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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 June | + | 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 June 24, 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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#Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M, (2016) "Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development." <i>Cell</i> <b>166</b>(3):664–78; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27397507 27397507]; doi: [https://dx.doi.org/10.1016/j.cell.2016.06.015 10.1016/j.cell.2016.06.015]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27397507 18]. | #Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M, (2016) "Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development." <i>Cell</i> <b>166</b>(3):664–78; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27397507 27397507]; doi: [https://dx.doi.org/10.1016/j.cell.2016.06.015 10.1016/j.cell.2016.06.015]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27397507 18]. | ||
#Konstantinell A, Bruun JA, Olsen R, Aspar A, Škalko-Basnet N, Sveinbjørnsson B, Moens U, (2016) "Secretomic analysis of extracellular vesicles originating from polyomavirus-negative and polyomavirus-positive Merkel cell carcinoma cell lines." <i>Proteomics</i> <b>16</b>(19):2587–2591; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27402257 27402257]; doi: [https://dx.doi.org/10.1002/pmic.201600223 10.1002/pmic.201600223]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27402257 28]. | #Konstantinell A, Bruun JA, Olsen R, Aspar A, Škalko-Basnet N, Sveinbjørnsson B, Moens U, (2016) "Secretomic analysis of extracellular vesicles originating from polyomavirus-negative and polyomavirus-positive Merkel cell carcinoma cell lines." <i>Proteomics</i> <b>16</b>(19):2587–2591; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27402257 27402257]; doi: [https://dx.doi.org/10.1002/pmic.201600223 10.1002/pmic.201600223]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27402257 28]. | ||
+ | #Xue L, Blythe EE, Freiberger EC, Mamrosh JL, Hebert AS, Reitsma JM, Hess S, Coon JJ, Deshaies RJ, (2016) "Valosin-containing protein (VCP)-Adaptor Interactions are Exceptionally Dynamic and Subject to Differential Modulation by a VCP Inhibitor." <i>Mol Cell Proteomics</i> <b>15</b>(9):2970–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27406709 27406709]; doi: [https://dx.doi.org/10.1074/mcp.M116.061036 10.1074/mcp.M116.061036]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27406709 148]. | ||
#Shraibman B, Kadosh DM, Barnea E, Admon A, (2016) "Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy." <i>Mol Cell Proteomics</i> <b>15</b>(9):3058–70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27412690 27412690]; doi: [https://dx.doi.org/10.1074/mcp.M116.060350 10.1074/mcp.M116.060350]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27412690 60]. | #Shraibman B, Kadosh DM, Barnea E, Admon A, (2016) "Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy." <i>Mol Cell Proteomics</i> <b>15</b>(9):3058–70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27412690 27412690]; doi: [https://dx.doi.org/10.1074/mcp.M116.060350 10.1074/mcp.M116.060350]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27412690 60]. | ||
#Müller S, Balaz M, Stefanicka P, Varga L, Amri EZ, Ukropec J, Wollscheid B, Wolfrum C, (2016) "Proteomic Analysis of Human Brown Adipose Tissue Reveals Utilization of Coupled and Uncoupled Energy Expenditure Pathways." <i>Sci Rep</i> <b>6</b>:30030; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418403 27418403]; doi: [https://dx.doi.org/10.1038/srep30030 10.1038/srep30030]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27418403 32]. | #Müller S, Balaz M, Stefanicka P, Varga L, Amri EZ, Ukropec J, Wollscheid B, Wolfrum C, (2016) "Proteomic Analysis of Human Brown Adipose Tissue Reveals Utilization of Coupled and Uncoupled Energy Expenditure Pathways." <i>Sci Rep</i> <b>6</b>:30030; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418403 27418403]; doi: [https://dx.doi.org/10.1038/srep30030 10.1038/srep30030]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27418403 32]. | ||
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#De Muyt A, Pyatnitskaya A, Andréani J, Ranjha L, Ramus C, Laureau R, Fernandez-Vega A, Holoch D, Girard E, Govin J, Margueron R, Couté Y, Cejka P, Guérois R, Borde V, (2018) "A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation." <i>Genes Dev</i> <b>32</b>(3-4):283–296; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29440262 29440262]; doi: [https://dx.doi.org/10.1101/gad.308510.117 10.1101/gad.308510.117]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29440262 19]. | #De Muyt A, Pyatnitskaya A, Andréani J, Ranjha L, Ramus C, Laureau R, Fernandez-Vega A, Holoch D, Girard E, Govin J, Margueron R, Couté Y, Cejka P, Guérois R, Borde V, (2018) "A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation." <i>Genes Dev</i> <b>32</b>(3-4):283–296; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29440262 29440262]; doi: [https://dx.doi.org/10.1101/gad.308510.117 10.1101/gad.308510.117]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29440262 19]. | ||
#Schanzenbächer CT, Langer JD, Schuman EM, (2018) "Time- and polarity-dependent proteomic changes associated with homeostatic scaling at central synapses." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29447110 29447110]; doi: [https://dx.doi.org/10.7554/eLife.33322 10.7554/eLife.33322]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29447110 78]. | #Schanzenbächer CT, Langer JD, Schuman EM, (2018) "Time- and polarity-dependent proteomic changes associated with homeostatic scaling at central synapses." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29447110 29447110]; doi: [https://dx.doi.org/10.7554/eLife.33322 10.7554/eLife.33322]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29447110 78]. | ||
