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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 April | + | 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 April 30, 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]. | ||
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#Larkin SE, Johnston HE, Jackson TR, Jamieson DG, Roumeliotis TI, Mockridge CI, Michael A, Manousopoulou A, Papachristou EK, Brown MD, Clarke NW, Pandha H, Aukim-Hastie CL, Cragg MS, Garbis SD, Townsend PA, (2016) "Detection of candidate biomarkers of prostate cancer progression in serum: a depletion-free 3D LC/MS quantitative proteomics pilot study." <i>Br J Cancer</i> <b>115</b>(9):1078–1086; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27685442 27685442]; doi: [https://dx.doi.org/10.1038/bjc.2016.291 10.1038/bjc.2016.291]; GPMDB: [http://gpmdb.org/data/keyword/27685442 8]. | #Larkin SE, Johnston HE, Jackson TR, Jamieson DG, Roumeliotis TI, Mockridge CI, Michael A, Manousopoulou A, Papachristou EK, Brown MD, Clarke NW, Pandha H, Aukim-Hastie CL, Cragg MS, Garbis SD, Townsend PA, (2016) "Detection of candidate biomarkers of prostate cancer progression in serum: a depletion-free 3D LC/MS quantitative proteomics pilot study." <i>Br J Cancer</i> <b>115</b>(9):1078–1086; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27685442 27685442]; doi: [https://dx.doi.org/10.1038/bjc.2016.291 10.1038/bjc.2016.291]; GPMDB: [http://gpmdb.org/data/keyword/27685442 8]. | ||
#Martello R, Leutert M, Jungmichel S, Bilan V, Larsen SC, Young C, Hottiger MO, Nielsen ML, (2016) "Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue." <i>Nat Commun</i> <b>7</b>:12917; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27686526 27686526]; doi: [https://dx.doi.org/10.1038/ncomms12917 10.1038/ncomms12917]; GPMDB: [http://gpmdb.org/data/keyword/27686526 15]. | #Martello R, Leutert M, Jungmichel S, Bilan V, Larsen SC, Young C, Hottiger MO, Nielsen ML, (2016) "Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue." <i>Nat Commun</i> <b>7</b>:12917; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27686526 27686526]; doi: [https://dx.doi.org/10.1038/ncomms12917 10.1038/ncomms12917]; GPMDB: [http://gpmdb.org/data/keyword/27686526 15]. | ||
+ | #Mathieu AA, Ohl-Séguy E, Dubois ML, Jean D, Jones C, Boudreau F, Boisvert FM, (2016) "Subcellular proteomics analysis of different stages of colorectal cancer cell lines." <i>Proteomics</i> <b>16</b>(23):3009–3018; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27689624 27689624]; doi: [https://dx.doi.org/10.1002/pmic.201600314 10.1002/pmic.201600314]; GPMDB: [http://gpmdb.org/data/keyword/27689624 52]. | ||
#Greenwood EJ, Matheson NJ, Wals K, van den Boomen DJ, Antrobus R, Williamson JC, Lehner PJ, (2016) "Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27690223 27690223]; doi: [https://dx.doi.org/10.7554/eLife.18296 10.7554/eLife.18296]; GPMDB: [http://gpmdb.org/data/keyword/27690223 10]. | #Greenwood EJ, Matheson NJ, Wals K, van den Boomen DJ, Antrobus R, Williamson JC, Lehner PJ, (2016) "Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27690223 27690223]; doi: [https://dx.doi.org/10.7554/eLife.18296 10.7554/eLife.18296]; GPMDB: [http://gpmdb.org/data/keyword/27690223 10]. | ||
#Gautier V, Cayrol C, Farache D, Roga S, Monsarrat B, Burlet-Schiltz O, Gonzalez de Peredo A, Girard JP, (2016) "Extracellular IL-33 cytokine, but not endogenous nuclear IL-33, regulates protein expression in endothelial cells." <i>Sci Rep</i> <b>6</b>:34255; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27694941 27694941]; doi: [https://dx.doi.org/10.1038/srep34255 10.1038/srep34255]; GPMDB: [http://gpmdb.org/data/keyword/27694941 252]. | #Gautier V, Cayrol C, Farache D, Roga S, Monsarrat B, Burlet-Schiltz O, Gonzalez de Peredo A, Girard JP, (2016) "Extracellular IL-33 cytokine, but not endogenous nuclear IL-33, regulates protein expression in endothelial cells." <i>Sci Rep</i> <b>6</b>:34255; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27694941 27694941]; doi: [https://dx.doi.org/10.1038/srep34255 10.1038/srep34255]; GPMDB: [http://gpmdb.org/data/keyword/27694941 252]. | ||
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#Emmott E, Sorgeloos F, Caddy SL, Vashist S, Sosnovtsev S, Lloyd R, Heesom K, Locker N, Goodfellow I, (2017) "Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087593 28087593]; doi: [https://dx.doi.org/10.1074/mcp.M116.062448 10.1074/mcp.M116.062448]; GPMDB: [http://gpmdb.org/data/keyword/28087593 3]. | #Emmott E, Sorgeloos F, Caddy SL, Vashist S, Sosnovtsev S, Lloyd R, Heesom K, Locker N, Goodfellow I, (2017) "Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087593 28087593]; doi: [https://dx.doi.org/10.1074/mcp.M116.062448 10.1074/mcp.M116.062448]; GPMDB: [http://gpmdb.org/data/keyword/28087593 3]. | ||
