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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 March | + | 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 March 12, 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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#Kulej K, Avgousti DC, Sidoli S, Herrmann C, Della Fera AN, Kim ET, Garcia BA, Weitzman MD, (2017) "Time-resolved global and chromatin proteomics during herpes simplex virus (HSV-1) infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28179408 28179408]; doi: [https://dx.doi.org/10.1074/mcp.M116.065987 10.1074/mcp.M116.065987]; GPMDB: [http://gpmdb.org/data/keyword/28179408 63]. | #Kulej K, Avgousti DC, Sidoli S, Herrmann C, Della Fera AN, Kim ET, Garcia BA, Weitzman MD, (2017) "Time-resolved global and chromatin proteomics during herpes simplex virus (HSV-1) infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28179408 28179408]; doi: [https://dx.doi.org/10.1074/mcp.M116.065987 10.1074/mcp.M116.065987]; GPMDB: [http://gpmdb.org/data/keyword/28179408 63]. | ||
#Schm Oumllders J, Manske C, Otto A, Hoffmann C, Steiner B, Welin A, Becher DO, Hilbi H, (2017) "Comparative proteomics of purified pathogen vacuoles correlates intracellular replication of <i>Legionella pneumophila</i> with the small GTPase Rap1." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28183814 28183814]; doi: [https://dx.doi.org/10.1074/mcp.M116.063453 10.1074/mcp.M116.063453]; GPMDB: [http://gpmdb.org/data/keyword/28183814 118]. | #Schm Oumllders J, Manske C, Otto A, Hoffmann C, Steiner B, Welin A, Becher DO, Hilbi H, (2017) "Comparative proteomics of purified pathogen vacuoles correlates intracellular replication of <i>Legionella pneumophila</i> with the small GTPase Rap1." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28183814 28183814]; doi: [https://dx.doi.org/10.1074/mcp.M116.063453 10.1074/mcp.M116.063453]; GPMDB: [http://gpmdb.org/data/keyword/28183814 118]. | ||
+ | #Greseth MD, Carter DM, Terhune SS, Traktman P, (2017) "Proteomic screen for cellular targets of the vaccinia virus F10 protein kinase reveals that phosphorylation of mDia regulates stress fiber formation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28183815 28183815]; doi: [https://dx.doi.org/10.1074/mcp.M116.065003 10.1074/mcp.M116.065003]; GPMDB: [http://gpmdb.org/data/keyword/28183815 9]. | ||
#Fielding CA, Weekes MP, Nobre LV, Ruckova E, Wilkie GS, Paulo JA, Chang C, Suárez NM, Davies JA, Antrobus R, Stanton RJ, Aicheler RJ, Nichols H, Vojtesek B, Trowsdale J, Davison AJ, Gygi SP, Tomasec P, Lehner PJ, Wilkinson GW, (2017) "Control of immune ligands by members of a cytomegalovirus gene expansion suppresses natural killer cell activation." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28186488 28186488]; doi: [https://dx.doi.org/10.7554/eLife.22206 10.7554/eLife.22206]; GPMDB: [http://gpmdb.org/data/keyword/28186488 9]. | #Fielding CA, Weekes MP, Nobre LV, Ruckova E, Wilkie GS, Paulo JA, Chang C, Suárez NM, Davies JA, Antrobus R, Stanton RJ, Aicheler RJ, Nichols H, Vojtesek B, Trowsdale J, Davison AJ, Gygi SP, Tomasec P, Lehner PJ, Wilkinson GW, (2017) "Control of immune ligands by members of a cytomegalovirus gene expansion suppresses natural killer cell activation." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28186488 28186488]; doi: [https://dx.doi.org/10.7554/eLife.22206 10.7554/eLife.22206]; GPMDB: [http://gpmdb.org/data/keyword/28186488 9]. | ||
