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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 (1,245 publications) was current, as of September 4, 2016. | 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 (1,245 publications) was current, as of September 4, 2016. | ||
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#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]. | ||
#Liu T, Qian WJ, Strittmatter EF, Camp DG 2nd, Anderson GA, Thrall BD, Smith RD, (2004) "High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." <i>Anal Chem</i> <b>76</b>(18):5345–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/15362891 15362891]; doi: [https://dx.doi.org/10.1021/ac049485q 10.1021/ac049485q]; GPMDB: [http://gpmdb.org/data/keyword/15362891 6]. | #Liu T, Qian WJ, Strittmatter EF, Camp DG 2nd, Anderson GA, Thrall BD, Smith RD, (2004) "High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." <i>Anal Chem</i> <b>76</b>(18):5345–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/15362891 15362891]; doi: [https://dx.doi.org/10.1021/ac049485q 10.1021/ac049485q]; GPMDB: [http://gpmdb.org/data/keyword/15362891 6]. | ||
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#Zhang H, Ramakrishnan SK, Triner D, Centofanti B, Maitra D, Győrffy B, Sebolt-Leopold JS, Dame MK, Varani J, Brenner DE, Fearon ER, Omary MB, Shah YM, (2015) "Tumor-selective proteotoxicity of verteporfin inhibits colon cancer progression independently of YAP1." <i>Sci Signal</i> <b>8</b>(397):ra98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26443705 26443705]; doi: [https://dx.doi.org/10.1126/scisignal.aac5418 10.1126/scisignal.aac5418]; GPMDB: [http://gpmdb.org/data/keyword/26443705 2]. | #Zhang H, Ramakrishnan SK, Triner D, Centofanti B, Maitra D, Győrffy B, Sebolt-Leopold JS, Dame MK, Varani J, Brenner DE, Fearon ER, Omary MB, Shah YM, (2015) "Tumor-selective proteotoxicity of verteporfin inhibits colon cancer progression independently of YAP1." <i>Sci Signal</i> <b>8</b>(397):ra98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26443705 26443705]; doi: [https://dx.doi.org/10.1126/scisignal.aac5418 10.1126/scisignal.aac5418]; GPMDB: [http://gpmdb.org/data/keyword/26443705 2]. | ||
#Kwon OK, Kim SJ, Lee YM, Lee YH, Bae YS, Kim JY, Peng X, Cheng Z, Zhao Y, Lee S, (2016) "Global analysis of phosphoproteome dynamics in embryonic development of zebrafish (Danio rerio)." <i>Proteomics</i> <b>16</b>(1):136–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26449285 26449285]; doi: [https://dx.doi.org/10.1002/pmic.201500017 10.1002/pmic.201500017]; GPMDB: [http://gpmdb.org/data/keyword/26449285 32]. | #Kwon OK, Kim SJ, Lee YM, Lee YH, Bae YS, Kim JY, Peng X, Cheng Z, Zhao Y, Lee S, (2016) "Global analysis of phosphoproteome dynamics in embryonic development of zebrafish (Danio rerio)." <i>Proteomics</i> <b>16</b>(1):136–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26449285 26449285]; doi: [https://dx.doi.org/10.1002/pmic.201500017 10.1002/pmic.201500017]; GPMDB: [http://gpmdb.org/data/keyword/26449285 32]. | ||
+ | #Núñez Galindo A, Kussmann M, Dayon L, (2015) "Proteomics of Cerebrospinal Fluid: Throughput and Robustness Using a Scalable Automated Analysis Pipeline for Biomarker Discovery." <i>Anal Chem</i> <b>87</b>(21):10755–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26452177 26452177]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b02748 10.1021/acs.analchem.5b02748]; GPMDB: [http://gpmdb.org/data/keyword/26452177 66]. | ||
#Geddes JM, Croll D, Caza M, Stoynov N, Foster LJ, Kronstad JW, (2015) "Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A." <i>BMC Microbiol</i> <b>15</b>:206; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26453029 26453029]; doi: [https://dx.doi.org/10.1186/s12866-015-0532-3 10.1186/s12866-015-0532-3]; GPMDB: [http://gpmdb.org/data/keyword/26453029 48]. | #Geddes JM, Croll D, Caza M, Stoynov N, Foster LJ, Kronstad JW, (2015) "Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A." <i>BMC Microbiol</i> <b>15</b>:206; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26453029 26453029]; doi: [https://dx.doi.org/10.1186/s12866-015-0532-3 10.1186/s12866-015-0532-3]; GPMDB: [http://gpmdb.org/data/keyword/26453029 48]. | ||
#Gomez-Auli A, Hillebrand LE, Biniossek ML, Peters C, Reinheckel T, Schilling O, (2016) "Impact of cathepsin B on the interstitial fluid proteome of murine breast cancers." <i>Biochimie</i> <b>122</b>:88–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26455267 26455267]; doi: [https://dx.doi.org/10.1016/j.biochi.2015.10.009 10.1016/j.biochi.2015.10.009]; GPMDB: [http://gpmdb.org/data/keyword/26455267 1]. | #Gomez-Auli A, Hillebrand LE, Biniossek ML, Peters C, Reinheckel T, Schilling O, (2016) "Impact of cathepsin B on the interstitial fluid proteome of murine breast cancers." <i>Biochimie</i> <b>122</b>:88–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26455267 26455267]; doi: [https://dx.doi.org/10.1016/j.biochi.2015.10.009 10.1016/j.biochi.2015.10.009]; GPMDB: [http://gpmdb.org/data/keyword/26455267 1]. |
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 (1,245 publications) was current, as of September 4, 2016.