Line 24: | Line 24: | ||
==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 June | + | 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 June 19, 2016. |
#Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." <i>Infect Immun</i> <b>57</b>(3):999–1001; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2645217 2645217]; GPMDB: [http://gpmdb.org/data/keyword/2645217 66]. | #Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." <i>Infect Immun</i> <b>57</b>(3):999–1001; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2645217 2645217]; GPMDB: [http://gpmdb.org/data/keyword/2645217 66]. | ||
Line 990: | Line 990: | ||
#Kito K, Ito H, Nohara T, Ohnishi M, Ishibashi Y, Takeda D, (2016) "Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication." <i>Mol Cell Proteomics</i> <b>15</b>(1):218–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26560065 26560065]; doi: [https://dx.doi.org/10.1074/mcp.M115.051854 10.1074/mcp.M115.051854]; GPMDB: [http://gpmdb.org/data/keyword/26560065 150]. | #Kito K, Ito H, Nohara T, Ohnishi M, Ishibashi Y, Takeda D, (2016) "Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication." <i>Mol Cell Proteomics</i> <b>15</b>(1):218–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26560065 26560065]; doi: [https://dx.doi.org/10.1074/mcp.M115.051854 10.1074/mcp.M115.051854]; GPMDB: [http://gpmdb.org/data/keyword/26560065 150]. | ||
#Zhao Y, Valbuena G, Walker DH, Gazi M, Hidalgo M, DeSousa R, Oteo JA, Goez Y, Brasier AR, (2016) "Endothelial Cell Proteomic Response to Rickettsia conorii Infection Reveals Activation of the Janus Kinase (JAK)-Signal Transducer and Activator of Transcription (STAT)-Inferferon Stimulated Gene (ISG)15 Pathway and Reprogramming Plasma Membrane Integrin/Cadherin Signaling." <i>Mol Cell Proteomics</i> <b>15</b>(1):289–304; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26560068 26560068]; doi: [https://dx.doi.org/10.1074/mcp.M115.054361 10.1074/mcp.M115.054361]; GPMDB: [http://gpmdb.org/data/keyword/26560068 7]. | #Zhao Y, Valbuena G, Walker DH, Gazi M, Hidalgo M, DeSousa R, Oteo JA, Goez Y, Brasier AR, (2016) "Endothelial Cell Proteomic Response to Rickettsia conorii Infection Reveals Activation of the Janus Kinase (JAK)-Signal Transducer and Activator of Transcription (STAT)-Inferferon Stimulated Gene (ISG)15 Pathway and Reprogramming Plasma Membrane Integrin/Cadherin Signaling." <i>Mol Cell Proteomics</i> <b>15</b>(1):289–304; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26560068 26560068]; doi: [https://dx.doi.org/10.1074/mcp.M115.054361 10.1074/mcp.M115.054361]; GPMDB: [http://gpmdb.org/data/keyword/26560068 7]. | ||
+ | #Tutakhel OA, Jeleń S, Valdez-Flores M, Dimke H, Piersma SR, Jimenez CR, Deinum J, Lenders JW, Hoenderop JG, Bindels RJ, (2016) "Alternative splice variant of the thiazide-sensitive NaCl cotransporter: a novel player in renal salt handling." <i>Am J Physiol Renal Physiol</i> <b>310</b>(3):F204–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26561651 26561651]; doi: [https://dx.doi.org/10.1152/ajprenal.00429.2015 10.1152/ajprenal.00429.2015]; GPMDB: [http://gpmdb.org/data/keyword/26561651 1]. | ||
#Sun S, Shah P, Eshghi ST, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Höti N, Zhang Z, Chan DW, Zhang H, (2016) "Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides." <i>Nat Biotechnol</i> <b>34</b>(1):84–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26571101 26571101]; doi: [https://dx.doi.org/10.1038/nbt.3403 10.1038/nbt.3403]; GPMDB: [http://gpmdb.org/data/keyword/26571101 55]. | #Sun S, Shah P, Eshghi ST, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Höti N, Zhang Z, Chan DW, Zhang H, (2016) "Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides." <i>Nat Biotechnol</i> <b>34</b>(1):84–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26571101 26571101]; doi: [https://dx.doi.org/10.1038/nbt.3403 10.1038/nbt.3403]; GPMDB: [http://gpmdb.org/data/keyword/26571101 55]. | ||
#Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H, Beli P, (2016) "ATR inhibition rewires cellular signaling networks induced by replication stress." <i>Proteomics</i> <b>16</b>(3):402–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26572502 26572502]; doi: [https://dx.doi.org/10.1002/pmic.201500172 10.1002/pmic.201500172]; GPMDB: [http://gpmdb.org/data/keyword/26572502 20]. | #Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H, Beli P, (2016) "ATR inhibition rewires cellular signaling networks induced by replication stress." <i>Proteomics</i> <b>16</b>(3):402–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26572502 26572502]; doi: [https://dx.doi.org/10.1002/pmic.201500172 10.1002/pmic.201500172]; GPMDB: [http://gpmdb.org/data/keyword/26572502 20]. | ||
Line 1,009: | Line 1,010: | ||
#Padden J, Ahrens M, Kälsch J, Bertram S, Megger DA, Bracht T, Eisenacher M, Kocabayoglu P, Meyer HE, Sipos B, Baba HA, Sitek B, (2016) "Immunohistochemical Markers Distinguishing Cholangiocellular Carcinoma (CCC) from Pancreatic Ductal Adenocarcinoma (PDAC) Discovered by Proteomic Analysis of Microdissected Cells." <i>Mol Cell Proteomics</i> <b>15</b>(3):1072–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26644413 26644413]; doi: [https://dx.doi.org/10.1074/mcp.M115.054585 10.1074/mcp.M115.054585]; GPMDB: [http://gpmdb.org/data/keyword/26644413 66]. | #Padden J, Ahrens M, Kälsch J, Bertram S, Megger DA, Bracht T, Eisenacher M, Kocabayoglu P, Meyer HE, Sipos B, Baba HA, Sitek B, (2016) "Immunohistochemical Markers Distinguishing Cholangiocellular Carcinoma (CCC) from Pancreatic Ductal Adenocarcinoma (PDAC) Discovered by Proteomic Analysis of Microdissected Cells." <i>Mol Cell Proteomics</i> <b>15</b>(3):1072–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26644413 26644413]; doi: [https://dx.doi.org/10.1074/mcp.M115.054585 10.1074/mcp.M115.054585]; GPMDB: [http://gpmdb.org/data/keyword/26644413 66]. | ||
#Xu J, Gao J, Yu C, He H, Yang Y, Figeys D, Zhou H, (2016) "Development of Online pH Gradient-Eluted Strong Cation Exchange Nanoelectrospray-Tandem Mass Spectrometry for Proteomic Analysis Facilitating Basic and Histidine-Containing Peptides Identification." <i>Anal Chem</i> <b>88</b>(1):583–91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26646553 26646553]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b04000 10.1021/acs.analchem.5b04000]; GPMDB: [http://gpmdb.org/data/keyword/26646553 6]. | #Xu J, Gao J, Yu C, He H, Yang Y, Figeys D, Zhou H, (2016) "Development of Online pH Gradient-Eluted Strong Cation Exchange Nanoelectrospray-Tandem Mass Spectrometry for Proteomic Analysis Facilitating Basic and Histidine-Containing Peptides Identification." <i>Anal Chem</i> <b>88</b>(1):583–91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26646553 26646553]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b04000 10.1021/acs.analchem.5b04000]; GPMDB: [http://gpmdb.org/data/keyword/26646553 6]. | ||
- | #Iglesias-Gato D, Wikström P, Tyanova S, Lavallee C, Thysell E, Carlsson J, Hägglöf C, Cox J, Andrén O, Stattin P, Egevad L, Widmark A, Bjartell A, Collins CC, Bergh A, Geiger T, Mann M, Flores-Morales A, ( | + | #Iglesias-Gato D, Wikström P, Tyanova S, Lavallee C, Thysell E, Carlsson J, Hägglöf C, Cox J, Andrén O, Stattin P, Egevad L, Widmark A, Bjartell A, Collins CC, Bergh A, Geiger T, Mann M, Flores-Morales A, (2016) "The Proteome of Primary Prostate Cancer." <i>Eur Urol</i> <b>69</b>(5):942–52; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26651926 26651926]; doi: [https://dx.doi.org/10.1016/j.eururo.2015.10.053 10.1016/j.eururo.2015.10.053]; GPMDB: [http://gpmdb.org/data/keyword/26651926 36]. |
#Kasvandik S, Samuel K, Peters M, Eimre M, Peet N, Roost AM, Padrik L, Paju K, Peil L, Salumets A, (2016) "Deep Quantitative Proteomics Reveals Extensive Metabolic Reprogramming and Cancer-Like Changes of Ectopic Endometriotic Stromal Cells." <i>J Proteome Res</i> <b>15</b>(2):572–84; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26654049 26654049]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00965 10.1021/acs.jproteome.5b00965]; GPMDB: [http://gpmdb.org/data/keyword/26654049 21]. | #Kasvandik S, Samuel K, Peters M, Eimre M, Peet N, Roost AM, Padrik L, Paju K, Peil L, Salumets A, (2016) "Deep Quantitative Proteomics Reveals Extensive Metabolic Reprogramming and Cancer-Like Changes of Ectopic Endometriotic Stromal Cells." <i>J Proteome Res</i> <b>15</b>(2):572–84; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26654049 26654049]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00965 10.1021/acs.jproteome.5b00965]; GPMDB: [http://gpmdb.org/data/keyword/26654049 21]. | ||
