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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 9, 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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#Kristensen TN, Kjeldal H, Schou MF, Nielsen JL, (2016) "Proteomic data reveal a physiological basis for costs and benefits associated with thermal acclimation." <i>J Exp Biol</i> <b>219</b>(Pt 7):969–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26823104 26823104]; doi: [https://dx.doi.org/10.1242/jeb.132696 10.1242/jeb.132696]; GPMDB: [http://gpmdb.org/data/keyword/26823104 9]. | #Kristensen TN, Kjeldal H, Schou MF, Nielsen JL, (2016) "Proteomic data reveal a physiological basis for costs and benefits associated with thermal acclimation." <i>J Exp Biol</i> <b>219</b>(Pt 7):969–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26823104 26823104]; doi: [https://dx.doi.org/10.1242/jeb.132696 10.1242/jeb.132696]; GPMDB: [http://gpmdb.org/data/keyword/26823104 9]. | ||
#Steger M, Tonelli F, Ito G, Davies P, Trost M, Vetter M, Wachter S, Lorentzen E, Duddy G, Wilson S, Baptista MA, Fiske BK, Fell MJ, Morrow JA, Reith AD, Alessi DR, Mann M, (2016) "Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26824392 26824392]; doi: [https://dx.doi.org/10.7554/eLife.12813 10.7554/eLife.12813]; GPMDB: [http://gpmdb.org/data/keyword/26824392 216]. | #Steger M, Tonelli F, Ito G, Davies P, Trost M, Vetter M, Wachter S, Lorentzen E, Duddy G, Wilson S, Baptista MA, Fiske BK, Fell MJ, Morrow JA, Reith AD, Alessi DR, Mann M, (2016) "Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26824392 26824392]; doi: [https://dx.doi.org/10.7554/eLife.12813 10.7554/eLife.12813]; GPMDB: [http://gpmdb.org/data/keyword/26824392 216]. | ||
+ | #Wiśniewski JR, Vildhede A, Norén A, Artursson P, (2016) "In-depth quantitative analysis and comparison of the human hepatocyte and hepatoma cell line HepG2 proteomes." <i>J Proteomics</i> <b>136</b>:234–47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26825538 26825538]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.01.016 10.1016/j.jprot.2016.01.016]; GPMDB: [http://gpmdb.org/data/keyword/26825538 122]. | ||
#Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE, (2016) "Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases." <i>Cell Rep</i> <b>14</b>(5):1049–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832403 26832403]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.01.009 10.1016/j.celrep.2016.01.009]; GPMDB: [http://gpmdb.org/data/keyword/26832403 486]. | #Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE, (2016) "Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases." <i>Cell Rep</i> <b>14</b>(5):1049–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832403 26832403]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.01.009 10.1016/j.celrep.2016.01.009]; GPMDB: [http://gpmdb.org/data/keyword/26832403 486]. | ||
#Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE, (2016) "miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells." <i>Cancer Cell</i> <b>29</b>(2):214–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832662 26832662]; doi: [https://dx.doi.org/10.1016/j.ccell.2015.12.011 10.1016/j.ccell.2015.12.011]; GPMDB: [http://gpmdb.org/data/keyword/26832662 72]. | #Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE, (2016) "miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells." <i>Cancer Cell</i> <b>29</b>(2):214–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832662 26832662]; doi: [https://dx.doi.org/10.1016/j.ccell.2015.12.011 10.1016/j.ccell.2015.12.011]; GPMDB: [http://gpmdb.org/data/keyword/26832662 72]. | ||
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#Ibáñez MI, Cabello P, Luque-Almagro VM, Sáez LP, Olaya A, Sánchez de Medina V, Luque de Castro MD, Moreno-Vivián C, Roldán MD, (2017) "Quantitative proteomic analysis of Pseudomonas pseudoalcaligenes CECT5344 in response to industrial cyanide-containing wastewaters using Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS)." <i>PLoS One</i> <b>12</b>(3):e0172908; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28253357 28253357]; doi: [https://dx.doi.org/10.1371/journal.pone.0172908 10.1371/journal.pone.0172908]; GPMDB: [http://gpmdb.org/data/keyword/28253357 8]. | #Ibáñez MI, Cabello P, Luque-Almagro VM, Sáez LP, Olaya A, Sánchez de Medina V, Luque de Castro MD, Moreno-Vivián C, Roldán MD, (2017) "Quantitative proteomic analysis of Pseudomonas pseudoalcaligenes CECT5344 in response to industrial cyanide-containing wastewaters using Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS)." <i>PLoS One</i> <b>12</b>(3):e0172908; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28253357 28253357]; doi: [https://dx.doi.org/10.1371/journal.pone.0172908 10.1371/journal.pone.0172908]; GPMDB: [http://gpmdb.org/data/keyword/28253357 8]. | ||