#Barnea E, Melamed Kadosh D, Haimovich Y, Satumtira N, Dorris ML, Nguyen MT, Hammer RE, Tran TM, Colbert RA, Taurog JD, Admon A, (2017) "The HLA-B27 peptidome in vivo in spondyloarthritis-susceptible HLA-B27 transgenic rats and the effect of ERAP1 deletion." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28188227 28188227]; doi: [https://dx.doi.org/10.1074/mcp.M116.066241 10.1074/mcp.M116.066241]; GPMDB: [http://gpmdb.org/data/keyword/28188227 49]. | #Barnea E, Melamed Kadosh D, Haimovich Y, Satumtira N, Dorris ML, Nguyen MT, Hammer RE, Tran TM, Colbert RA, Taurog JD, Admon A, (2017) "The HLA-B27 peptidome in vivo in spondyloarthritis-susceptible HLA-B27 transgenic rats and the effect of ERAP1 deletion." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28188227 28188227]; doi: [https://dx.doi.org/10.1074/mcp.M116.066241 10.1074/mcp.M116.066241]; GPMDB: [http://gpmdb.org/data/keyword/28188227 49]. | ||
#Howie D, Cobbold SP, Adams E, Ten Bokum A, Necula AS, Zhang W, Huang H, Roberts DJ, Thomas B, Hester SS, Vaux DJ, Betz AG, Waldmann H, (2017) "Foxp3 drives oxidative phosphorylation and protection from lipotoxicity." <i>JCI Insight</i> <b>2</b>(3):e89160; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28194435 28194435]; doi: [https://dx.doi.org/10.1172/jci.insight.89160 10.1172/jci.insight.89160]; GPMDB: [http://gpmdb.org/data/keyword/28194435 7]. | #Howie D, Cobbold SP, Adams E, Ten Bokum A, Necula AS, Zhang W, Huang H, Roberts DJ, Thomas B, Hester SS, Vaux DJ, Betz AG, Waldmann H, (2017) "Foxp3 drives oxidative phosphorylation and protection from lipotoxicity." <i>JCI Insight</i> <b>2</b>(3):e89160; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28194435 28194435]; doi: [https://dx.doi.org/10.1172/jci.insight.89160 10.1172/jci.insight.89160]; GPMDB: [http://gpmdb.org/data/keyword/28194435 7]. | ||
- | #Liu NQ, Ter Huurne M, Nguyen LN, Peng T, Wang SY, Studd JB, Joshi O, Ongen H, Bramsen JB, Yan J, Andersen CL, Taipale J, Dermitzakis ET, Houlston RS, Hubner NC, Stunnenberg HG, (2017) "The non-coding variant rs1800734 enhances DCLK3 expression through long-range interaction and promotes colorectal cancer progression." <i>Nat Commun</i> <b>8</b>:14418; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28195176 28195176]; doi: [https://dx.doi.org/10.1038/ncomms14418 10.1038/ncomms14418]; GPMDB: [http://gpmdb.org/data/keyword/28195176 | + | #Liu NQ, Ter Huurne M, Nguyen LN, Peng T, Wang SY, Studd JB, Joshi O, Ongen H, Bramsen JB, Yan J, Andersen CL, Taipale J, Dermitzakis ET, Houlston RS, Hubner NC, Stunnenberg HG, (2017) "The non-coding variant rs1800734 enhances DCLK3 expression through long-range interaction and promotes colorectal cancer progression." <i>Nat Commun</i> <b>8</b>:14418; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28195176 28195176]; doi: [https://dx.doi.org/10.1038/ncomms14418 10.1038/ncomms14418]; GPMDB: [http://gpmdb.org/data/keyword/28195176 250]. |
#Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM, (2017) "Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28195392 28195392]; doi: [https://dx.doi.org/10.1002/pmic.201600300 10.1002/pmic.201600300]; GPMDB: [http://gpmdb.org/data/keyword/28195392 36]. | #Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM, (2017) "Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28195392 28195392]; doi: [https://dx.doi.org/10.1002/pmic.201600300 10.1002/pmic.201600300]; GPMDB: [http://gpmdb.org/data/keyword/28195392 36]. | ||
