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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 | + | 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 2, 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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#Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villén J, Haas W, Sowa ME, Gygi SP, (2010) "A tissue-specific atlas of mouse protein phosphorylation and expression." <i>Cell</i> <b>143</b>(7):1174–89; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21183079 21183079]; doi: [https://dx.doi.org/10.1016/j.cell.2010.12.001 10.1016/j.cell.2010.12.001]; GPMDB: [http://gpmdb.org/data/keyword/21183079 313]. | #Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villén J, Haas W, Sowa ME, Gygi SP, (2010) "A tissue-specific atlas of mouse protein phosphorylation and expression." <i>Cell</i> <b>143</b>(7):1174–89; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21183079 21183079]; doi: [https://dx.doi.org/10.1016/j.cell.2010.12.001 10.1016/j.cell.2010.12.001]; GPMDB: [http://gpmdb.org/data/keyword/21183079 313]. | ||
#Brockmeyer C, Paster W, Pepper D, Tan CP, Trudgian DC, McGowan S, Fu G, Gascoigne NR, Acuto O, Salek M, (2011) "T cell receptor (TCR)-induced tyrosine phosphorylation dynamics identifies THEMIS as a new TCR signalosome component." <i>J Biol Chem</i> <b>286</b>(9):7535–47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21189249 21189249]; doi: [https://dx.doi.org/10.1074/jbc.M110.201236 10.1074/jbc.M110.201236]; GPMDB: [http://gpmdb.org/data/keyword/21189249 4]. | #Brockmeyer C, Paster W, Pepper D, Tan CP, Trudgian DC, McGowan S, Fu G, Gascoigne NR, Acuto O, Salek M, (2011) "T cell receptor (TCR)-induced tyrosine phosphorylation dynamics identifies THEMIS as a new TCR signalosome component." <i>J Biol Chem</i> <b>286</b>(9):7535–47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21189249 21189249]; doi: [https://dx.doi.org/10.1074/jbc.M110.201236 10.1074/jbc.M110.201236]; GPMDB: [http://gpmdb.org/data/keyword/21189249 4]. | ||
- | #Manes NP, Dong L, Zhou W, Du X, Reghu N, Kool AC, Choi D, Bailey CL, Petricoin EF 3rd, Liotta LA, Popov SG, (2011) "Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry." <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.000927; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21189417 21189417]; doi: [https://dx.doi.org/10.1074/mcp.M110.000927 10.1074/mcp.M110.000927]; GPMDB: [http://gpmdb.org/data/keyword/21189417 | + | #Manes NP, Dong L, Zhou W, Du X, Reghu N, Kool AC, Choi D, Bailey CL, Petricoin EF 3rd, Liotta LA, Popov SG, (2011) "Discovery of mouse spleen signaling responses to anthrax using label-free quantitative phosphoproteomics via mass spectrometry." <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.000927; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21189417 21189417]; doi: [https://dx.doi.org/10.1074/mcp.M110.000927 10.1074/mcp.M110.000927]; GPMDB: [http://gpmdb.org/data/keyword/21189417 133]. |
#Hansson J, Panchaud A, Favre L, Bosco N, Mansourian R, Benyacoub J, Blum S, Jensen ON, Kussmann M, (2011) "Time-resolved quantitative proteome analysis of in vivo intestinal development." <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.005231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21191033 21191033]; doi: [https://dx.doi.org/10.1074/mcp.M110.005231 10.1074/mcp.M110.005231]; GPMDB: [http://gpmdb.org/data/keyword/21191033 48]. | #Hansson J, Panchaud A, Favre L, Bosco N, Mansourian R, Benyacoub J, Blum S, Jensen ON, Kussmann M, (2011) "Time-resolved quantitative proteome analysis of in vivo intestinal development." <i>Mol Cell Proteomics</i> <b>10</b>(3):M110.005231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21191033 21191033]; doi: [https://dx.doi.org/10.1074/mcp.M110.005231 10.1074/mcp.M110.005231]; GPMDB: [http://gpmdb.org/data/keyword/21191033 48]. | ||
#Singh SK, Lakshmi MG, Saxena S, Swamy CV, Idris MM, (2011) "Proteome profile of zebrafish caudal fin based on one-dimensional gel electrophoresis LCMS/MS and two-dimensional gel electrophoresis MALDI MS/MS analysis." <i>J Sep Sci</i> <b>34</b>(2):225–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21246729 21246729]; doi: [https://dx.doi.org/10.1002/jssc.201000626 10.1002/jssc.201000626]; GPMDB: [http://gpmdb.org/data/keyword/21246729 17]. | #Singh SK, Lakshmi MG, Saxena S, Swamy CV, Idris MM, (2011) "Proteome profile of zebrafish caudal fin based on one-dimensional gel electrophoresis LCMS/MS and two-dimensional gel electrophoresis MALDI MS/MS analysis." <i>J Sep Sci</i> <b>34</b>(2):225–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21246729 21246729]; doi: [https://dx.doi.org/10.1002/jssc.201000626 10.1002/jssc.201000626]; GPMDB: [http://gpmdb.org/data/keyword/21246729 17]. | ||
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#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]. | ||
+ | #Cutler JA, Tahir R, Sreenivasamurthy SK, Mitchell C, Renuse S, Nirujogi RS, Patil AH, Heydarian M, Wong X, Wu X, Huang TC, Kim MS, Reddy KL, Pandey A, (2017) "Differential signaling through p190 and p210 BCR-ABL fusion proteins revealed by interactome and phosphoproteome analysis." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28210003 28210003]; doi: [https://dx.doi.org/10.1038/leu.2017.61 10.1038/leu.2017.61]; GPMDB: [http://gpmdb.org/data/keyword/28210003 20]. | ||