+ | #Mathieson T, Franken H, Kosinski J, Kurzawa N, Zinn N, Sweetman G, Poeckel D, Ratnu VS, Schramm M, Becher I, Steidel M, Noh KM, Bergamini G, Beck M, Bantscheff M, Savitski MM, (2018) "Systematic analysis of protein turnover in primary cells." <i>Nat Commun</i> <b>9</b>(1):689; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29449567 29449567]; doi: [https://dx.doi.org/10.1038/s41467-018-03106-1 10.1038/s41467-018-03106-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29449567 883]. | ||
#Lan J, Núñez Galindo A, Doecke J, Fowler C, Martins RN, Rainey-Smith SR, Cominetti O, Dayon L, (2018) "Systematic Evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29451788 29451788]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00788 10.1021/acs.jproteome.7b00788]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29451788 36]. | #Lan J, Núñez Galindo A, Doecke J, Fowler C, Martins RN, Rainey-Smith SR, Cominetti O, Dayon L, (2018) "Systematic Evaluation of the Use of Human Plasma and Serum for Mass-Spectrometry-Based Shotgun Proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29451788 29451788]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00788 10.1021/acs.jproteome.7b00788]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29451788 36]. | ||
#Bergmann TJ, Fregno I, Fumagalli F, Rinaldi A, Bertoni F, Boersema PJ, Picotti P, Molinari M, (2018) "Chemical stresses fail to mimic the unfolded protein response resulting from luminal load with unfolded polypeptides." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29453283 29453283]; doi: [https://dx.doi.org/10.1074/jbc.RA117.001484 10.1074/jbc.RA117.001484]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29453283 39]. | #Bergmann TJ, Fregno I, Fumagalli F, Rinaldi A, Bertoni F, Boersema PJ, Picotti P, Molinari M, (2018) "Chemical stresses fail to mimic the unfolded protein response resulting from luminal load with unfolded polypeptides." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29453283 29453283]; doi: [https://dx.doi.org/10.1074/jbc.RA117.001484 10.1074/jbc.RA117.001484]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29453283 39]. | ||
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#Mohammad I, Nousiainen K, Bhosale SD, Starskaia I, Moulder R, Rokka A, Cheng F, Mohanasundaram P, Eriksson JE, Goodlett DR, Lähdesmäki H, Chen Z, (2018) "Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells." <i>PLoS Biol</i> <b>16</b>(5):e2004194; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29851958 29851958]; doi: [https://dx.doi.org/10.1371/journal.pbio.2004194 10.1371/journal.pbio.2004194]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29851958 45]. | #Mohammad I, Nousiainen K, Bhosale SD, Starskaia I, Moulder R, Rokka A, Cheng F, Mohanasundaram P, Eriksson JE, Goodlett DR, Lähdesmäki H, Chen Z, (2018) "Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells." <i>PLoS Biol</i> <b>16</b>(5):e2004194; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29851958 29851958]; doi: [https://dx.doi.org/10.1371/journal.pbio.2004194 10.1371/journal.pbio.2004194]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29851958 45]. | ||
#Marín E, Haesaert A, Padilla L, Adán J, Hernáez ML, Monteoliva L, Gil C, (2018) "Unraveling <i>Gardnerella vaginalis</i> Surface Proteins Using Cell Shaving Proteomics." <i>Front Microbiol</i> <b>9</b>:975; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29867878 29867878]; doi: [https://dx.doi.org/10.3389/fmicb.2018.00975 10.3389/fmicb.2018.00975]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29867878 3]. | #Marín E, Haesaert A, Padilla L, Adán J, Hernáez ML, Monteoliva L, Gil C, (2018) "Unraveling <i>Gardnerella vaginalis</i> Surface Proteins Using Cell Shaving Proteomics." <i>Front Microbiol</i> <b>9</b>:975; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29867878 29867878]; doi: [https://dx.doi.org/10.3389/fmicb.2018.00975 10.3389/fmicb.2018.00975]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29867878 3]. | ||
+ | #Portela M, Yang L, Paul S, Li X, Veraksa A, Parsons LM, Richardson HE, (2018) "Lgl reduces endosomal vesicle acidification and Notch signaling by promoting the interaction between Vap33 and the V-ATPase complex." <i>Sci Signal</i> <b>11</b>(533):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29871910 29871910]; doi: [https://dx.doi.org/10.1126/scisignal.aar1976 10.1126/scisignal.aar1976]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29871910 11]. | ||
+ | #Madeira JP, Alpha-Bazin B, Armengaud J, Duport C, (2018) "Time-course proteomics dataset to monitor protein-bound methionine oxidation <i>in Bacillus cereus</i> ATCC 14579." <i>Data Brief</i> <b>18</b>:394–398; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29896523 29896523]; doi: [https://dx.doi.org/10.1016/j.dib.2018.03.030 10.1016/j.dib.2018.03.030]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29896523 18]. | ||
+ | #Adav SS, Wei J, Terence Y, Ang BC, Yip LW, Sze SK, (2018) "Proteomic Analysis of Aqueous Humor from Primary Open Angle Glaucoma Patients on Drug Treatment Revealed Altered Complement Activation Cascade." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29901396 29901396]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00244 10.1021/acs.jproteome.8b00244]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29901396 80]. | ||
+ | #Steenbeek SC, Pham TV, de Ligt J, Zomer A, Knol JC, Piersma SR, Schelfhorst T, Huisjes R, Schiffelers RM, Cuppen E, Jimenez CR, van Rheenen J, (2018) "Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29907695 29907695]; doi: [https://dx.doi.org/10.15252/embj.201798357 10.15252/embj.201798357]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29907695 11]. |
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 June 24, 2018.