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#Eitzinger N, Wagner V, Weisheit W, Geimer S, Boness D, Kreimer G, Mittag M, (2015) "Proteomic Analysis of a Fraction with Intact Eyespots of Chlamydomonas reinhardtii and Assignment of Protein Methylation." <i>Front Plant Sci</i> <b>6</b>:1085; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26697039 26697039]; doi: [https://dx.doi.org/10.3389/fpls.2015.01085 10.3389/fpls.2015.01085]; GPMDB: [http://gpmdb.org/data/keyword/26697039 128]. | #Eitzinger N, Wagner V, Weisheit W, Geimer S, Boness D, Kreimer G, Mittag M, (2015) "Proteomic Analysis of a Fraction with Intact Eyespots of Chlamydomonas reinhardtii and Assignment of Protein Methylation." <i>Front Plant Sci</i> <b>6</b>:1085; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26697039 26697039]; doi: [https://dx.doi.org/10.3389/fpls.2015.01085 10.3389/fpls.2015.01085]; GPMDB: [http://gpmdb.org/data/keyword/26697039 128]. | ||
#Kozlov SV, Waardenberg AJ, Engholm-Keller K, Arthur JW, Graham ME, Lavin MF, (2015) "ROS-activated ATM-dependent phosphorylation of cytoplasmic substrates identified by large scale phosphoproteomics screen." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26699800 26699800]; doi: [https://dx.doi.org/10.1074/mcp.M115.055723 10.1074/mcp.M115.055723]; GPMDB: [http://gpmdb.org/data/keyword/26699800 141]. | #Kozlov SV, Waardenberg AJ, Engholm-Keller K, Arthur JW, Graham ME, Lavin MF, (2015) "ROS-activated ATM-dependent phosphorylation of cytoplasmic substrates identified by large scale phosphoproteomics screen." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26699800 26699800]; doi: [https://dx.doi.org/10.1074/mcp.M115.055723 10.1074/mcp.M115.055723]; GPMDB: [http://gpmdb.org/data/keyword/26699800 141]. | ||
+ | #El Ouaamari A, Dirice E, Gedeon N, Hu J, Zhou JY, Shirakawa J, Hou L, Goodman J, Karampelias C, Qiang G, Boucher J, Martinez R, Gritsenko MA, De Jesus DF, Kahraman S, Bhatt S, Smith RD, Beer HD, Jungtrakoon P, Gong Y, Goldfine AB, Liew CW, Doria A, Andersson O, Qian WJ, Remold-O'Donnell E, Kulkarni RN, (2016) "SerpinB1 Promotes Pancreatic β Cell Proliferation." <i>Cell Metab</i> <b>23</b>(1):194–205; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26701651 26701651]; doi: [https://dx.doi.org/10.1016/j.cmet.2015.12.001 10.1016/j.cmet.2015.12.001]; GPMDB: [http://gpmdb.org/data/keyword/26701651 4]. | ||
#Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L, (2015) "Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26702875 26702875]; doi: [https://dx.doi.org/10.1002/pmic.201500187 10.1002/pmic.201500187]; GPMDB: [http://gpmdb.org/data/keyword/26702875 2]. | #Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L, (2015) "Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26702875 26702875]; doi: [https://dx.doi.org/10.1002/pmic.201500187 10.1002/pmic.201500187]; GPMDB: [http://gpmdb.org/data/keyword/26702875 2]. | ||
#Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S, (2016) "Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains." <i>Mol Cell</i> <b>61</b>(1):125–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26711008 26711008]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.11.016 10.1016/j.molcel.2015.11.016]; GPMDB: [http://gpmdb.org/data/keyword/26711008 44]. | #Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S, (2016) "Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains." <i>Mol Cell</i> <b>61</b>(1):125–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26711008 26711008]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.11.016 10.1016/j.molcel.2015.11.016]; GPMDB: [http://gpmdb.org/data/keyword/26711008 44]. | ||
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#Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T, (2016) "Proteomic maps of breast cancer subtypes." <i>Nat Commun</i> <b>7</b>:10259; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26725330 26725330]; doi: [https://dx.doi.org/10.1038/ncomms10259 10.1038/ncomms10259]; GPMDB: [http://gpmdb.org/data/keyword/26725330 255]. | #Tyanova S, Albrechtsen R, Kronqvist P, Cox J, Mann M, Geiger T, (2016) "Proteomic maps of breast cancer subtypes." <i>Nat Commun</i> <b>7</b>:10259; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26725330 26725330]; doi: [https://dx.doi.org/10.1038/ncomms10259 10.1038/ncomms10259]; GPMDB: [http://gpmdb.org/data/keyword/26725330 255]. | ||