#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]. | ||
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#Funnell T, Tasaki S, Oloumi A, Araki S, Kong E, Yap D, Nakayama Y, Hughes CS, Cheng SG, Tozaki H, Iwatani M, Sasaki S, Ohashi T, Miyazaki T, Morishita N, Morishita D, Ogasawara-Shimizu M, Ohori M, Nakao S, Karashima M, Sano M, Murai A, Nomura T, Uchiyama N, Kawamoto T, Hara R, Nakanishi O, Shumansky K, Rosner J, Wan A, McKinney S, Morin GB, Nakanishi A, Shah S, Toyoshiba H, Aparicio S, (2017) "CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor." <i>Nat Commun</i> <b>8</b>(1):7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28232751 28232751]; doi: [https://dx.doi.org/10.1038/s41467-016-0008-7 10.1038/s41467-016-0008-7]; GPMDB: [http://gpmdb.org/data/keyword/28232751 3]. | #Funnell T, Tasaki S, Oloumi A, Araki S, Kong E, Yap D, Nakayama Y, Hughes CS, Cheng SG, Tozaki H, Iwatani M, Sasaki S, Ohashi T, Miyazaki T, Morishita N, Morishita D, Ogasawara-Shimizu M, Ohori M, Nakao S, Karashima M, Sano M, Murai A, Nomura T, Uchiyama N, Kawamoto T, Hara R, Nakanishi O, Shumansky K, Rosner J, Wan A, McKinney S, Morin GB, Nakanishi A, Shah S, Toyoshiba H, Aparicio S, (2017) "CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor." <i>Nat Commun</i> <b>8</b>(1):7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28232751 28232751]; doi: [https://dx.doi.org/10.1038/s41467-016-0008-7 10.1038/s41467-016-0008-7]; GPMDB: [http://gpmdb.org/data/keyword/28232751 3]. | ||
#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]. | ||
+ | #Arend KC, Lenarcic EM, Vincent HA, Rashid N, Lazear E, McDonald IM, Gilbert TS, East MP, Herring LE, Johnson GL, Graves L, Moorman NJ, (2017) "Kinome Profiling Identifies Druggable Targets For Novel HCMV Antivirals." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28237943 28237943]; doi: [https://dx.doi.org/10.1074/mcp.M116.065375 10.1074/mcp.M116.065375]; GPMDB: [http://gpmdb.org/data/keyword/28237943 14]. | ||
#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]. | #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]. | ||
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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 71]. | ||
#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 | + | #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]. |
#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]. | #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 57]. | #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]. | ||
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#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 20]. | #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 20]. | ||
#Blattner M, Liu D, Robinson BD, Huang D, Poliakov A, Gao D, Nataraj S, Deonarine LD, Augello MA, Sailer V, Ponnala L, Ittmann M, Chinnaiyan AM, Sboner A, Chen Y, Rubin MA, Barbieri CE, (2017) "SPOP Mutation Drives Prostate Tumorigenesis In Vivo through Coordinate Regulation of PI3K/mTOR and AR Signaling." <i>Cancer Cell</i> <b>31</b>(3):436–451; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28292441 28292441]; doi: [https://dx.doi.org/10.1016/j.ccell.2017.02.004 10.1016/j.ccell.2017.02.004]; GPMDB: [http://gpmdb.org/data/keyword/28292441 96]. | #Blattner M, Liu D, Robinson BD, Huang D, Poliakov A, Gao D, Nataraj S, Deonarine LD, Augello MA, Sailer V, Ponnala L, Ittmann M, Chinnaiyan AM, Sboner A, Chen Y, Rubin MA, Barbieri CE, (2017) "SPOP Mutation Drives Prostate Tumorigenesis In Vivo through Coordinate Regulation of PI3K/mTOR and AR Signaling." <i>Cancer Cell</i> <b>31</b>(3):436–451; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28292441 28292441]; doi: [https://dx.doi.org/10.1016/j.ccell.2017.02.004 10.1016/j.ccell.2017.02.004]; GPMDB: [http://gpmdb.org/data/keyword/28292441 96]. | ||
- | #Bundy JL, Vied C, Nowakowski RS, (2017) "Sex differences in the molecular signature of the developing mouse hippocampus." <i>BMC Genomics</i> <b>18</b>(1):237; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28302071 28302071]; doi: [https://dx.doi.org/10.1186/s12864-017-3608-7 10.1186/s12864-017-3608-7]; GPMDB: [http://gpmdb.org/data/keyword/28302071 | + | #Bundy JL, Vied C, Nowakowski RS, (2017) "Sex differences in the molecular signature of the developing mouse hippocampus." <i>BMC Genomics</i> <b>18</b>(1):237; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28302071 28302071]; doi: [https://dx.doi.org/10.1186/s12864-017-3608-7 10.1186/s12864-017-3608-7]; GPMDB: [http://gpmdb.org/data/keyword/28302071 51]. |
+ | #Winter M, Dokic I, Schlegel J, Warnken U, Debus J, Abdollahi A, Schnölzer M, (2017) "Deciphering the acute cellular phosphoproteome response to irradiation with X-rays, protons and carbon ions." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28302921 28302921]; doi: [https://dx.doi.org/10.1074/mcp.M116.066597 10.1074/mcp.M116.066597]; GPMDB: [http://gpmdb.org/data/keyword/28302921 269]. | ||
+ | #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]. |
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 2, 2017.