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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 August | + | 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 August 19, 2018. |
#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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#Zhang J, Lu S, Zhou Y, Meng K, Chen Z, Cui Y, Shi Y, Wang T, He QY, (2017) "Motile hepatocellular carcinoma cells preferentially secret sugar metabolism regulatory proteins via exosomes." <i>Proteomics</i> <b>17</b>(13-14):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28590090 28590090]; doi: [https://dx.doi.org/10.1002/pmic.201700103 10.1002/pmic.201700103]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28590090 6]. | #Zhang J, Lu S, Zhou Y, Meng K, Chen Z, Cui Y, Shi Y, Wang T, He QY, (2017) "Motile hepatocellular carcinoma cells preferentially secret sugar metabolism regulatory proteins via exosomes." <i>Proteomics</i> <b>17</b>(13-14):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28590090 28590090]; doi: [https://dx.doi.org/10.1002/pmic.201700103 10.1002/pmic.201700103]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28590090 6]. | ||
#Jensen SR, Schoof EM, Wheeler SE, Hvid H, Ahnfelt-Rønne J, Hansen BF, Nishimura E, Olsen GS, Kislinger T, Brubaker PL, (2017) "Quantitative Proteomics of Intestinal Mucosa From Male Mice Lacking Intestinal Epithelial Insulin Receptors." <i>Endocrinology</i> <b>158</b>(8):2470–2485; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28591806 28591806]; doi: [https://dx.doi.org/10.1210/en.2017-00194 10.1210/en.2017-00194]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28591806 10]. | #Jensen SR, Schoof EM, Wheeler SE, Hvid H, Ahnfelt-Rønne J, Hansen BF, Nishimura E, Olsen GS, Kislinger T, Brubaker PL, (2017) "Quantitative Proteomics of Intestinal Mucosa From Male Mice Lacking Intestinal Epithelial Insulin Receptors." <i>Endocrinology</i> <b>158</b>(8):2470–2485; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28591806 28591806]; doi: [https://dx.doi.org/10.1210/en.2017-00194 10.1210/en.2017-00194]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28591806 10]. | ||
+ | #Pearson LJ, Klaharn IY, Thongsawang B, Manuprasert W, Saejew T, Somparn P, Chuengsaman P, Kanjanabuch T, Pisitkun T, (2017) "Multiple extracellular vesicle types in peritoneal dialysis effluent are prominent and contain known biomarkers." <i>PLoS One</i> <b>12</b>(6):e0178601; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28594924 28594924]; doi: [https://dx.doi.org/10.1371/journal.pone.0178601 10.1371/journal.pone.0178601]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28594924 90]. | ||
#Bekker-Jensen DB, Kelstrup CD, Batth TS, Larsen SC, Haldrup C, Bramsen JB, Sørensen KD, Høyer S, Ørntoft TF, Andersen CL, Nielsen ML, Olsen JV, (2017) "An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes." <i>Cell Syst</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28601559 28601559]; doi: [https://dx.doi.org/10.1016/j.cels.2017.05.009 10.1016/j.cels.2017.05.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28601559 93]. | #Bekker-Jensen DB, Kelstrup CD, Batth TS, Larsen SC, Haldrup C, Bramsen JB, Sørensen KD, Høyer S, Ørntoft TF, Andersen CL, Nielsen ML, Olsen JV, (2017) "An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes." <i>Cell Syst</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28601559 28601559]; doi: [https://dx.doi.org/10.1016/j.cels.2017.05.009 10.1016/j.cels.2017.05.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28601559 93]. | ||
#Haas TL, Sciuto MR, Brunetto L, Valvo C, Signore M, Fiori ME, di Martino S, Giannetti S, Morgante L, Boe A, Patrizii M, Warnken U, Schnölzer M, Ciolfi A, Di Stefano C, Biffoni M, Ricci-Vitiani L, Pallini R, De Maria R, (2017) "Integrin α7 Is a Functional Marker and Potential Therapeutic Target in Glioblastoma." <i>Cell Stem Cell</i> <b>21</b>(1):35–50.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28602620 28602620]; doi: [https://dx.doi.org/10.1016/j.stem.2017.04.009 10.1016/j.stem.2017.04.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28602620 3]. | #Haas TL, Sciuto MR, Brunetto L, Valvo C, Signore M, Fiori ME, di Martino S, Giannetti S, Morgante L, Boe A, Patrizii M, Warnken U, Schnölzer M, Ciolfi A, Di Stefano C, Biffoni M, Ricci-Vitiani L, Pallini R, De Maria R, (2017) "Integrin α7 Is a Functional Marker and Potential Therapeutic Target in Glioblastoma." <i>Cell Stem Cell</i> <b>21</b>(1):35–50.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28602620 28602620]; doi: [https://dx.doi.org/10.1016/j.stem.2017.04.009 10.1016/j.stem.2017.04.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28602620 3]. | ||
