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==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 December 4, 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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#Zhou Y, Xiong L, Zhang Y, Yu R, Jiang X, Xu G, (2016) "Quantitative proteomics identifies myoferlin as a novel regulator of A Disintegrin and Metalloproteinase 12 in HeLa cells." <i>J Proteomics</i> <b>148</b>:94–104; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432471 27432471]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.07.015 10.1016/j.jprot.2016.07.015]; GPMDB: [http://gpmdb.org/data/keyword/27432471 14]. | #Zhou Y, Xiong L, Zhang Y, Yu R, Jiang X, Xu G, (2016) "Quantitative proteomics identifies myoferlin as a novel regulator of A Disintegrin and Metalloproteinase 12 in HeLa cells." <i>J Proteomics</i> <b>148</b>:94–104; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432471 27432471]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.07.015 10.1016/j.jprot.2016.07.015]; GPMDB: [http://gpmdb.org/data/keyword/27432471 14]. | ||
#Li X, Tran KM, Aziz KE, Sorokin AV, Chen J, Wang W, (2016) "Defining the Protein-Protein Interaction Network of the Human Protein Tyrosine Phosphatase Family." <i>Mol Cell Proteomics</i> <b>15</b>(9):3030–44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432908 27432908]; doi: [https://dx.doi.org/10.1074/mcp.M116.060277 10.1074/mcp.M116.060277]; GPMDB: [http://gpmdb.org/data/keyword/27432908 88]. | #Li X, Tran KM, Aziz KE, Sorokin AV, Chen J, Wang W, (2016) "Defining the Protein-Protein Interaction Network of the Human Protein Tyrosine Phosphatase Family." <i>Mol Cell Proteomics</i> <b>15</b>(9):3030–44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432908 27432908]; doi: [https://dx.doi.org/10.1074/mcp.M116.060277 10.1074/mcp.M116.060277]; GPMDB: [http://gpmdb.org/data/keyword/27432908 88]. | ||
- | #Suárez-Cortés P, Sharma V, Bertuccini L, Costa G, Bannerman NL, | + | #Suárez-Cortés P, Sharma V, Bertuccini L, Costa G, Bannerman NL, Sannella AR, Williamson K, Klemba M, Levashina EA, Lasonder E, Alano P, (2016) "Comparative Proteomics and Functional Analysis Reveal a Role of Plasmodium falciparum Osmiophilic Bodies in Malaria Parasite Transmission." <i>Mol Cell Proteomics</i> <b>15</b>(10):3243–3255; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432909 27432909]; doi: [https://dx.doi.org/10.1074/mcp.M116.060681 10.1074/mcp.M116.060681]; GPMDB: [http://gpmdb.org/data/keyword/27432909 162]. |
#Vandenbrouck Y, Lane L, Carapito C, Duek P, Rondel K, Bruley C, Macron C, Gonzalez de Peredo A, Couté Y, Chaoui K, Com E, Gateau A, Hesse AM, Marcellin M, Méar L, Mouton-Barbosa E, Robin T, Burlet-Schiltz O, Cianferani S, Ferro M, Fréour T, Lindskog C, Garin J, Pineau C, (2016) "Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update." <i>J Proteome Res</i> <b>15</b>(11):3998–4019; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27444420 27444420]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00400 10.1021/acs.jproteome.6b00400]; GPMDB: [http://gpmdb.org/data/keyword/27444420 108]. | #Vandenbrouck Y, Lane L, Carapito C, Duek P, Rondel K, Bruley C, Macron C, Gonzalez de Peredo A, Couté Y, Chaoui K, Com E, Gateau A, Hesse AM, Marcellin M, Méar L, Mouton-Barbosa E, Robin T, Burlet-Schiltz O, Cianferani S, Ferro M, Fréour T, Lindskog C, Garin J, Pineau C, (2016) "Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update." <i>J Proteome Res</i> <b>15</b>(11):3998–4019; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27444420 27444420]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00400 10.1021/acs.jproteome.6b00400]; GPMDB: [http://gpmdb.org/data/keyword/27444420 108]. | ||
#Martinez-Val A, Garcia F, Ximénez-Embún P, Ibarz N, Zarzuela E, Ruppen I, Mohammed S, Munoz J, (2016) "On the Statistical Significance of Compressed Ratios in Isobaric Labeling: A Cross-Platform Comparison." <i>J Proteome Res</i> <b>15</b>(9):3029–38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27452035 27452035]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00151 10.1021/acs.jproteome.6b00151]; GPMDB: [http://gpmdb.org/data/keyword/27452035 18]. | #Martinez-Val A, Garcia F, Ximénez-Embún P, Ibarz N, Zarzuela E, Ruppen I, Mohammed S, Munoz J, (2016) "On the Statistical Significance of Compressed Ratios in Isobaric Labeling: A Cross-Platform Comparison." <i>J Proteome Res</i> <b>15</b>(9):3029–38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27452035 27452035]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00151 10.1021/acs.jproteome.6b00151]; GPMDB: [http://gpmdb.org/data/keyword/27452035 18]. | ||
