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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 March 5, 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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#Grundner-Culemann K, Dybowski JN, Klammer M, Tebbe A, Schaab C, Daub H, (2016) "Comparative proteome analysis across non-small cell lung cancer cell lines." <i>J Proteomics</i> <b>130</b>:1–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26361996 26361996]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.09.003 10.1016/j.jprot.2015.09.003]; GPMDB: [http://gpmdb.org/data/keyword/26361996 23]. | #Grundner-Culemann K, Dybowski JN, Klammer M, Tebbe A, Schaab C, Daub H, (2016) "Comparative proteome analysis across non-small cell lung cancer cell lines." <i>J Proteomics</i> <b>130</b>:1–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26361996 26361996]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.09.003 10.1016/j.jprot.2015.09.003]; GPMDB: [http://gpmdb.org/data/keyword/26361996 23]. | ||
#Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M, Obermayer B, (2015) "Extensive identification and analysis of conserved small ORFs in animals." <i>Genome Biol</i> <b>16</b>:179; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26364619 26364619]; doi: [https://dx.doi.org/10.1186/s13059-015-0742-x 10.1186/s13059-015-0742-x]; GPMDB: [http://gpmdb.org/data/keyword/26364619 19]. | #Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M, Obermayer B, (2015) "Extensive identification and analysis of conserved small ORFs in animals." <i>Genome Biol</i> <b>16</b>:179; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26364619 26364619]; doi: [https://dx.doi.org/10.1186/s13059-015-0742-x 10.1186/s13059-015-0742-x]; GPMDB: [http://gpmdb.org/data/keyword/26364619 19]. | ||
- | #Preil SA, Kristensen LP, Beck HC, Jensen PS, Nielsen PS, Steiniche T, Bjørling-Poulsen M, Larsen MR, Hansen ML, Rasmussen LM, (2015) "Quantitative Proteome Analysis Reveals Increased Content of Basement Membrane Proteins in Arteries From Patients With Type 2 Diabetes Mellitus and Lower Levels Among Metformin Users." <i>Circ Cardiovasc Genet</i> <b>8</b>(5):727–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26371159 26371159]; doi: [https://dx.doi.org/10.1161/CIRCGENETICS.115.001165 10.1161/CIRCGENETICS.115.001165]; GPMDB: [http://gpmdb.org/data/keyword/26371159 | + | #Preil SA, Kristensen LP, Beck HC, Jensen PS, Nielsen PS, Steiniche T, Bjørling-Poulsen M, Larsen MR, Hansen ML, Rasmussen LM, (2015) "Quantitative Proteome Analysis Reveals Increased Content of Basement Membrane Proteins in Arteries From Patients With Type 2 Diabetes Mellitus and Lower Levels Among Metformin Users." <i>Circ Cardiovasc Genet</i> <b>8</b>(5):727–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26371159 26371159]; doi: [https://dx.doi.org/10.1161/CIRCGENETICS.115.001165 10.1161/CIRCGENETICS.115.001165]; GPMDB: [http://gpmdb.org/data/keyword/26371159 19]. |
#Lin MH, Sugiyama N, Ishihama Y, (2015) "Systematic profiling of the bacterial phosphoproteome reveals bacterium-specific features of phosphorylation." <i>Sci Signal</i> <b>8</b>(394):rs10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26373674 26373674]; doi: [https://dx.doi.org/10.1126/scisignal.aaa3117 10.1126/scisignal.aaa3117]; GPMDB: [http://gpmdb.org/data/keyword/26373674 73]. | #Lin MH, Sugiyama N, Ishihama Y, (2015) "Systematic profiling of the bacterial phosphoproteome reveals bacterium-specific features of phosphorylation." <i>Sci Signal</i> <b>8</b>(394):rs10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26373674 26373674]; doi: [https://dx.doi.org/10.1126/scisignal.aaa3117 10.1126/scisignal.aaa3117]; GPMDB: [http://gpmdb.org/data/keyword/26373674 73]. | ||
