [http://gpmdb.org/data/keyword/25257309 2]. | ||
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#Carabetta VJ, Greco TM, Tanner AW, Cristea IM, Dubnau D, (2016) "Temporal Regulation of the <i>Bacillus subtilis</i> Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall Growth." <i>mSystems</i> <b>1</b>(3):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27376153 27376153]; doi: [https://dx.doi.org/10.1128/mSystems.00005-16 10.1128/mSystems.00005-16]; GPMDB: [http://gpmdb.org/data/keyword/27376153 30]. | #Carabetta VJ, Greco TM, Tanner AW, Cristea IM, Dubnau D, (2016) "Temporal Regulation of the <i>Bacillus subtilis</i> Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall Growth." <i>mSystems</i> <b>1</b>(3):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27376153 27376153]; doi: [https://dx.doi.org/10.1128/mSystems.00005-16 10.1128/mSystems.00005-16]; GPMDB: [http://gpmdb.org/data/keyword/27376153 30]. | ||
#Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsveld J, Hentze MW, Castello A, Ephrussi A, (2016) "Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila." <i>Nat Commun</i> <b>7</b>:12128; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27378189 27378189]; doi: [https://dx.doi.org/10.1038/ncomms12128 10.1038/ncomms12128]; GPMDB: [http://gpmdb.org/data/keyword/27378189 25]. | #Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsveld J, Hentze MW, Castello A, Ephrussi A, (2016) "Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila." <i>Nat Commun</i> <b>7</b>:12128; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27378189 27378189]; doi: [https://dx.doi.org/10.1038/ncomms12128 10.1038/ncomms12128]; GPMDB: [http://gpmdb.org/data/keyword/27378189 25]. | ||
+ | #Ashford P, Hernandez A, Greco TM, Buch A, Sodeik B, Cristea IM, Grunewald K, Shepherd A, Topf M, (2016) "HVint: A strategy for identifying novel protein-protein interactions in herpes simplex virus type 1." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27384951 27384951]; doi: [https://dx.doi.org/10.1074/mcp.M116.058552 10.1074/mcp.M116.058552]; GPMDB: [http://gpmdb.org/data/keyword/27384951 19]. | ||
#Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M, (2016) "Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development." <i>Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27397507 27397507]; doi: [https://dx.doi.org/10.1016/j.cell.2016.06.015 10.1016/j.cell.2016.06.015]; GPMDB: [http://gpmdb.org/data/keyword/27397507 18]. | #Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M, (2016) "Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development." <i>Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27397507 27397507]; doi: [https://dx.doi.org/10.1016/j.cell.2016.06.015 10.1016/j.cell.2016.06.015]; GPMDB: [http://gpmdb.org/data/keyword/27397507 18]. |
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 July 17, 2016.