Line 25: | Line 25: | ||
==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 May | + | 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 May 14, 2017. |
#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]. | ||
Line 1,520: | Line 1,520: | ||
#Worst TS, von Hardenberg J, Gross JC, Erben P, Schnoelzer M, Hausser I, Bugert P, Michel MS, Boutros M, (2017) "A database-augmented, exosome-based mass spectrometry approach exemplarily identifies circulating claudin 3 as biomarker in prostate cancer." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28396511 28396511]; doi: [https://dx.doi.org/10.1074/mcp.M117.068577 10.1074/mcp.M117.068577]; GPMDB: [http://gpmdb.org/data/keyword/28396511 17]. | #Worst TS, von Hardenberg J, Gross JC, Erben P, Schnoelzer M, Hausser I, Bugert P, Michel MS, Boutros M, (2017) "A database-augmented, exosome-based mass spectrometry approach exemplarily identifies circulating claudin 3 as biomarker in prostate cancer." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28396511 28396511]; doi: [https://dx.doi.org/10.1074/mcp.M117.068577 10.1074/mcp.M117.068577]; GPMDB: [http://gpmdb.org/data/keyword/28396511 17]. | ||
#Rinschen MM, Grahammer F, Hoppe AK, Kohli P, Hagmann H, Kretz O, Bertsch S, Höhne M, Göbel H, Bartram MP, Gandhirajan RK, Krüger M, Brinkkoetter PT, Huber TB, Kann M, Wickström SA, Benzing T, Schermer B, (2017) "YAP-mediated mechanotransduction determines the podocyte's response to damage." <i>Sci Signal</i> <b>10</b>(474):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28400537 28400537]; doi: [https://dx.doi.org/10.1126/scisignal.aaf8165 10.1126/scisignal.aaf8165]; GPMDB: [http://gpmdb.org/data/keyword/28400537 20]. | #Rinschen MM, Grahammer F, Hoppe AK, Kohli P, Hagmann H, Kretz O, Bertsch S, Höhne M, Göbel H, Bartram MP, Gandhirajan RK, Krüger M, Brinkkoetter PT, Huber TB, Kann M, Wickström SA, Benzing T, Schermer B, (2017) "YAP-mediated mechanotransduction determines the podocyte's response to damage." <i>Sci Signal</i> <b>10</b>(474):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28400537 28400537]; doi: [https://dx.doi.org/10.1126/scisignal.aaf8165 10.1126/scisignal.aaf8165]; GPMDB: [http://gpmdb.org/data/keyword/28400537 20]. | ||
- | #Müller MM, Lehmann R, Klassert TE, Reifenstein S, Conrad T, Moore C, Kuhn A, Behnert A, Guthke R, Driesch D, Slevogt H, (2017) "Global analysis of glycoproteins identifies markers of endotoxin tolerant monocytes and GPR84 as a modulator of TNFα expression." <i>Sci Rep</i> <b>7</b>(1):838; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28404994 28404994]; doi: [https://dx.doi.org/10.1038/s41598-017-00828-y 10.1038/s41598-017-00828-y]; GPMDB: [http://gpmdb.org/data/keyword/28404994 | + | #Müller MM, Lehmann R, Klassert TE, Reifenstein S, Conrad T, Moore C, Kuhn A, Behnert A, Guthke R, Driesch D, Slevogt H, (2017) "Global analysis of glycoproteins identifies markers of endotoxin tolerant monocytes and GPR84 as a modulator of TNFα expression." <i>Sci Rep</i> <b>7</b>(1):838; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28404994 28404994]; doi: [https://dx.doi.org/10.1038/s41598-017-00828-y 10.1038/s41598-017-00828-y]; GPMDB: [http://gpmdb.org/data/keyword/28404994 138]. |