+ | #Lorey MB, Rossi K, Eklund KK, Nyman TA, Matikainen S, (2017) "Global characterization of protein secretion from human macrophages following non-canonical caspase-4/5 inflammasome activation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28196878 28196878]; doi: [https://dx.doi.org/10.1074/mcp.M116.064840 10.1074/mcp.M116.064840]; GPMDB: [http://gpmdb.org/data/keyword/28196878 60]. | ||
+ | #Suh MJ, Keasey SL, Brueggemann EE, Ulrich RG, (2017) "Antibiotic-dependent perturbations of extended spectrum beta-lactamase producing Klebsiella pneumoniae proteome." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28198105 28198105]; doi: [https://dx.doi.org/10.1002/pmic.201700003 10.1002/pmic.201700003]; GPMDB: [http://gpmdb.org/data/keyword/28198105 24]. | ||
#Potu H, Peterson LF, Kandarpa M, Pal A, Sun H, Durham A, Harms PW, Hollenhorst PC, Eskiocak U, Talpaz M, Donato NJ, (2017) "Usp9x regulates Ets-1 ubiquitination and stability to control NRAS expression and tumorigenicity in melanoma." <i>Nat Commun</i> <b>8</b>:14449; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28198367 28198367]; doi: [https://dx.doi.org/10.1038/ncomms14449 10.1038/ncomms14449]; GPMDB: [http://gpmdb.org/data/keyword/28198367 6]. | #Potu H, Peterson LF, Kandarpa M, Pal A, Sun H, Durham A, Harms PW, Hollenhorst PC, Eskiocak U, Talpaz M, Donato NJ, (2017) "Usp9x regulates Ets-1 ubiquitination and stability to control NRAS expression and tumorigenicity in melanoma." <i>Nat Commun</i> <b>8</b>:14449; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28198367 28198367]; doi: [https://dx.doi.org/10.1038/ncomms14449 10.1038/ncomms14449]; GPMDB: [http://gpmdb.org/data/keyword/28198367 6]. | ||
#Tahir A, Bileck A, Muqaku B, Niederstaetter L, Kreutz D, Mayer RL, Wolrab D, Meier SM, Slany A, Gerner C, (2017) "Combined Proteome and Eicosanoid Profiling Approach for Revealing Implications of Human Fibroblasts in Chronic Inflammation." <i>Anal Chem</i> <b>89</b>(3):1945–1954; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28208246 28208246]; doi: [https://dx.doi.org/10.1021/acs.analchem.6b04433 10.1021/acs.analchem.6b04433]; GPMDB: [http://gpmdb.org/data/keyword/28208246 32]. | #Tahir A, Bileck A, Muqaku B, Niederstaetter L, Kreutz D, Mayer RL, Wolrab D, Meier SM, Slany A, Gerner C, (2017) "Combined Proteome and Eicosanoid Profiling Approach for Revealing Implications of Human Fibroblasts in Chronic Inflammation." <i>Anal Chem</i> <b>89</b>(3):1945–1954; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28208246 28208246]; doi: [https://dx.doi.org/10.1021/acs.analchem.6b04433 10.1021/acs.analchem.6b04433]; GPMDB: [http://gpmdb.org/data/keyword/28208246 32]. | ||
+ | #Al Shweiki MR, Mönchgesang S, Majovsky P, Thieme D, Trutschel D, Hoehenwarter W, (2017) "Assessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28217993 28217993]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00645 10.1021/acs.jproteome.6b00645]; GPMDB: [http://gpmdb.org/data/keyword/28217993 54]. | ||
#Swertfeger DK, Li H, Rebholz S, Zhu X, Shah AS, Davidson WS, Lu LJ, (2017) "Mapping atheroprotective functions and related proteins/lipoproteins in size fractionated human plasma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28223350 28223350]; doi: [https://dx.doi.org/10.1074/mcp.M116.066290 10.1074/mcp.M116.066290]; GPMDB: [http://gpmdb.org/data/keyword/28223350 180]. | #Swertfeger DK, Li H, Rebholz S, Zhu X, Shah AS, Davidson WS, Lu LJ, (2017) "Mapping atheroprotective functions and related proteins/lipoproteins in size fractionated human plasma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28223350 28223350]; doi: [https://dx.doi.org/10.1074/mcp.M116.066290 10.1074/mcp.M116.066290]; GPMDB: [http://gpmdb.org/data/keyword/28223350 180]. | ||