#Weinert BT, Satpathy S, Hansen BK, Lyon D, Jensen LJ, Choudhary C, (2017) "Accurate quantification of site-specific acetylation stoichiometry reveals the impact of sirtuin deacetylase CobB on the <i>E. coli</i> acetylome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28254776 28254776]; doi: [https://dx.doi.org/10.1074/mcp.M117.067587 10.1074/mcp.M117.067587]; GPMDB: [http://gpmdb.org/data/keyword/28254776 140]. | #Weinert BT, Satpathy S, Hansen BK, Lyon D, Jensen LJ, Choudhary C, (2017) "Accurate quantification of site-specific acetylation stoichiometry reveals the impact of sirtuin deacetylase CobB on the <i>E. coli</i> acetylome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28254776 28254776]; doi: [https://dx.doi.org/10.1074/mcp.M117.067587 10.1074/mcp.M117.067587]; GPMDB: [http://gpmdb.org/data/keyword/28254776 140]. | ||
- | #Casanovas A, Pinto-Llorente R, Carrascal M, Abian J, (2017) "Large-Scale Filter-Aided Sample Preparation Method for the Analysis of the Ubiquitinome." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28260372 28260372]; doi: [https://dx.doi.org/10.1021/acs.analchem.6b04804 10.1021/acs.analchem.6b04804]; GPMDB: [http://gpmdb.org/data/keyword/28260372 | + | #Casanovas A, Pinto-Llorente R, Carrascal M, Abian J, (2017) "Large-Scale Filter-Aided Sample Preparation Method for the Analysis of the Ubiquitinome." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28260372 28260372]; doi: [https://dx.doi.org/10.1021/acs.analchem.6b04804 10.1021/acs.analchem.6b04804]; GPMDB: [http://gpmdb.org/data/keyword/28260372 76]. |
#Giddey AD, de Kock E, Nakedi KC, Garnett S, Nel AJ, Soares NC, Blackburn JM, (2017) "A temporal proteome dynamics study reveals the molecular basis of induced phenotypic resistance in Mycobacterium smegmatis at sub-lethal rifampicin concentrations." <i>Sci Rep</i> <b>7</b>:43858; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28262820 28262820]; doi: [https://dx.doi.org/10.1038/srep43858 10.1038/srep43858]; GPMDB: [http://gpmdb.org/data/keyword/28262820 18]. | #Giddey AD, de Kock E, Nakedi KC, Garnett S, Nel AJ, Soares NC, Blackburn JM, (2017) "A temporal proteome dynamics study reveals the molecular basis of induced phenotypic resistance in Mycobacterium smegmatis at sub-lethal rifampicin concentrations." <i>Sci Rep</i> <b>7</b>:43858; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28262820 28262820]; doi: [https://dx.doi.org/10.1038/srep43858 10.1038/srep43858]; GPMDB: [http://gpmdb.org/data/keyword/28262820 18]. | ||
#Rieckmann JC, Geiger R, Hornburg D, Wolf T, Kveler K, Jarrossay D, Sallusto F, Shen-Orr SS, Lanzavecchia A, Mann M, Meissner F, (2017) "Social network architecture of human immune cells unveiled by quantitative proteomics." <i>Nat Immunol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28263321 28263321]; doi: [https://dx.doi.org/10.1038/ni.3693 10.1038/ni.3693]; GPMDB: [http://gpmdb.org/data/keyword/28263321 454]. | #Rieckmann JC, Geiger R, Hornburg D, Wolf T, Kveler K, Jarrossay D, Sallusto F, Shen-Orr SS, Lanzavecchia A, Mann M, Meissner F, (2017) "Social network architecture of human immune cells unveiled by quantitative proteomics." <i>Nat Immunol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28263321 28263321]; doi: [https://dx.doi.org/10.1038/ni.3693 10.1038/ni.3693]; GPMDB: [http://gpmdb.org/data/keyword/28263321 454]. | ||
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#Kliza K, Taumer C, Pinzuti I, Franz-Wachtel M, Kunzelmann S, Stieglitz B, Macek B, Husnjak K, (2017) "Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28319114 28319114]; doi: [https://dx.doi.org/10.1038/nmeth.4228 10.1038/nmeth.4228]; GPMDB: [http://gpmdb.org/data/keyword/28319114 32]. | #Kliza K, Taumer C, Pinzuti I, Franz-Wachtel M, Kunzelmann S, Stieglitz B, Macek B, Husnjak K, (2017) "Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28319114 28319114]; doi: [https://dx.doi.org/10.1038/nmeth.4228 10.1038/nmeth.4228]; GPMDB: [http://gpmdb.org/data/keyword/28319114 32]. | ||
#Tien JF, Mazloomian A, Cheng SG, Hughes CS, Chow CC, Canapi LT, Oloumi A, Trigo-Gonzalez G, Bashashati A, Xu J, Chang VC, Shah SP, Aparicio S, Morin GB, (2017) "CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28334900 28334900]; doi: [https://dx.doi.org/10.1093/nar/gkx187 10.1093/nar/gkx187]; GPMDB: [http://gpmdb.org/data/keyword/28334900 11]. | #Tien JF, Mazloomian A, Cheng SG, Hughes CS, Chow CC, Canapi LT, Oloumi A, Trigo-Gonzalez G, Bashashati A, Xu J, Chang VC, Shah SP, Aparicio S, Morin GB, (2017) "CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28334900 28334900]; doi: [https://dx.doi.org/10.1093/nar/gkx187 10.1093/nar/gkx187]; GPMDB: [http://gpmdb.org/data/keyword/28334900 11]. | ||
+ | #O'Neill JR, Pak HS, Pairo-Castineira E, Save V, Paterson-Brown S, Nenutil R, Vojtěšek B, Overton I, Scherl A, Hupp TR, (2017) "Quantitative shotgun proteomics unveils candidate novel oesophageal adenocarcinoma-specific proteins." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28336725 28336725]; doi: [https://dx.doi.org/10.1074/mcp.M116.065078 10.1074/mcp.M116.065078]; GPMDB: [http://gpmdb.org/data/keyword/28336725 7]. | ||
+ | #Francavilla C, Lupia M, Tsafou K, Villa A, Kowalczyk K, Rakownikow Jersie-Christensen R, Bertalot G, Confalonieri S, Brunak S, Jensen LJ, Cavallaro U, Olsen JV, (2017) "Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer." <i>Cell Rep</i> <b>18</b>(13):3242–3256; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28355574 28355574]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.03.015 10.1016/j.celrep.2017.03.015]; GPMDB: [http://gpmdb.org/data/keyword/28355574 38]. |
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 9, 2017.