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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 19, 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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#Degroote RL, Uhl PB, Amann B, Krackhardt AM, Ueffing M, Hauck SM, Deeg CA, (2017) "Formin like 1 expression is increased on CD4+ T lymphocytes in spontaneous autoimmune uveitis." <i>J Proteomics</i> <b>154</b>:102–108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28057602 28057602]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.12.015 10.1016/j.jprot.2016.12.015]; GPMDB: [http://gpmdb.org/data/keyword/28057602 6]. | #Degroote RL, Uhl PB, Amann B, Krackhardt AM, Ueffing M, Hauck SM, Deeg CA, (2017) "Formin like 1 expression is increased on CD4+ T lymphocytes in spontaneous autoimmune uveitis." <i>J Proteomics</i> <b>154</b>:102–108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28057602 28057602]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.12.015 10.1016/j.jprot.2016.12.015]; GPMDB: [http://gpmdb.org/data/keyword/28057602 6]. | ||
#Braakman RB, Stingl C, Tilanus-Linthorst MM, Deurzen CH, Timmermans MA, Smid M, Foekens JA, Luider TM, Martens JW, Umar A, (2017) "Proteomic characterization of microdissected breast tissue environment provides a protein-level overview of malignant transformation." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28058811 28058811]; doi: [https://dx.doi.org/10.1002/pmic.201600213 10.1002/pmic.201600213]; GPMDB: [http://gpmdb.org/data/keyword/28058811 70]. | #Braakman RB, Stingl C, Tilanus-Linthorst MM, Deurzen CH, Timmermans MA, Smid M, Foekens JA, Luider TM, Martens JW, Umar A, (2017) "Proteomic characterization of microdissected breast tissue environment provides a protein-level overview of malignant transformation." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28058811 28058811]; doi: [https://dx.doi.org/10.1002/pmic.201600213 10.1002/pmic.201600213]; GPMDB: [http://gpmdb.org/data/keyword/28058811 70]. | ||
+ | #Beck F, Geiger J, Gambaryan S, Solari FA, Dell'Aica M, Loroch S, Mattheij NJ, Mindukshev I, Pötz O, Jurk K, Burkhart JM, Fufezan C, Heemskerk JW, Walter U, Zahedi RP, Sickmann A, (2017) "Temporal quantitative phosphoproteomics of ADP stimulation reveals novel central nodes in platelet activation and inhibition." <i>Blood</i> <b>129</b>(2):e1–e12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28060719 28060719]; doi: [https://dx.doi.org/10.1182/blood-2016-05-714048 10.1182/blood-2016-05-714048]; GPMDB: [http://gpmdb.org/data/keyword/28060719 4]. | ||
#Clotet S, Soler MJ, Riera M, Pascual J, Fang F, Zhou J, Batruch I, Vasiliou SK, Dimitromanolakis A, Barrios C, Diamandis E, Scholey J, Konvalinka A, (2017) "SILAC-Based Proteomics of Primary Human Kidney Cells Reveals a Novel Link between Male Sex Hormones and Impaired Energy Metabolism in Diabetic Kidney Disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062795 28062795]; doi: [https://dx.doi.org/10.1074/mcp.M116.061903 10.1074/mcp.M116.061903]; GPMDB: [http://gpmdb.org/data/keyword/28062795 11]. | #Clotet S, Soler MJ, Riera M, Pascual J, Fang F, Zhou J, Batruch I, Vasiliou SK, Dimitromanolakis A, Barrios C, Diamandis E, Scholey J, Konvalinka A, (2017) "SILAC-Based Proteomics of Primary Human Kidney Cells Reveals a Novel Link between Male Sex Hormones and Impaired Energy Metabolism in Diabetic Kidney Disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062795 28062795]; doi: [https://dx.doi.org/10.1074/mcp.M116.061903 10.1074/mcp.M116.061903]; GPMDB: [http://gpmdb.org/data/keyword/28062795 11]. | ||
#Johnston HE, Carter MJ, Cox KL, Dunscombe M, Manousopoulou A, Townsend PA, Garbis SD, Cragg MS, (2017) "Integrated Cellular and Plasma Proteomics of Contrasting B-cell Cancers Reveals Common, Unique and Systemic Signatures." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062796 28062796]; doi: [https://dx.doi.org/10.1074/mcp.M116.063511 10.1074/mcp.M116.063511]; GPMDB: [http://gpmdb.org/data/keyword/28062796 166]. | #Johnston HE, Carter MJ, Cox KL, Dunscombe M, Manousopoulou A, Townsend PA, Garbis SD, Cragg MS, (2017) "Integrated Cellular and Plasma Proteomics of Contrasting B-cell Cancers Reveals Common, Unique and Systemic Signatures." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062796 28062796]; doi: [https://dx.doi.org/10.1074/mcp.M116.063511 10.1074/mcp.M116.063511]; GPMDB: [http://gpmdb.org/data/keyword/28062796 166]. | ||
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#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]. | #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]. | ||
+ | #Abelin JG, Keskin DB, Sarkizova S, Hartigan CR, Zhang W, Sidney J, Stevens J, Lane W, Zhang GL, Eisenhaure TM, Clauser KR, Hacohen N, Rooney MS, Carr SA, Wu CJ, (2017) "Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction." <i>Immunity</i> <b>46</b>(2):315–326; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28228285 28228285]; doi: [https://dx.doi.org/10.1016/j.immuni.2017.02.007 10.1016/j.immuni.2017.02.007]; GPMDB: [http://gpmdb.org/data/keyword/28228285 87]. | ||
+ | #Groves JA, Maduka AO, O'Meally RN, Cole RN, Zachara NE, (2017) "Fatty acid synthase inhibits the O-GlcNAcase during oxidative stress." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28232487 28232487]; doi: [https://dx.doi.org/10.1074/jbc.M116.760785 10.1074/jbc.M116.760785]; GPMDB: [http://gpmdb.org/data/keyword/28232487 2]. | ||
#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]. | #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]. | ||
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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]. | ||
- | #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 | + | #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 32]. |
- | #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 | + | #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 57]. |
#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]. | #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]. | ||
+ | #Zhang T, Wei W, Dirsch O, Krüger T, Kan C, Xie C, Kniemeyer O, Fang H, Settmacher U, Dahmen U, (2017) "Identification of Proteins Interacting with Cytoplasmic High-Mobility Group Box 1 during the Hepatocellular Response to Ischemia Reperfusion Injury." <i>Int J Mol Sci</i> <b>18</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28275217 28275217]; doi: [https://dx.doi.org/10.3390/ijms18010167 10.3390/ijms18010167]; GPMDB: [http://gpmdb.org/data/keyword/28275217 4]. | ||
+ | #Sadewasser A, Paki K, Eichelbaum K, Bogdanow B, Saenger S, Budt M, Lesch M, Hinz KP, Herrmann A, Meyer TF, Karlas A, Selbach M, Wolff T, (2017) "Quantitative proteomic approach identifies Vpr binding protein as novel host factor supporting influenza A virus infections in human cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28289176 28289176]; doi: [https://dx.doi.org/10.1074/mcp.M116.065904 10.1074/mcp.M116.065904]; GPMDB: [http://gpmdb.org/data/keyword/28289176 14]. |
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 19, 2017.