#Farina F, Gaillard J, Guérin C, Couté Y, Sillibourne J, Blanchoin L, Théry M, (2016) "The centrosome is an actin-organizing centre." <i>Nat Cell Biol</i> <b>18</b>(1):65–75; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26655833 26655833]; doi: [https://dx.doi.org/10.1038/ncb3285 10.1038/ncb3285]; GPMDB: [http://gpmdb.org/data/keyword/26655833 2]. | #Farina F, Gaillard J, Guérin C, Couté Y, Sillibourne J, Blanchoin L, Théry M, (2016) "The centrosome is an actin-organizing centre." <i>Nat Cell Biol</i> <b>18</b>(1):65–75; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26655833 26655833]; doi: [https://dx.doi.org/10.1038/ncb3285 10.1038/ncb3285]; GPMDB: [http://gpmdb.org/data/keyword/26655833 2]. | ||
Line 1,164: | Line 1,165: | ||
#Wang B, Pfeiffer MJ, Drexler HC, Fuellen G, Boiani M, (2016) "Proteomic analysis of mouse oocytes identifies PRMT7 as reprogramming factor that replaces SOX2 in the induction of pluripotent stem cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27225728 27225728]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01083 10.1021/acs.jproteome.5b01083]; GPMDB: [http://gpmdb.org/data/keyword/27225728 14]. | #Wang B, Pfeiffer MJ, Drexler HC, Fuellen G, Boiani M, (2016) "Proteomic analysis of mouse oocytes identifies PRMT7 as reprogramming factor that replaces SOX2 in the induction of pluripotent stem cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27225728 27225728]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01083 10.1021/acs.jproteome.5b01083]; GPMDB: [http://gpmdb.org/data/keyword/27225728 14]. | ||
#Lodrini M, Poschmann G, Schmidt V, Wünschel J, Dreidax D, Witt O, Höfer T, Meyer HE, Stühler K, Eggert A, Deubzer HE, (2016) "Minichromosome Maintenance Complex Is a Critical Node in the miR-183 Signaling Network of MYCN-Amplified Neuroblastoma Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27239679 27239679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00134 10.1021/acs.jproteome.6b00134]; GPMDB: [http://gpmdb.org/data/keyword/27239679 12]. | #Lodrini M, Poschmann G, Schmidt V, Wünschel J, Dreidax D, Witt O, Höfer T, Meyer HE, Stühler K, Eggert A, Deubzer HE, (2016) "Minichromosome Maintenance Complex Is a Critical Node in the miR-183 Signaling Network of MYCN-Amplified Neuroblastoma Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27239679 27239679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00134 10.1021/acs.jproteome.6b00134]; GPMDB: [http://gpmdb.org/data/keyword/27239679 12]. | ||
+ | #Bullen JW, Tchernyshyov I, Holewinski RJ, DeVine L, Wu F, Venkatraman V, Kass DL, Cole RN, Van Eyk J, Semenza GL, (2016) "Protein kinase A-dependent phosphorylation stimulates the transcriptional activity of hypoxia-inducible factor 1." <i>Sci Signal</i> <b>9</b>(430):ra56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27245613 27245613]; doi: [https://dx.doi.org/10.1126/scisignal.aaf0583 10.1126/scisignal.aaf0583]; GPMDB: [http://gpmdb.org/data/keyword/27245613 14]. | ||
+ | #Patella F, Neilson LJ, Athineos D, Erami Z, Anderson KI, Blyth K, Ryan KM, Zanivan S, (2016) "In-Depth Proteomics Identifies a Role for Autophagy in Controlling Reactive Oxygen Species Mediated Endothelial Permeability." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27246970 27246970]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00166 10.1021/acs.jproteome.6b00166]; GPMDB: [http://gpmdb.org/data/keyword/27246970 10]. | ||
+ | #Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC, (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [http://gpmdb.org/data/keyword/27251275 1265]. | ||
+ | #Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of novel pancreatic ductal adenocarcinoma subtypes by global phosphotyrosine profiling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [http://gpmdb.org/data/keyword/27259358 112]. |
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 June 19, 2016.