#Park AJ, Murphy K, Surette MD, Bandoro C, Krieger JR, Taylor P, Khursigara CM, (2015) "Tracking the Dynamic Relationship between Cellular Systems and Extracellular Subproteomes in Pseudomonas aeruginosa Biofilms." <i>J Proteome Res</i> <b>14</b>(11):4524–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26378716 26378716]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00262 10.1021/acs.jproteome.5b00262]; GPMDB: [http://gpmdb.org/data/keyword/26378716 34]. | #Park AJ, Murphy K, Surette MD, Bandoro C, Krieger JR, Taylor P, Khursigara CM, (2015) "Tracking the Dynamic Relationship between Cellular Systems and Extracellular Subproteomes in Pseudomonas aeruginosa Biofilms." <i>J Proteome Res</i> <b>14</b>(11):4524–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26378716 26378716]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00262 10.1021/acs.jproteome.5b00262]; GPMDB: [http://gpmdb.org/data/keyword/26378716 34]. | ||
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#Geddes JM, Croll D, Caza M, Stoynov N, Foster LJ, Kronstad JW, (2015) "Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A." <i>BMC Microbiol</i> <b>15</b>:206; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26453029 26453029]; doi: [https://dx.doi.org/10.1186/s12866-015-0532-3 10.1186/s12866-015-0532-3]; GPMDB: [http://gpmdb.org/data/keyword/26453029 48]. | #Geddes JM, Croll D, Caza M, Stoynov N, Foster LJ, Kronstad JW, (2015) "Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A." <i>BMC Microbiol</i> <b>15</b>:206; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26453029 26453029]; doi: [https://dx.doi.org/10.1186/s12866-015-0532-3 10.1186/s12866-015-0532-3]; GPMDB: [http://gpmdb.org/data/keyword/26453029 48]. | ||
#Gomez-Auli A, Hillebrand LE, Biniossek ML, Peters C, Reinheckel T, Schilling O, (2016) "Impact of cathepsin B on the interstitial fluid proteome of murine breast cancers." <i>Biochimie</i> <b>122</b>:88–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26455267 26455267]; doi: [https://dx.doi.org/10.1016/j.biochi.2015.10.009 10.1016/j.biochi.2015.10.009]; GPMDB: [http://gpmdb.org/data/keyword/26455267 1]. | #Gomez-Auli A, Hillebrand LE, Biniossek ML, Peters C, Reinheckel T, Schilling O, (2016) "Impact of cathepsin B on the interstitial fluid proteome of murine breast cancers." <i>Biochimie</i> <b>122</b>:88–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26455267 26455267]; doi: [https://dx.doi.org/10.1016/j.biochi.2015.10.009 10.1016/j.biochi.2015.10.009]; GPMDB: [http://gpmdb.org/data/keyword/26455267 1]. | ||
+ | #Roos A, Kollipara L, Buchkremer S, Labisch T, Brauers E, Gatz C, Lentz C, Gerardo-Nava J, Weis J, Zahedi RP, (2016) "Cellular Signature of SIL1 Depletion: Disease Pathogenesis due to Alterations in Protein Composition Beyond the ER Machinery." <i>Mol Neurobiol</i> <b>53</b>(8):5527–41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26468156 26468156]; doi: [https://dx.doi.org/10.1007/s12035-015-9456-z 10.1007/s12035-015-9456-z]; GPMDB: [http://gpmdb.org/data/keyword/26468156 18]. | ||
#Poli M, Ori A, Child T, Jaroudi S, Spath K, Beck M, Wells D, (2015) "Characterization and quantification of proteins secreted by single human embryos prior to implantation." <i>EMBO Mol Med</i> <b>7</b>(11):1465–79; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26471863 26471863]; doi: [https://dx.doi.org/10.15252/emmm.201505344 10.15252/emmm.201505344]; GPMDB: [http://gpmdb.org/data/keyword/26471863 11]. | #Poli M, Ori A, Child T, Jaroudi S, Spath K, Beck M, Wells D, (2015) "Characterization and quantification of proteins secreted by single human embryos prior to implantation." <i>EMBO Mol Med</i> <b>7</b>(11):1465–79; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26471863 26471863]; doi: [https://dx.doi.org/10.15252/emmm.201505344 10.15252/emmm.201505344]; GPMDB: [http://gpmdb.org/data/keyword/26471863 11]. | ||
#Schlage P, Kockmann T, Sabino F, Kizhakkedathu JN, Auf dem Keller U, (2015) "Matrix Metalloproteinase 10 Degradomics in Keratinocytes and Epidermal Tissue Identifies Bioactive Substrates With Pleiotropic Functions." <i>Mol Cell Proteomics</i> <b>14</b>(12):3234–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26475864 26475864]; doi: [https://dx.doi.org/10.1074/mcp.M115.053520 10.1074/mcp.M115.053520]; GPMDB: [http://gpmdb.org/data/keyword/26475864 25]. | #Schlage P, Kockmann T, Sabino F, Kizhakkedathu JN, Auf dem Keller U, (2015) "Matrix Metalloproteinase 10 Degradomics in Keratinocytes and Epidermal Tissue Identifies Bioactive Substrates With Pleiotropic Functions." <i>Mol Cell Proteomics</i> <b>14</b>(12):3234–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26475864 26475864]; doi: [https://dx.doi.org/10.1074/mcp.M115.053520 10.1074/mcp.M115.053520]; GPMDB: [http://gpmdb.org/data/keyword/26475864 25]. | ||