#Guo Z, Kong Q, Liu C, Zhang S, Zou L, Yan F, Whitmire JK, Xiong Y, Chen X, Wan YY, (2016) "DCAF1 controls T-cell function via p53-dependent and -independent mechanisms." <i>Nat Commun</i> <b>7</b>:10307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26728942 26728942]; doi: [https://dx.doi.org/10.1038/ncomms10307 10.1038/ncomms10307]; GPMDB: [http://gpmdb.org/data/keyword/26728942 120]. | #Guo Z, Kong Q, Liu C, Zhang S, Zou L, Yan F, Whitmire JK, Xiong Y, Chen X, Wan YY, (2016) "DCAF1 controls T-cell function via p53-dependent and -independent mechanisms." <i>Nat Commun</i> <b>7</b>:10307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26728942 26728942]; doi: [https://dx.doi.org/10.1038/ncomms10307 10.1038/ncomms10307]; GPMDB: [http://gpmdb.org/data/keyword/26728942 120]. | ||
- | #Clark DJ, Fondrie WE, Yang A, Mao L, ( | + | #Clark DJ, Fondrie WE, Yang A, Mao L, (2016) "Triple SILAC quantitative proteomic analysis reveals differential abundance of cell signaling proteins between normal and lung cancer-derived exosomes." <i>J Proteomics</i> <b>133</b>:161–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26739763 26739763]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.12.023 10.1016/j.jprot.2015.12.023]; GPMDB: [http://gpmdb.org/data/keyword/26739763 3]. |
#Wandinger SK, Lahortiga I, Jacobs K, Klammer M, Jordan N, Elschenbroich S, Parade M, Jacoby E, Linders JT, Brehmer D, Cools J, Daub H, (2016) "Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling." <i>PLoS One</i> <b>11</b>(1):e0146100; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26745281 26745281]; doi: [https://dx.doi.org/10.1371/journal.pone.0146100 10.1371/journal.pone.0146100]; GPMDB: [http://gpmdb.org/data/keyword/26745281 72]. | #Wandinger SK, Lahortiga I, Jacobs K, Klammer M, Jordan N, Elschenbroich S, Parade M, Jacoby E, Linders JT, Brehmer D, Cools J, Daub H, (2016) "Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling." <i>PLoS One</i> <b>11</b>(1):e0146100; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26745281 26745281]; doi: [https://dx.doi.org/10.1371/journal.pone.0146100 10.1371/journal.pone.0146100]; GPMDB: [http://gpmdb.org/data/keyword/26745281 72]. | ||
#Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Arias AM, Lilley KS, (2016) "A draft map of the mouse pluripotent stem cell spatial proteome." <i>Nat Commun</i> <b>7</b>:9992; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26754106 26754106]; doi: [https://dx.doi.org/10.1038/ncomms9992 10.1038/ncomms9992]; GPMDB: [http://gpmdb.org/data/keyword/26754106 2]. | #Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Arias AM, Lilley KS, (2016) "A draft map of the mouse pluripotent stem cell spatial proteome." <i>Nat Commun</i> <b>7</b>:9992; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26754106 26754106]; doi: [https://dx.doi.org/10.1038/ncomms9992 10.1038/ncomms9992]; GPMDB: [http://gpmdb.org/data/keyword/26754106 2]. | ||
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#Neubert P, Halim A, Zauser M, Essig A, Joshi HJ, Zatorska E, Larsen IS, Loibl M, Castells-Ballester J, Aebi M, Clausen H, Strahl S, (2016) "Mapping the O-mannose glycoproteome in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26764011 26764011]; doi: [https://dx.doi.org/10.1074/mcp.M115.057505 10.1074/mcp.M115.057505]; GPMDB: [http://gpmdb.org/data/keyword/26764011 6]. | #Neubert P, Halim A, Zauser M, Essig A, Joshi HJ, Zatorska E, Larsen IS, Loibl M, Castells-Ballester J, Aebi M, Clausen H, Strahl S, (2016) "Mapping the O-mannose glycoproteome in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26764011 26764011]; doi: [https://dx.doi.org/10.1074/mcp.M115.057505 10.1074/mcp.M115.057505]; GPMDB: [http://gpmdb.org/data/keyword/26764011 6]. | ||
#Kümper S, Mardakheh FK, McCarthy A, Yeo M, Stamp GW, Paul A, Worboys J, Sadok A, Jørgensen C, Guichard S, Marshall CJ, (2016) "Rho-associated kinase (ROCK) function is essential for cell cycle progression, senescence and tumorigenesis." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26765561 26765561]; doi: [https://dx.doi.org/10.7554/eLife.12203 10.7554/eLife.12203]; GPMDB: [http://gpmdb.org/data/keyword/26765561 28]. | #Kümper S, Mardakheh FK, McCarthy A, Yeo M, Stamp GW, Paul A, Worboys J, Sadok A, Jørgensen C, Guichard S, Marshall CJ, (2016) "Rho-associated kinase (ROCK) function is essential for cell cycle progression, senescence and tumorigenesis." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26765561 26765561]; doi: [https://dx.doi.org/10.7554/eLife.12203 10.7554/eLife.12203]; GPMDB: [http://gpmdb.org/data/keyword/26765561 28]. | ||
+ | #Peleg S, Feller C, Forne I, Schiller E, Sévin DC, Schauer T, Regnard C, Straub T, Prestel M, Klima C, Schmitt Nogueira M, Becker L, Klopstock T, Sauer U, Becker PB, Imhof A, Ladurner AG, (2016) "Life span extension by targeting a link between metabolism and histone acetylation in Drosophila." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26781291 26781291]; doi: [https://dx.doi.org/10.15252/embr.201541132 10.15252/embr.201541132]; GPMDB: [http://gpmdb.org/data/keyword/26781291 20]. |
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.