Line 24: | Line 24: | ||
==Data from publications== | ==Data from publications== | ||
- | The following is a 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 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 29, 2016. |
#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 942: | Line 942: | ||
#Shrivastava AN, Redeker V, Fritz N, Pieri L, Almeida LG, Spolidoro M, Liebmann T, Bousset L, Renner M, Léna C, Aperia A, Melki R, Triller A, (2015) "α-synuclein assemblies sequester neuronal α3-Na+/K+-ATPase and impair Na+ gradient." <i>EMBO J</i> <b>34</b>(19):2408–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26323479 26323479]; doi: [https://dx.doi.org/10.15252/embj.201591397 10.15252/embj.201591397]; GPMDB: [http://gpmdb.org/data/keyword/26323479 23]. | #Shrivastava AN, Redeker V, Fritz N, Pieri L, Almeida LG, Spolidoro M, Liebmann T, Bousset L, Renner M, Léna C, Aperia A, Melki R, Triller A, (2015) "α-synuclein assemblies sequester neuronal α3-Na+/K+-ATPase and impair Na+ gradient." <i>EMBO J</i> <b>34</b>(19):2408–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26323479 26323479]; doi: [https://dx.doi.org/10.15252/embj.201591397 10.15252/embj.201591397]; GPMDB: [http://gpmdb.org/data/keyword/26323479 23]. | ||
#Chu XL, Feng MG, Ying SH, (2016) "Qualitative ubiquitome unveils the potential significances of protein lysine ubiquitination in hyphal growth of Aspergillus nidulans." <i>Curr Genet</i> <b>62</b>(1):191–201; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26328806 26328806]; doi: [https://dx.doi.org/10.1007/s00294-015-0517-7 10.1007/s00294-015-0517-7]; GPMDB: [http://gpmdb.org/data/keyword/26328806 1]. | #Chu XL, Feng MG, Ying SH, (2016) "Qualitative ubiquitome unveils the potential significances of protein lysine ubiquitination in hyphal growth of Aspergillus nidulans." <i>Curr Genet</i> <b>62</b>(1):191–201; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26328806 26328806]; doi: [https://dx.doi.org/10.1007/s00294-015-0517-7 10.1007/s00294-015-0517-7]; GPMDB: [http://gpmdb.org/data/keyword/26328806 1]. | ||
+ | #Wu X, Zahari MS, Renuse S, Nirujogi RS, Kim MS, Manda SS, Stearns V, Gabrielson E, Sukumar S, Pandey A, (2015) "Phosphoproteomic Analysis Identifies Focal Adhesion Kinase 2 (FAK2) as a Potential Therapeutic Target for Tamoxifen Resistance in Breast Cancer." <i>Mol Cell Proteomics</i> <b>14</b>(11):2887–900; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26330541 26330541]; doi: [https://dx.doi.org/10.1074/mcp.M115.050484 10.1074/mcp.M115.050484]; GPMDB: [http://gpmdb.org/data/keyword/26330541 15]. | ||
#Duhamel M, Rodet F, Delhem N, Vanden Abeele F, Kobeissy F, Nataf S, Pays L, Desjardins R, Gagnon H, Wisztorski M, Fournier I, Day R, Salzet M, (2015) "Molecular Consequences of Proprotein Convertase 1/3 (PC1/3) Inhibition in Macrophages for Application to Cancer Immunotherapy: A Proteomic Study." <i>Mol Cell Proteomics</i> <b>14</b>(11):2857–77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26330543 26330543]; doi: [https://dx.doi.org/10.1074/mcp.M115.052480 10.1074/mcp.M115.052480]; GPMDB: [http://gpmdb.org/data/keyword/26330543 18]. | #Duhamel M, Rodet F, Delhem N, Vanden Abeele F, Kobeissy F, Nataf S, Pays L, Desjardins R, Gagnon H, Wisztorski M, Fournier I, Day R, Salzet M, (2015) "Molecular Consequences of Proprotein Convertase 1/3 (PC1/3) Inhibition in Macrophages for Application to Cancer Immunotherapy: A Proteomic Study." <i>Mol Cell Proteomics</i> <b>14</b>(11):2857–77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26330543 26330543]; doi: [https://dx.doi.org/10.1074/mcp.M115.052480 10.1074/mcp.M115.052480]; GPMDB: [http://gpmdb.org/data/keyword/26330543 18]. | ||