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#Shishkova E, Hebert AS, Coon JJ, (2016) "Now, More Than Ever, Proteomics Needs Better Chromatography." <i>Cell Syst</i> <b>3</b>(4):321–324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27788355 27788355]; doi: [https://dx.doi.org/10.1016/j.cels.2016.10.007 10.1016/j.cels.2016.10.007]; GPMDB: [http://gpmdb.org/data/keyword/27788355 35]. | #Shishkova E, Hebert AS, Coon JJ, (2016) "Now, More Than Ever, Proteomics Needs Better Chromatography." <i>Cell Syst</i> <b>3</b>(4):321–324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27788355 27788355]; doi: [https://dx.doi.org/10.1016/j.cels.2016.10.007 10.1016/j.cels.2016.10.007]; GPMDB: [http://gpmdb.org/data/keyword/27788355 35]. | ||
#Zhao M, Xu F, Wu F, Yu D, Su N, Zhang Y, Cheng L, Xu P, (2016) "iTRAQ-Based Membrane Proteomics Reveals Plasma Membrane Proteins Change During HepaRG Cell Differentiation." <i>J Proteome Res</i> <b>15</b>(12):4245–4257; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27790907 27790907]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00305 10.1021/acs.jproteome.6b00305]; GPMDB: [http://gpmdb.org/data/keyword/27790907 1]. | #Zhao M, Xu F, Wu F, Yu D, Su N, Zhang Y, Cheng L, Xu P, (2016) "iTRAQ-Based Membrane Proteomics Reveals Plasma Membrane Proteins Change During HepaRG Cell Differentiation." <i>J Proteome Res</i> <b>15</b>(12):4245–4257; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27790907 27790907]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00305 10.1021/acs.jproteome.6b00305]; GPMDB: [http://gpmdb.org/data/keyword/27790907 1]. | ||
+ | #Ren Y, Yeoh KW, Hao P, Kon OL, Sze SK, (2016) "Irradiation of Epithelial Carcinoma Cells Upregulates Calcium-Binding Proteins That Promote Survival under Hypoxic Conditions." <i>J Proteome Res</i> <b>15</b>(12):4258–4264; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27790916 27790916]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00340 10.1021/acs.jproteome.6b00340]; GPMDB: [http://gpmdb.org/data/keyword/27790916 3]. | ||
#Lundquist PK, Mantegazza O, Stefanski A, Stühler K, Weber AP, (2016) "Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts." <i>Mol Plant</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27794502 27794502]; doi: [https://dx.doi.org/10.1016/j.molp.2016.10.011 10.1016/j.molp.2016.10.011]; GPMDB: [http://gpmdb.org/data/keyword/27794502 42]. | #Lundquist PK, Mantegazza O, Stefanski A, Stühler K, Weber AP, (2016) "Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts." <i>Mol Plant</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27794502 27794502]; doi: [https://dx.doi.org/10.1016/j.molp.2016.10.011 10.1016/j.molp.2016.10.011]; GPMDB: [http://gpmdb.org/data/keyword/27794502 42]. | ||
#Fournier M, Orpinell M, Grauffel C, Scheer E, Garnier JM, Ye T, Chavant V, Joint M, Esashi F, Dejaegere A, Gönczy P, Tora L, (2016) "KAT2A/KAT2B-targeted acetylome reveals a role for PLK4 acetylation in preventing centrosome amplification." <i>Nat Commun</i> <b>7</b>:13227; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27796307 27796307]; doi: [https://dx.doi.org/10.1038/ncomms13227 10.1038/ncomms13227]; GPMDB: [http://gpmdb.org/data/keyword/27796307 114]. | #Fournier M, Orpinell M, Grauffel C, Scheer E, Garnier JM, Ye T, Chavant V, Joint M, Esashi F, Dejaegere A, Gönczy P, Tora L, (2016) "KAT2A/KAT2B-targeted acetylome reveals a role for PLK4 acetylation in preventing centrosome amplification." <i>Nat Commun</i> <b>7</b>:13227; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27796307 27796307]; doi: [https://dx.doi.org/10.1038/ncomms13227 10.1038/ncomms13227]; GPMDB: [http://gpmdb.org/data/keyword/27796307 114]. | ||