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#Baas R, Sijm A, van Teeffelen HA, van Es R, Vos HR, Marc Timmers HT, (2016) "Quantitative Proteomics of the SMAD (Suppressor of Mothers against Decapentaplegic) Transcription Factor Family Identifies Importin 5 as a Bone Morphogenic Protein Receptor SMAD-specific Importin." <i>J Biol Chem</i> <b>291</b>(46):24121–24132; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27703004 27703004]; doi: [https://dx.doi.org/10.1074/jbc.M116.748582 10.1074/jbc.M116.748582]; GPMDB: [http://gpmdb.org/data/keyword/27703004 108]. | #Baas R, Sijm A, van Teeffelen HA, van Es R, Vos HR, Marc Timmers HT, (2016) "Quantitative Proteomics of the SMAD (Suppressor of Mothers against Decapentaplegic) Transcription Factor Family Identifies Importin 5 as a Bone Morphogenic Protein Receptor SMAD-specific Importin." <i>J Biol Chem</i> <b>291</b>(46):24121–24132; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27703004 27703004]; doi: [https://dx.doi.org/10.1074/jbc.M116.748582 10.1074/jbc.M116.748582]; GPMDB: [http://gpmdb.org/data/keyword/27703004 108]. | ||
#Hughes CS, McConechy MK, Cochrane DR, Nazeran T, Karnezis AN, Huntsman DG, Morin GB, (2016) "Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research." <i>Sci Rep</i> <b>6</b>:34949; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27713570 27713570]; doi: [https://dx.doi.org/10.1038/srep34949 10.1038/srep34949]; GPMDB: [http://gpmdb.org/data/keyword/27713570 172]. | #Hughes CS, McConechy MK, Cochrane DR, Nazeran T, Karnezis AN, Huntsman DG, Morin GB, (2016) "Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research." <i>Sci Rep</i> <b>6</b>:34949; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27713570 27713570]; doi: [https://dx.doi.org/10.1038/srep34949 10.1038/srep34949]; GPMDB: [http://gpmdb.org/data/keyword/27713570 172]. | ||
- | #Sivadasan R, Hornburg D, Drepper C, Frank N, Jablonka S, Hansel A, Lojewski X, Sterneckert J, Hermann A, Shaw PJ, Ince PG, Mann M, Meissner F, Sendtner M, (2016) "C9ORF72 interaction with cofilin modulates actin dynamics in motor neurons." <i>Nat Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27723745 27723745]; doi: [https://dx.doi.org/10.1038/nn.4407 10.1038/nn.4407]; GPMDB: [http://gpmdb.org/data/keyword/27723745 6]. | + | #McShane E, Sin C, Zauber H, Wells JN, Donnelly N, Wang X, Hou J, Chen W, Storchova Z, Marsh JA, Valleriani A, Selbach M, (2016) "Kinetic Analysis of Protein Stability Reveals Age-Dependent Degradation." <i>Cell</i> <b>167</b>(3):803–815.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27720452 27720452]; doi: [https://dx.doi.org/10.1016/j.cell.2016.09.015 10.1016/j.cell.2016.09.015]; GPMDB: [http://gpmdb.org/data/keyword/27720452 43]. |
+ | #Sivadasan R, Hornburg D, Drepper C, Frank N, Jablonka S, Hansel A, Lojewski X, Sterneckert J, Hermann A, Shaw PJ, Ince PG, Mann M, Meissner F, Sendtner M, (2016) "C9ORF72 interaction with cofilin modulates actin dynamics in motor neurons." <i>Nat Neurosci</i> <b>19</b>(12):1610–1618; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27723745 27723745]; doi: [https://dx.doi.org/10.1038/nn.4407 10.1038/nn.4407]; GPMDB: [http://gpmdb.org/data/keyword/27723745 6]. | ||
#Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE, (2016) "Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27726376 27726376]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00386 10.1021/acs.jproteome.6b00386]; GPMDB: [http://gpmdb.org/data/keyword/27726376 61]. | #Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE, (2016) "Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27726376 27726376]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00386 10.1021/acs.jproteome.6b00386]; GPMDB: [http://gpmdb.org/data/keyword/27726376 61]. | ||
#Al-Daghri NM, Alokail MS, Manousopoulou A, Heinson A, Al-Attas O, Al-Saleh Y, Sabico S, Yakout S, Woelk CH, Chrousos GP, Garbis SD, (2016) "Sex-specific vitamin D effects on blood coagulation among overweight adults." <i>Eur J Clin Invest</i> <b>46</b>(12):1031–1040; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27727459 27727459]; doi: [https://dx.doi.org/10.1111/eci.12688 10.1111/eci.12688]; GPMDB: [http://gpmdb.org/data/keyword/27727459 50]. | #Al-Daghri NM, Alokail MS, Manousopoulou A, Heinson A, Al-Attas O, Al-Saleh Y, Sabico S, Yakout S, Woelk CH, Chrousos GP, Garbis SD, (2016) "Sex-specific vitamin D effects on blood coagulation among overweight adults." <i>Eur J Clin Invest</i> <b>46</b>(12):1031–1040; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27727459 27727459]; doi: [https://dx.doi.org/10.1111/eci.12688 10.1111/eci.12688]; GPMDB: [http://gpmdb.org/data/keyword/27727459 50]. | ||
#Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myhr KM, Torkildsen Ø, Berven FS, (2016) "In-depth cerebrospinal fluid quantitative proteome and deglycoproteome analysis; presenting a comprehensive picture of pathways and processes affected by multiple sclerosis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27728768 27728768]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00659 10.1021/acs.jproteome.6b00659]; GPMDB: [http://gpmdb.org/data/keyword/27728768 26]. | #Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myhr KM, Torkildsen Ø, Berven FS, (2016) "In-depth cerebrospinal fluid quantitative proteome and deglycoproteome analysis; presenting a comprehensive picture of pathways and processes affected by multiple sclerosis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27728768 27728768]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00659 10.1021/acs.jproteome.6b00659]; GPMDB: [http://gpmdb.org/data/keyword/27728768 26]. | ||
+ | #Zammit CM, Weiland F, Brugger J, Wade B, Winderbaum LJ, Nies DH, Southam G, Hoffmann P, Reith F, (2016) "Proteomic responses to gold(iii)-toxicity in the bacterium Cupriavidus metallidurans CH34." <i>Metallomics</i> <b>8</b>(11):1204–1216; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27757465 27757465]; doi: [https://dx.doi.org/10.1039/c6mt00142d 10.1039/c6mt00142d]; GPMDB: [http://gpmdb.org/data/keyword/27757465 56]. | ||
+ | #Sarvaiya HA, Lazar IM, (2016) "Insulin stimulated MCF7 breast cancer cells: Proteome dataset." <i>Data Brief</i> <b>9</b>:579–584; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27761513 27761513]; doi: [https://dx.doi.org/10.1016/j.dib.2016.09.025 10.1016/j.dib.2016.09.025]; GPMDB: [http://gpmdb.org/data/keyword/27761513 1]. | ||
#Duncan O, Trösch J, Fenske R, Taylor NL, Millar AH, (2016) "Mapping the Triticum aestivum proteome." <i>Plant J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27775198 27775198]; doi: [https://dx.doi.org/10.1111/tpj.13402 10.1111/tpj.13402]; GPMDB: [http://gpmdb.org/data/keyword/27775198 28]. | #Duncan O, Trösch J, Fenske R, Taylor NL, Millar AH, (2016) "Mapping the Triticum aestivum proteome." <i>Plant J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27775198 27775198]; doi: [https://dx.doi.org/10.1111/tpj.13402 10.1111/tpj.13402]; GPMDB: [http://gpmdb.org/data/keyword/27775198 28]. | ||
+ | #Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS, (2016) "A flexible data analysis pipeline for high-confidence proteogenomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27786492 27786492]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00765 10.1021/acs.jproteome.6b00765]; GPMDB: [http://gpmdb.org/data/keyword/27786492 35]. | ||
#Mardakheh FK, Self A, Marshall CJ, (2016) "RHO binding to FAM65A regulates Golgi reorientation during cell migration." <i>J Cell Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807006 27807006]; doi: [https://dx.doi.org/10.1242/jcs.198614 10.1242/jcs.198614]; GPMDB: [http://gpmdb.org/data/keyword/27807006 18]. | #Mardakheh FK, Self A, Marshall CJ, (2016) "RHO binding to FAM65A regulates Golgi reorientation during cell migration." <i>J Cell Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807006 27807006]; doi: [https://dx.doi.org/10.1242/jcs.198614 10.1242/jcs.198614]; GPMDB: [http://gpmdb.org/data/keyword/27807006 18]. | ||
+ | #Bassani-Sternberg M, Bräunlein E, Klar R, Engleitner T, Sinitcyn P, Audehm S, Straub M, Weber J, Slotta-Huspenina J, Specht K, Martignoni ME, Werner A, Hein R, H Busch D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM, (2016) "Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry." <i>Nat Commun</i> <b>7</b>:13404; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27869121 27869121]; doi: [https://dx.doi.org/10.1038/ncomms13404 10.1038/ncomms13404]; GPMDB: [http://gpmdb.org/data/keyword/27869121 22]. | ||
#St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JD, Rajendran D, Couzens AL, Currie KW, Tkach JM, Cheung SW, Pelletier L, Gingras AC, (2016) "Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators." <i>Cell Rep</i> <b>17</b>(9):2488–2501; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27880917 27880917]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.10.078 10.1016/j.celrep.2016.10.078]; GPMDB: [http://gpmdb.org/data/keyword/27880917 315]. | #St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JD, Rajendran D, Couzens AL, Currie KW, Tkach JM, Cheung SW, Pelletier L, Gingras AC, (2016) "Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators." <i>Cell Rep</i> <b>17</b>(9):2488–2501; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27880917 27880917]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.10.078 10.1016/j.celrep.2016.10.078]; GPMDB: [http://gpmdb.org/data/keyword/27880917 315]. |
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 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 December 4, 2016.