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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 December | + | 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 26, 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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#Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | #Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | ||
#Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | #Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | ||
+ | #Finamore F, Reny JL, Malacarne S, Fontana P, Sanchez JC, (2018) "A high glucose level is associated with decreased aspirin-mediated acetylation of platelet cyclooxygenase (COX)-1 at serine 529: A pilot study." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30240925 30240925]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.09.007 10.1016/j.jprot.2018.09.007]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30240925 18]. | ||
#Sun J, Shi J, Wang Y, Chen Y, Li Y, Kong D, Chang L, Liu F, Lv Z, Zhou Y, He F, Zhang Y, Xu P, (2018) "Multiproteases Combined with High-pH Reverse-Phase Separation Strategy Verified Fourteen Missing Proteins in Human Testis Tissue." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30280576 30280576]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00397 10.1021/acs.jproteome.8b00397]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30280576 108]. | #Sun J, Shi J, Wang Y, Chen Y, Li Y, Kong D, Chang L, Liu F, Lv Z, Zhou Y, He F, Zhang Y, Xu P, (2018) "Multiproteases Combined with High-pH Reverse-Phase Separation Strategy Verified Fourteen Missing Proteins in Human Testis Tissue." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30280576 30280576]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00397 10.1021/acs.jproteome.8b00397]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30280576 108]. | ||
+ | #Sepil I, Hopkins BR, Dean R, Thézénas ML, Charles PD, Konietzny R, Fischer R, Kessler B, Wigby S, (2018) "Quantitative proteomics identification of seminal fluid proteins in male <i>Drosophila melanogaster</i>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30287546 30287546]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000831 10.1074/mcp.RA118.000831]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30287546 87]. | ||
#Erdmann J, Preusse M, Khaledi A, Pich A, Häussler S, (2018) "Environment-driven changes of mRNA and protein levels in Pseudomonas aeruginosa." <i>Environ Microbiol</i> <b>20</b>(11):3952–3963; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30346651 30346651]; doi: [https://dx.doi.org/10.1111/1462-2920.14419 10.1111/1462-2920.14419]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30346651 253]. | #Erdmann J, Preusse M, Khaledi A, Pich A, Häussler S, (2018) "Environment-driven changes of mRNA and protein levels in Pseudomonas aeruginosa." <i>Environ Microbiol</i> <b>20</b>(11):3952–3963; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30346651 30346651]; doi: [https://dx.doi.org/10.1111/1462-2920.14419 10.1111/1462-2920.14419]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30346651 253]. | ||
#Krahmer N, Najafi B, Schueder F, Quagliarini F, Steger M, Seitz S, Kasper R, Salinas F, Cox J, Uhlenhaut NH, Walther TC, Jungmann R, Zeigerer A, Borner GHH, Mann M, (2018) "Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis." <i>Dev Cell</i> <b>47</b>(2):205–221.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352176 30352176]; doi: [https://dx.doi.org/10.1016/j.devcel.2018.09.017 10.1016/j.devcel.2018.09.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352176 134]. | #Krahmer N, Najafi B, Schueder F, Quagliarini F, Steger M, Seitz S, Kasper R, Salinas F, Cox J, Uhlenhaut NH, Walther TC, Jungmann R, Zeigerer A, Borner GHH, Mann M, (2018) "Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis." <i>Dev Cell</i> <b>47</b>(2):205–221.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352176 30352176]; doi: [https://dx.doi.org/10.1016/j.devcel.2018.09.017 10.1016/j.devcel.2018.09.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352176 134]. | ||
#van Mierlo G, Wester RA, Marks H, (2018) "Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in the pluripotent ground state." <i>Stem Cell Res</i> <b>33</b>:135–145; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352361 30352361]; doi: [https://dx.doi.org/10.1016/j.scr.2018.09.017 10.1016/j.scr.2018.09.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352361 6]. | #van Mierlo G, Wester RA, Marks H, (2018) "Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in the pluripotent ground state." <i>Stem Cell Res</i> <b>33</b>:135–145; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352361 30352361]; doi: [https://dx.doi.org/10.1016/j.scr.2018.09.017 10.1016/j.scr.2018.09.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352361 6]. | ||