#White CH, Johnston HE, Moesker B, Manousopoulou A, Margolis DM, Richman DD, Spina CA, Garbis SD, Woelk CH, Beliakova-Bethell N, (2015) "Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency." <i>Antiviral Res</i> <b>123</b>:78–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26343910 26343910]; doi: [https://dx.doi.org/10.1016/j.antiviral.2015.09.002 10.1016/j.antiviral.2015.09.002]; GPMDB: [http://gpmdb.org/data/keyword/26343910 172]. | #White CH, Johnston HE, Moesker B, Manousopoulou A, Margolis DM, Richman DD, Spina CA, Garbis SD, Woelk CH, Beliakova-Bethell N, (2015) "Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency." <i>Antiviral Res</i> <b>123</b>:78–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26343910 26343910]; doi: [https://dx.doi.org/10.1016/j.antiviral.2015.09.002 10.1016/j.antiviral.2015.09.002]; GPMDB: [http://gpmdb.org/data/keyword/26343910 172]. | ||
Line 1,136: | Line 1,137: | ||
#Eyckerman S, Titeca K, Van Quickelberghe E, Cloots E, Verhee A, Samyn N, De Ceuninck L, Timmerman E, De Sutter D, Lievens S, Van Calenbergh S, Gevaert K, Tavernier J, (2016) "Trapping mammalian protein complexes in viral particles." <i>Nat Commun</i> <b>7</b>:11416; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27122307 27122307]; doi: [https://dx.doi.org/10.1038/ncomms11416 10.1038/ncomms11416]; GPMDB: [http://gpmdb.org/data/keyword/27122307 58]. | #Eyckerman S, Titeca K, Van Quickelberghe E, Cloots E, Verhee A, Samyn N, De Ceuninck L, Timmerman E, De Sutter D, Lievens S, Van Calenbergh S, Gevaert K, Tavernier J, (2016) "Trapping mammalian protein complexes in viral particles." <i>Nat Commun</i> <b>7</b>:11416; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27122307 27122307]; doi: [https://dx.doi.org/10.1038/ncomms11416 10.1038/ncomms11416]; GPMDB: [http://gpmdb.org/data/keyword/27122307 58]. | ||
#Ono M, Yamada K, Bensaddek D, Afzal V, Biddlestone J, Ortmann B, Mudie S, Boivin V, Scott MS, Rocha S, Lamond AI, (2016) "Enhanced snoMEN Vectors Facilitate Establishment of GFP-HIF-1α Protein Replacement Human Cell Lines." <i>PLoS One</i> <b>11</b>(4):e0154759; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27128805 27128805]; doi: [https://dx.doi.org/10.1371/journal.pone.0154759 10.1371/journal.pone.0154759]; GPMDB: [http://gpmdb.org/data/keyword/27128805 72]. | #Ono M, Yamada K, Bensaddek D, Afzal V, Biddlestone J, Ortmann B, Mudie S, Boivin V, Scott MS, Rocha S, Lamond AI, (2016) "Enhanced snoMEN Vectors Facilitate Establishment of GFP-HIF-1α Protein Replacement Human Cell Lines." <i>PLoS One</i> <b>11</b>(4):e0154759; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27128805 27128805]; doi: [https://dx.doi.org/10.1371/journal.pone.0154759 10.1371/journal.pone.0154759]; GPMDB: [http://gpmdb.org/data/keyword/27128805 72]. | ||
+ | #Petrone A, Adamo ME, Cheg C, Kettenbach AN, (2016) "Identification of candidate CDK1 substrates in mitosis by quantitative phosphoproteomics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27134283 27134283]; doi: [https://dx.doi.org/10.1074/mcp.M116.059394 10.1074/mcp.M116.059394]; GPMDB: [http://gpmdb.org/data/keyword/27134283 90]. | ||
#Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M, (2015) "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats." <i>Cell Syst</i> <b>1</b>(3):224–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27135913 27135913]; doi: [https://dx.doi.org/10.1016/j.cels.2015.08.012 10.1016/j.cels.2015.08.012]; GPMDB: [http://gpmdb.org/data/keyword/27135913 190]. | #Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M, (2015) "Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats." <i>Cell Syst</i> <b>1</b>(3):224–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27135913 27135913]; doi: [https://dx.doi.org/10.1016/j.cels.2015.08.012 10.1016/j.cels.2015.08.012]; GPMDB: [http://gpmdb.org/data/keyword/27135913 190]. | ||