#Niklasson M, Maddalo G, Sramkova Z, Mutlu E, Wee S, Sekyrova P, Schmidt L, Fritz N, Dehnisch I, Kyriatzis G, Krafcikova M, Carson BB, Feenstra J, Marinescu VD, Segerman A, Haraldsson M, Gustavsson AL, Hammarström LG, Jenmalm-Jensen A, Uhrbom L, Altelaar AF, Linnarsson S, Uhlén P, Trantirek L, Vincent CT, Nelander S, Enger PØ, Andäng M, (2017) "Membrane-depolarizing channel blockers induce selective glioma cell death by impairing nutrient transport and unfolded protein/amino acid responses." <i>Cancer Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087597 28087597]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-16-2274 10.1158/0008-5472.CAN-16-2274]; GPMDB: [http://gpmdb.org/data/keyword/28087597 6]. | #Niklasson M, Maddalo G, Sramkova Z, Mutlu E, Wee S, Sekyrova P, Schmidt L, Fritz N, Dehnisch I, Kyriatzis G, Krafcikova M, Carson BB, Feenstra J, Marinescu VD, Segerman A, Haraldsson M, Gustavsson AL, Hammarström LG, Jenmalm-Jensen A, Uhrbom L, Altelaar AF, Linnarsson S, Uhlén P, Trantirek L, Vincent CT, Nelander S, Enger PØ, Andäng M, (2017) "Membrane-depolarizing channel blockers induce selective glioma cell death by impairing nutrient transport and unfolded protein/amino acid responses." <i>Cancer Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087597 28087597]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-16-2274 10.1158/0008-5472.CAN-16-2274]; GPMDB: [http://gpmdb.org/data/keyword/28087597 6]. | ||
+ | #Gao Y, Chen Y, Zhan S, Zhang W, Xiong F, Ge W, (2017) "Comprehensive proteome analysis of lysosomes reveals the diverse function of macrophages in immune responses." <i>Oncotarget</i> <b>8</b>(5):7420–7440; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28088779 28088779]; doi: [https://dx.doi.org/10.18632/oncotarget.14558 10.18632/oncotarget.14558]; GPMDB: [http://gpmdb.org/data/keyword/28088779 2]. | ||
#Riesner K, Shi Y, Jacobi A, Kraeter M, Kalupa M, McGearey A, Mertlitz S, Cordes S, Schrezenmeier JF, Mengwasser J, Westphal S, Perez-Hernandez D, Schmitt C, Dittmar G, Guck J, Penack O, (2017) "Initiation of acute graft-versus-host disease by angiogenesis." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096092 28096092]; doi: [https://dx.doi.org/10.1182/blood-2016-08-736314 10.1182/blood-2016-08-736314]; GPMDB: [http://gpmdb.org/data/keyword/28096092 1]. | #Riesner K, Shi Y, Jacobi A, Kraeter M, Kalupa M, McGearey A, Mertlitz S, Cordes S, Schrezenmeier JF, Mengwasser J, Westphal S, Perez-Hernandez D, Schmitt C, Dittmar G, Guck J, Penack O, (2017) "Initiation of acute graft-versus-host disease by angiogenesis." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096092 28096092]; doi: [https://dx.doi.org/10.1182/blood-2016-08-736314 10.1182/blood-2016-08-736314]; GPMDB: [http://gpmdb.org/data/keyword/28096092 1]. | ||
#Princz LN, Wild P, Bittmann J, Aguado FJ, Blanco MG, Matos J, Pfander B, (2017) "Dbf4-dependent kinase and the Rtt107 scaffold promote Mus81-Mms4 resolvase activation during mitosis." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096179 28096179]; doi: [https://dx.doi.org/10.15252/embj.201694831 10.15252/embj.201694831]; GPMDB: [http://gpmdb.org/data/keyword/28096179 130]. | #Princz LN, Wild P, Bittmann J, Aguado FJ, Blanco MG, Matos J, Pfander B, (2017) "Dbf4-dependent kinase and the Rtt107 scaffold promote Mus81-Mms4 resolvase activation during mitosis." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096179 28096179]; doi: [https://dx.doi.org/10.15252/embj.201694831 10.15252/embj.201694831]; GPMDB: [http://gpmdb.org/data/keyword/28096179 130]. | ||
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#Young C, Podtelejnikov AV, Nielsen ML, (2017) "Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28387123 28387123]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01055 10.1021/acs.jproteome.6b01055]; GPMDB: [http://gpmdb.org/data/keyword/28387123 12]. | #Young C, Podtelejnikov AV, Nielsen ML, (2017) "Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28387123 28387123]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01055 10.1021/acs.jproteome.6b01055]; GPMDB: [http://gpmdb.org/data/keyword/28387123 12]. | ||
#Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu PH, Hua B, Silberman RE, Springer M, Amon A, (2017) "Aneuploidy Causes Non-genetic Individuality." <i>Cell</i> <b>169</b>(2):229–242.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388408 28388408]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.021 10.1016/j.cell.2017.03.021]; GPMDB: [http://gpmdb.org/data/keyword/28388408 3]. | #Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu PH, Hua B, Silberman RE, Springer M, Amon A, (2017) "Aneuploidy Causes Non-genetic Individuality." <i>Cell</i> <b>169</b>(2):229–242.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388408 28388408]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.021 10.1016/j.cell.2017.03.021]; GPMDB: [http://gpmdb.org/data/keyword/28388408 3]. | ||
+ | #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]. | ||
+ | #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 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 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 April 30, 2017.