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#Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." <i>Nat Commun</i> <b>7</b>:13595; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27882920 27882920]; doi: [https://dx.doi.org/10.1038/ncomms13595 10.1038/ncomms13595]; GPMDB: [http://gpmdb.org/data/keyword/27882920 9]. | #Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." <i>Nat Commun</i> <b>7</b>:13595; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27882920 27882920]; doi: [https://dx.doi.org/10.1038/ncomms13595 10.1038/ncomms13595]; GPMDB: [http://gpmdb.org/data/keyword/27882920 9]. | ||
#Hurwitz SN, Rider MA, Bundy JL, Liu X, Singh RK, Meckes DG Jr, (2016) "Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers." <i>Oncotarget</i> <b>7</b>(52):86999–87015; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27894104 27894104]; doi: [https://dx.doi.org/10.18632/oncotarget.13569 10.18632/oncotarget.13569]; GPMDB: [http://gpmdb.org/data/keyword/27894104 898]. | #Hurwitz SN, Rider MA, Bundy JL, Liu X, Singh RK, Meckes DG Jr, (2016) "Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers." <i>Oncotarget</i> <b>7</b>(52):86999–87015; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27894104 27894104]; doi: [https://dx.doi.org/10.18632/oncotarget.13569 10.18632/oncotarget.13569]; GPMDB: [http://gpmdb.org/data/keyword/27894104 898]. | ||
+ | #Sundberg M, Strage EM, Bergquist J, Holst BS, Ramström M, (2016) "Quantitative and Selective Analysis of Feline Growth Related Proteins Using Parallel Reaction Monitoring High Resolution Mass Spectrometry." <i>PLoS One</i> <b>11</b>(12):e0167138; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27907059 27907059]; doi: [https://dx.doi.org/10.1371/journal.pone.0167138 10.1371/journal.pone.0167138]; GPMDB: [http://gpmdb.org/data/keyword/27907059 3]. | ||
#Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT, (2016) "A proteomic approach to analyse the aspirin-mediated lysine acetylome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27913581 27913581]; doi: [https://dx.doi.org/10.1074/mcp.O116.065219 10.1074/mcp.O116.065219]; GPMDB: [http://gpmdb.org/data/keyword/27913581 40]. | #Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT, (2016) "A proteomic approach to analyse the aspirin-mediated lysine acetylome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27913581 27913581]; doi: [https://dx.doi.org/10.1074/mcp.O116.065219 10.1074/mcp.O116.065219]; GPMDB: [http://gpmdb.org/data/keyword/27913581 40]. | ||
#Beaumont V, Zhong S, Lin H, Xu W, Bradaia A, Steidl E, Gleyzes M, Wadel K, Buisson B, Padovan-Neto FE, Chakroborty S, Ward KM, Harms JF, Beltran J, Kwan M, Ghavami A, Häggkvist J, Tóth M, Halldin C, Varrone A, Schaab C, Dybowski JN, Elschenbroich S, Lehtimäki K, Heikkinen T, Park L, Rosinski J, Mrzljak L, Lavery D, West AR, Schmidt CJ, Zaleska MM, Munoz-Sanjuan I, (2016) "Phosphodiesterase 10A Inhibition Improves Cortico-Basal Ganglia Function in Huntington's Disease Models." <i>Neuron</i> <b>92</b>(6):1220–1237; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27916455 27916455]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.10.064 10.1016/j.neuron.2016.10.064]; GPMDB: [http://gpmdb.org/data/keyword/27916455 377]. | #Beaumont V, Zhong S, Lin H, Xu W, Bradaia A, Steidl E, Gleyzes M, Wadel K, Buisson B, Padovan-Neto FE, Chakroborty S, Ward KM, Harms JF, Beltran J, Kwan M, Ghavami A, Häggkvist J, Tóth M, Halldin C, Varrone A, Schaab C, Dybowski JN, Elschenbroich S, Lehtimäki K, Heikkinen T, Park L, Rosinski J, Mrzljak L, Lavery D, West AR, Schmidt CJ, Zaleska MM, Munoz-Sanjuan I, (2016) "Phosphodiesterase 10A Inhibition Improves Cortico-Basal Ganglia Function in Huntington's Disease Models." <i>Neuron</i> <b>92</b>(6):1220–1237; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27916455 27916455]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.10.064 10.1016/j.neuron.2016.10.064]; GPMDB: [http://gpmdb.org/data/keyword/27916455 377]. | ||