#Shen X, Shen S, Li J, Hu Q, Nie L, Tu C, Wang X, Orsburn B, Wang J, Qu J, (2017) "An IonStar experimental strategy for MS1 ion current-based quantification using ultra-high-field Orbitrap: reproducible, in-depth and accurate protein measurement in larger cohorts." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28412812 28412812]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00061 10.1021/acs.jproteome.7b00061]; GPMDB: [http://gpmdb.org/data/keyword/28412812 20]. | #Shen X, Shen S, Li J, Hu Q, Nie L, Tu C, Wang X, Orsburn B, Wang J, Qu J, (2017) "An IonStar experimental strategy for MS1 ion current-based quantification using ultra-high-field Orbitrap: reproducible, in-depth and accurate protein measurement in larger cohorts." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28412812 28412812]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00061 10.1021/acs.jproteome.7b00061]; GPMDB: [http://gpmdb.org/data/keyword/28412812 20]. | ||
#Perl K, Ushakov K, Pozniak Y, Yizhar-Barnea O, Bhonker Y, Shivatzki S, Geiger T, Avraham KB, Shamir R, (2017) "Reduced changes in protein compared to mRNA levels across non-proliferating tissues." <i>BMC Genomics</i> <b>18</b>(1):305; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28420336 28420336]; doi: [https://dx.doi.org/10.1186/s12864-017-3683-9 10.1186/s12864-017-3683-9]; GPMDB: [http://gpmdb.org/data/keyword/28420336 6]. | #Perl K, Ushakov K, Pozniak Y, Yizhar-Barnea O, Bhonker Y, Shivatzki S, Geiger T, Avraham KB, Shamir R, (2017) "Reduced changes in protein compared to mRNA levels across non-proliferating tissues." <i>BMC Genomics</i> <b>18</b>(1):305; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28420336 28420336]; doi: [https://dx.doi.org/10.1186/s12864-017-3683-9 10.1186/s12864-017-3683-9]; GPMDB: [http://gpmdb.org/data/keyword/28420336 6]. | ||
#Mendoza-Viveros L, Chiang CK, Ong JLK, Hegazi S, Cheng AH, Bouchard-Cannon P, Fana M, Lowden C, Zhang P, Bothorel B, Michniewicz MG, Magill ST, Holmes MM, Goodman RH, Simonneaux V, Figeys D, Cheng HM, (2017) "miR-132/212 Modulates Seasonal Adaptation and Dendritic Morphology of the Central Circadian Clock." <i>Cell Rep</i> <b>19</b>(3):505–520; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28423315 28423315]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.03.057 10.1016/j.celrep.2017.03.057]; GPMDB: [http://gpmdb.org/data/keyword/28423315 128]. | #Mendoza-Viveros L, Chiang CK, Ong JLK, Hegazi S, Cheng AH, Bouchard-Cannon P, Fana M, Lowden C, Zhang P, Bothorel B, Michniewicz MG, Magill ST, Holmes MM, Goodman RH, Simonneaux V, Figeys D, Cheng HM, (2017) "miR-132/212 Modulates Seasonal Adaptation and Dendritic Morphology of the Central Circadian Clock." <i>Cell Rep</i> <b>19</b>(3):505–520; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28423315 28423315]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.03.057 10.1016/j.celrep.2017.03.057]; GPMDB: [http://gpmdb.org/data/keyword/28423315 128]. | ||
#Beyene GT, Kalayou S, Riaz T, Tonjum T, (2017) "Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis." <i>BMC Microbiol</i> <b>17</b>(1):96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28431522 28431522]; doi: [https://dx.doi.org/10.1186/s12866-017-1004-8 10.1186/s12866-017-1004-8]; GPMDB: [http://gpmdb.org/data/keyword/28431522 108]. | #Beyene GT, Kalayou S, Riaz T, Tonjum T, (2017) "Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis." <i>BMC Microbiol</i> <b>17</b>(1):96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28431522 28431522]; doi: [https://dx.doi.org/10.1186/s12866-017-1004-8 10.1186/s12866-017-1004-8]; GPMDB: [http://gpmdb.org/data/keyword/28431522 108]. |
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 be approved our quality control AI 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 May 14, 2017.