+ | #El-Rami FE, Zielke RA, Wi T, Sikora AE, Unemo M, (2018) "Quantitative proteomics of the 2016 WHO <i>Neisseria gonorrhoeae</i> reference strains surveys vaccine candidates and antimicrobial resistance determinants." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352803 30352803]; doi: [https://dx.doi.org/10.1074/mcp.RA118.001125 10.1074/mcp.RA118.001125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352803 3]. | ||
#Serra A, Gallart-Palau X, Park JE, Lim GGY, Lim KL, Ho HH, Tam JP, Sze SK, (2018) "Vascular Bed Molecular Profiling by Differential Systemic Decellularization In Vivo." <i>Arterioscler Thromb Vasc Biol</i> <b>38</b>(10):2396–2409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30354219 30354219]; doi: [https://dx.doi.org/10.1161/ATVBAHA.118.311552 10.1161/ATVBAHA.118.311552]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30354219 16]. | #Serra A, Gallart-Palau X, Park JE, Lim GGY, Lim KL, Ho HH, Tam JP, Sze SK, (2018) "Vascular Bed Molecular Profiling by Differential Systemic Decellularization In Vivo." <i>Arterioscler Thromb Vasc Biol</i> <b>38</b>(10):2396–2409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30354219 30354219]; doi: [https://dx.doi.org/10.1161/ATVBAHA.118.311552 10.1161/ATVBAHA.118.311552]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30354219 16]. | ||
#Magagnotti C, Zerbini G, Fermo I, Carletti RM, Bonfanti R, Vallone F, Andolfo A, (2018) "Identification of nephropathy predictors in urine from children with a recent diagnosis of type 1 diabetes." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30366120 30366120]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.10.010 10.1016/j.jprot.2018.10.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30366120 51]. | #Magagnotti C, Zerbini G, Fermo I, Carletti RM, Bonfanti R, Vallone F, Andolfo A, (2018) "Identification of nephropathy predictors in urine from children with a recent diagnosis of type 1 diabetes." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30366120 30366120]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.10.010 10.1016/j.jprot.2018.10.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30366120 51]. | ||
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#Wolf A, Liesinger L, Spoerk S, Schittmayer M, Lang-Loidolt D, Birner-Gruenberger R, Tomazic PV, (2018) "Olfactory cleft proteome does not reflect olfactory performance in patients with idiopathic and postinfectious olfactory disorder: A pilot study." <i>Sci Rep</i> <b>8</b>(1):17554; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30510230 30510230]; doi: [https://dx.doi.org/10.1038/s41598-018-35776-8 10.1038/s41598-018-35776-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30510230 21]. | #Wolf A, Liesinger L, Spoerk S, Schittmayer M, Lang-Loidolt D, Birner-Gruenberger R, Tomazic PV, (2018) "Olfactory cleft proteome does not reflect olfactory performance in patients with idiopathic and postinfectious olfactory disorder: A pilot study." <i>Sci Rep</i> <b>8</b>(1):17554; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30510230 30510230]; doi: [https://dx.doi.org/10.1038/s41598-018-35776-8 10.1038/s41598-018-35776-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30510230 21]. | ||
#Tascher G, Gerbaix M, Maes P, Chazarin B, Ghislin S, Antropova E, Vassilieva G, Ouzren-Zarhloul N, Gauquelin-Koch G, Vico L, Frippiat JP, Bertile F, (2018) "Analysis of femurs from mice embarked on board BION-M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth." <i>FASEB J</i> <b></b>:fj201801463R; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30521760 30521760]; doi: [https://dx.doi.org/10.1096/fj.201801463R 10.1096/fj.201801463R]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30521760 36]. | #Tascher G, Gerbaix M, Maes P, Chazarin B, Ghislin S, Antropova E, Vassilieva G, Ouzren-Zarhloul N, Gauquelin-Koch G, Vico L, Frippiat JP, Bertile F, (2018) "Analysis of femurs from mice embarked on board BION-M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth." <i>FASEB J</i> <b></b>:fj201801463R; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30521760 30521760]; doi: [https://dx.doi.org/10.1096/fj.201801463R 10.1096/fj.201801463R]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30521760 36]. | ||
+ | #Roustan V, Weckwerth W, (2018) "Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in <i>Chlamydomonas reinhardtii</i>." <i>Front Plant Sci</i> <b>9</b>:1590; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30546371 30546371]; doi: [https://dx.doi.org/10.3389/fpls.2018.01590 10.3389/fpls.2018.01590]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30546371 54]. | ||
+ | #Yao Z, Jia X, Megger DA, Chen J, Liu Y, Li J, Sitek B, Yuan Z, (2018) "Label-free Proteomic Analysis of Exosomes Secreted from THP-1-derived Macrophages Treated with IFN-α Identifies Antiviral Proteins Enriched in Exosomes." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30550287 30550287]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00514 10.1021/acs.jproteome.8b00514]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30550287 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 December 26, 2018.