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#Shraibman B, Barnea E, Melamed Kadosh D, Haimovich Y, Slobodin G, Rosner I, López-Larrea C, Hilf N, Kuttruff S, Song C, Britten C, Castle J, Kreiter S, Frenzel K, Tatagiba M, Tabatabai G, Dietrich PY, Dutoit V, Wick W, Platten M, Winkler F, Von Deimling A, Kroep J, Sahuquillo J, Martinez-Ricarte F, Rodon J, Lassen U, Ottensmeier C, van der Burg SH, Thor Straten P, Poulsen HS, Ponsati B, Okada H, Rammensee HG, Sahin U, Singh H, Admon A, (2018) "Identification of tumor antigens among the HLA peptidomes of Glioblastoma tumors and plasma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30072578 30072578]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000792 10.1074/mcp.RA118.000792]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30072578 75]. | #Shraibman B, Barnea E, Melamed Kadosh D, Haimovich Y, Slobodin G, Rosner I, López-Larrea C, Hilf N, Kuttruff S, Song C, Britten C, Castle J, Kreiter S, Frenzel K, Tatagiba M, Tabatabai G, Dietrich PY, Dutoit V, Wick W, Platten M, Winkler F, Von Deimling A, Kroep J, Sahuquillo J, Martinez-Ricarte F, Rodon J, Lassen U, Ottensmeier C, van der Burg SH, Thor Straten P, Poulsen HS, Ponsati B, Okada H, Rammensee HG, Sahin U, Singh H, Admon A, (2018) "Identification of tumor antigens among the HLA peptidomes of Glioblastoma tumors and plasma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30072578 30072578]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000792 10.1074/mcp.RA118.000792]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30072578 75]. | ||
#Park S, Park JH, Jung HJ, Jang JH, Ahn S, Kim Y, Suh PG, Chae S, Yoon JH, Ryu SH, Hwang D, (2018) "A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cells." <i>Exp Mol Med</i> <b>50</b>(8):93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076294 30076294]; doi: [https://dx.doi.org/10.1038/s12276-018-0120-3 10.1038/s12276-018-0120-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076294 24]. | #Park S, Park JH, Jung HJ, Jang JH, Ahn S, Kim Y, Suh PG, Chae S, Yoon JH, Ryu SH, Hwang D, (2018) "A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cells." <i>Exp Mol Med</i> <b>50</b>(8):93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076294 30076294]; doi: [https://dx.doi.org/10.1038/s12276-018-0120-3 10.1038/s12276-018-0120-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076294 24]. | ||
+ | #Kumar G, Hummel K, Razzazi-Fazeli E, El-Matbouli M, (2018) "Proteome Profiles of Head Kidney and Spleen of Rainbow Trout (Oncorhynchus Mykiss)." <i>Proteomics</i> <b></b>:e1800101; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30094954 30094954]; doi: [https://dx.doi.org/10.1002/pmic.201800101 10.1002/pmic.201800101]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30094954 54]. | ||
+ | #Schiza C, Korbakis D, Panteleli E, Jarvi K, Drabovich AP, Diamandis EP, (2018) "Discovery of a human testis-specific protein complex TEX101-DPEP3 and selection of its disrupting antibodies." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30097533 30097533]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000749 10.1074/mcp.RA118.000749]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30097533 44]. | ||
+ | #Hwang H, Jeong JE, Lee HK, Yun KN, An HJ, Lee B, Paik YK, Jeong TS, Yee GT, Kim JY, Yoo JS, (2018) "Identification of Missing Proteins in Human Olfactory Epithelial Tissue by Liquid Chromatography-Tandem Mass Spectrometry." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30113170 30113170]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00408 10.1021/acs.jproteome.8b00408]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30113170 23]. |
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.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
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 August 19, 2018.