#Ulrich V, Rotllan N, Araldi E, Luciano A, Skroblin P, Abonnenc M, Perrotta P, Yin X, Bauer A, Leslie KL, Zhang P, Aryal B, Montgomery RL, Thum T, Martin K, Suarez Y, Mayr M, Fernandez-Hernando C, Sessa WC, (2016) "Chronic miR-29 antagonism promotes favorable plaque remodeling in atherosclerotic mice." <i>EMBO Mol Med</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27137489 27137489]; doi: [https://dx.doi.org/10.15252/emmm.201506031 10.15252/emmm.201506031]; GPMDB: [http://gpmdb.org/data/keyword/27137489 120]. | #Ulrich V, Rotllan N, Araldi E, Luciano A, Skroblin P, Abonnenc M, Perrotta P, Yin X, Bauer A, Leslie KL, Zhang P, Aryal B, Montgomery RL, Thum T, Martin K, Suarez Y, Mayr M, Fernandez-Hernando C, Sessa WC, (2016) "Chronic miR-29 antagonism promotes favorable plaque remodeling in atherosclerotic mice." <i>EMBO Mol Med</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27137489 27137489]; doi: [https://dx.doi.org/10.15252/emmm.201506031 10.15252/emmm.201506031]; GPMDB: [http://gpmdb.org/data/keyword/27137489 120]. | ||
#Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE, (2016) "Proteomics-driven antigen discovery for development of vaccines against gonorrhea." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141096 27141096]; doi: [https://dx.doi.org/10.1074/mcp.M116.058800 10.1074/mcp.M116.058800]; GPMDB: [http://gpmdb.org/data/keyword/27141096 3]. | #Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE, (2016) "Proteomics-driven antigen discovery for development of vaccines against gonorrhea." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27141096 27141096]; doi: [https://dx.doi.org/10.1074/mcp.M116.058800 10.1074/mcp.M116.058800]; GPMDB: [http://gpmdb.org/data/keyword/27141096 3]. | ||
- | #Ziganshin RH, Ivanova OM, Lomakin YA, Belogurov AA Jr, Kovalchuk SI, Azarkin IV, Arapidi GP, Anikanov NA, Shender VO, Piradov MA, Suponeva NA, Vorobyeva AA, Gabibov AG, Ivanov VT, Govorun VM, (2016) "The pathogenesis of demyelinating form of Guillain-Barre syndrome: proteo-peptidomic and immunological profiling of physiological fluids." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27143409 27143409]; doi: [https://dx.doi.org/10.1074/mcp.M115.056036 10.1074/mcp.M115.056036]; GPMDB: [http://gpmdb.org/data/keyword/27143409 | + | #Ziganshin RH, Ivanova OM, Lomakin YA, Belogurov AA Jr, Kovalchuk SI, Azarkin IV, Arapidi GP, Anikanov NA, Shender VO, Piradov MA, Suponeva NA, Vorobyeva AA, Gabibov AG, Ivanov VT, Govorun VM, (2016) "The pathogenesis of demyelinating form of Guillain-Barre syndrome: proteo-peptidomic and immunological profiling of physiological fluids." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27143409 27143409]; doi: [https://dx.doi.org/10.1074/mcp.M115.056036 10.1074/mcp.M115.056036]; GPMDB: [http://gpmdb.org/data/keyword/27143409 28]. |
#Kempf SJ, Metaxas A, Ibáñez-Vea M, Darvesh S, Finsen B, Larsen MR, (2016) "An integrated proteomics approach shows synaptic plasticity changes in an APP/PS1 Alzheimer's mouse model." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27144524 27144524]; doi: [https://dx.doi.org/10.18632/oncotarget.9092 10.18632/oncotarget.9092]; GPMDB: [http://gpmdb.org/data/keyword/27144524 104]. | #Kempf SJ, Metaxas A, Ibáñez-Vea M, Darvesh S, Finsen B, Larsen MR, (2016) "An integrated proteomics approach shows synaptic plasticity changes in an APP/PS1 Alzheimer's mouse model." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27144524 27144524]; doi: [https://dx.doi.org/10.18632/oncotarget.9092 10.18632/oncotarget.9092]; GPMDB: [http://gpmdb.org/data/keyword/27144524 104]. | ||
#Dørum S, Steinsbø Ø, Bergseng E, Arntzen MØ, de Souza GA, Sollid LM, (2016) "Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes." <i>Sci Rep</i> <b>6</b>:25565; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27146306 27146306]; doi: [https://dx.doi.org/10.1038/srep25565 10.1038/srep25565]; GPMDB: [http://gpmdb.org/data/keyword/27146306 27]. | #Dørum S, Steinsbø Ø, Bergseng E, Arntzen MØ, de Souza GA, Sollid LM, (2016) "Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes." <i>Sci Rep</i> <b>6</b>:25565; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27146306 27146306]; doi: [https://dx.doi.org/10.1038/srep25565 10.1038/srep25565]; GPMDB: [http://gpmdb.org/data/keyword/27146306 27]. | ||