+ | #Koppenol-Raab M, Sjoelund VH, Manes NP, Gottschalk RA, Dutta B, Benet ZL, Fraser ID, Nita-Lazar A, (2017) "Proteome and secretome analysis reveals differential post-transcriptional regulation of Toll-like receptor responses." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28235783 28235783]; doi: [https://dx.doi.org/10.1074/mcp.M116.064261 10.1074/mcp.M116.064261]; GPMDB: [http://gpmdb.org/data/keyword/28235783 629]. | ||
#Jia X, Chen J, Megger DA, Zhang X, Kozlowski M, Zhang L, Fang Z, Li J, Chu Q, Wu M, Li Y, Sitek B, Yuan Z, (2017) "Label-free Proteomic Analysis of Exosomes Derived from Inducible Hepatitis B Virus-Replicating HepAD38 Cell Line." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28242843 28242843]; doi: [https://dx.doi.org/10.1074/mcp.M116.063503 10.1074/mcp.M116.063503]; GPMDB: [http://gpmdb.org/data/keyword/28242843 12]. | #Jia X, Chen J, Megger DA, Zhang X, Kozlowski M, Zhang L, Fang Z, Li J, Chu Q, Wu M, Li Y, Sitek B, Yuan Z, (2017) "Label-free Proteomic Analysis of Exosomes Derived from Inducible Hepatitis B Virus-Replicating HepAD38 Cell Line." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28242843 28242843]; doi: [https://dx.doi.org/10.1074/mcp.M116.063503 10.1074/mcp.M116.063503]; GPMDB: [http://gpmdb.org/data/keyword/28242843 12]. | ||
+ | #Bayés À, Collins MO, Reig-Viader R, Gou G, Goulding D, Izquierdo A, Choudhary JS, Emes RD, Grant SG, (2017) "Evolution of complexity in the zebrafish synapse proteome." <i>Nat Commun</i> <b>8</b>:14613; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28252024 28252024]; doi: [https://dx.doi.org/10.1038/ncomms14613 10.1038/ncomms14613]; GPMDB: [http://gpmdb.org/data/keyword/28252024 17]. | ||
+ | #Liberton M, Chrisler WB, Nicora CD, Moore RJ, Smith RD, Koppenaal DW, Pakrasi HB, Jacobs JM, (2017) "Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803." <i>PLoS One</i> <b>12</b>(3):e0173251; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28253354 28253354]; doi: [https://dx.doi.org/10.1371/journal.pone.0173251 10.1371/journal.pone.0173251]; GPMDB: [http://gpmdb.org/data/keyword/28253354 36]. | ||
+ | #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]. | ||
+ | #Kanshin E, Giguere S, Cheng J, Tyers MD, Thibault P, (2017) "Machine learning of global phosphoproteomic profiles enables discrimination of direct versus indirect kinase substrates." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28265048 28265048]; doi: [https://dx.doi.org/10.1074/mcp.M116.066233 10.1074/mcp.M116.066233]; GPMDB: [http://gpmdb.org/data/keyword/28265048 2]. | ||
+ | #Espadas G, Borràs E, Chiva C, Sabidó E, (2017) "Evaluation of different peptide fragmentation types and mass analyzers in data-dependent methods using an Orbitrap Fusion Lumos Tribrid mass spectrometer." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28266123 28266123]; doi: [https://dx.doi.org/10.1002/pmic.201600416 10.1002/pmic.201600416]; GPMDB: [http://gpmdb.org/data/keyword/28266123 22]. | ||
+ | #Rapisarda V, Borghesan M, Miguela V, Encheva V, Snijders AP, Lujambio A, O'Loghlen A, (2017) "Integrin Beta 3 Regulates Cellular Senescence by Activating the TGF-β Pathway." <i>Cell Rep</i> <b>18</b>(10):2480–2493; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28273461 28273461]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.02.012 10.1016/j.celrep.2017.02.012]; GPMDB: [http://gpmdb.org/data/keyword/28273461 32]. |
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 March 12, 2017.