Line 1,147: | Line 1,149: | ||
#Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG, (2016) "Proteomic investigation of the secretome of cellvibrio japonicus during growth on chitin." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27169553 27169553]; doi: [https://dx.doi.org/10.1002/pmic.201500419 10.1002/pmic.201500419]; GPMDB: [http://gpmdb.org/data/keyword/27169553 18]. | #Tuveng TR, Arntzen MØ, Bengtsson O, Gardner JG, Vaaje-Kolstad G, Eijsink VG, (2016) "Proteomic investigation of the secretome of cellvibrio japonicus during growth on chitin." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27169553 27169553]; doi: [https://dx.doi.org/10.1002/pmic.201500419 10.1002/pmic.201500419]; GPMDB: [http://gpmdb.org/data/keyword/27169553 18]. | ||
#Rao SR, Flores-Rodriguez N, Page SL, Wong C, Robinson PJ, Chircop M, (2016) "The clathrin-dependent spindle proteome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27174698 27174698]; doi: [https://dx.doi.org/10.1074/mcp.M115.054809 10.1074/mcp.M115.054809]; GPMDB: [http://gpmdb.org/data/keyword/27174698 130]. | #Rao SR, Flores-Rodriguez N, Page SL, Wong C, Robinson PJ, Chircop M, (2016) "The clathrin-dependent spindle proteome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27174698 27174698]; doi: [https://dx.doi.org/10.1074/mcp.M115.054809 10.1074/mcp.M115.054809]; GPMDB: [http://gpmdb.org/data/keyword/27174698 130]. | ||
+ | #Kliuchnikova AA, Samokhina NI, Ilina IY, Karpov DS, Pyatnitskiy MA, Kuznetsova KG, Toropygin IY, Kochergin SA, Alekseev IB, Zgoda VG, Archakov AI, Moshkovskii SA, (2016) "Human aqueous humor proteome in cataract, glaucoma and pseudoexfoliation syndrome." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193151 27193151]; doi: [https://dx.doi.org/10.1002/pmic.201500423 10.1002/pmic.201500423]; GPMDB: [http://gpmdb.org/data/keyword/27193151 86]. | ||
+ | #Heaven MR, Flint D, Randall SM, Sosunov AA, Wilson LB, Barnes S, Goldman JE, Muddiman DC, Brenner M, (2016) "The Composition of Rosenthal Fibers, the Protein Aggregate Hallmark of Alexander Disease." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193225 27193225]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00316 10.1021/acs.jproteome.6b00316]; GPMDB: [http://gpmdb.org/data/keyword/27193225 8]. | ||
+ | #Yang W, Jackson B, Zhang H, (2016) "Identification of glycoproteins associated with HIV latently infected cells using quantitative glycoproteomics." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27195445 27195445]; doi: [https://dx.doi.org/10.1002/pmic.201500215 10.1002/pmic.201500215]; GPMDB: [http://gpmdb.org/data/keyword/27195445 12]. | ||
+ | #Liang W, Ward LJ, Karlsson H, Ljunggren SA, Li W, Lindahl M, Yuan XM, (2016) "Distinctive proteomic profiles among different regions of human carotid plaques in men and women." <i>Sci Rep</i> <b>6</b>:26231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27198765 27198765]; doi: [https://dx.doi.org/10.1038/srep26231 10.1038/srep26231]; GPMDB: [http://gpmdb.org/data/keyword/27198765 60]. | ||
+ | #Virant-Klun I, Leicht S, Hughes C, Krijgsveld J, (2016) "Identification of maturation-specific proteins by single-cell proteomics of human oocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27215607 27215607]; doi: [https://dx.doi.org/10.1074/mcp.M115.056887 10.1074/mcp.M115.056887]; GPMDB: [http://gpmdb.org/data/keyword/27215607 18]. |
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 pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a 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 29, 2016.