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#Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ, (2017) "Interactome disassembly during apoptosis occurs independent of caspase cleavage." <i>Mol Syst Biol</i> <b>13</b>(1):906; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28082348 28082348]; GPMDB: [http://gpmdb.org/data/keyword/28082348 521]. | #Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ, (2017) "Interactome disassembly during apoptosis occurs independent of caspase cleavage." <i>Mol Syst Biol</i> <b>13</b>(1):906; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28082348 28082348]; GPMDB: [http://gpmdb.org/data/keyword/28082348 521]. | ||
#Emmott E, Sorgeloos F, Caddy SL, Vashist S, Sosnovtsev S, Lloyd R, Heesom K, Locker N, Goodfellow I, (2017) "Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087593 28087593]; doi: [https://dx.doi.org/10.1074/mcp.M116.062448 10.1074/mcp.M116.062448]; GPMDB: [http://gpmdb.org/data/keyword/28087593 3]. | #Emmott E, Sorgeloos F, Caddy SL, Vashist S, Sosnovtsev S, Lloyd R, Heesom K, Locker N, Goodfellow I, (2017) "Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087593 28087593]; doi: [https://dx.doi.org/10.1074/mcp.M116.062448 10.1074/mcp.M116.062448]; GPMDB: [http://gpmdb.org/data/keyword/28087593 3]. | ||
- | #Niklasson M, Maddalo G, Sramkova Z, Mutlu E, Wee S, Sekyrova P, Schmidt L, Fritz N, Dehnisch I, Kyriatzis G, Krafcikova M, Carson BB, Feenstra J, Marinescu VD, Segerman A, Haraldsson M, Gustavsson AL, Hammarström LG, Jenmalm-Jensen A, Uhrbom L, Altelaar AF, Linnarsson S, Uhlén P, Trantirek L, Vincent CT, Nelander S, Enger PØ, Andäng M, (2017) "Membrane-depolarizing channel blockers induce selective glioma cell death by impairing nutrient transport and unfolded protein/amino acid responses." <i>Cancer Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087597 28087597]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-16-2274 10.1158/0008-5472.CAN-16-2274]; GPMDB: [http://gpmdb.org/data/keyword/28087597 | + | #Niklasson M, Maddalo G, Sramkova Z, Mutlu E, Wee S, Sekyrova P, Schmidt L, Fritz N, Dehnisch I, Kyriatzis G, Krafcikova M, Carson BB, Feenstra J, Marinescu VD, Segerman A, Haraldsson M, Gustavsson AL, Hammarström LG, Jenmalm-Jensen A, Uhrbom L, Altelaar AF, Linnarsson S, Uhlén P, Trantirek L, Vincent CT, Nelander S, Enger PØ, Andäng M, (2017) "Membrane-depolarizing channel blockers induce selective glioma cell death by impairing nutrient transport and unfolded protein/amino acid responses." <i>Cancer Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087597 28087597]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-16-2274 10.1158/0008-5472.CAN-16-2274]; GPMDB: [http://gpmdb.org/data/keyword/28087597 6]. |
#Riesner K, Shi Y, Jacobi A, Kraeter M, Kalupa M, McGearey A, Mertlitz S, Cordes S, Schrezenmeier JF, Mengwasser J, Westphal S, Perez-Hernandez D, Schmitt C, Dittmar G, Guck J, Penack O, (2017) "Initiation of acute graft-versus-host disease by angiogenesis." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096092 28096092]; doi: [https://dx.doi.org/10.1182/blood-2016-08-736314 10.1182/blood-2016-08-736314]; GPMDB: [http://gpmdb.org/data/keyword/28096092 1]. | #Riesner K, Shi Y, Jacobi A, Kraeter M, Kalupa M, McGearey A, Mertlitz S, Cordes S, Schrezenmeier JF, Mengwasser J, Westphal S, Perez-Hernandez D, Schmitt C, Dittmar G, Guck J, Penack O, (2017) "Initiation of acute graft-versus-host disease by angiogenesis." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096092 28096092]; doi: [https://dx.doi.org/10.1182/blood-2016-08-736314 10.1182/blood-2016-08-736314]; GPMDB: [http://gpmdb.org/data/keyword/28096092 1]. | ||
#Princz LN, Wild P, Bittmann J, Aguado FJ, Blanco MG, Matos J, Pfander B, (2017) "Dbf4-dependent kinase and the Rtt107 scaffold promote Mus81-Mms4 resolvase activation during mitosis." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096179 28096179]; doi: [https://dx.doi.org/10.15252/embj.201694831 10.15252/embj.201694831]; GPMDB: [http://gpmdb.org/data/keyword/28096179 130]. | #Princz LN, Wild P, Bittmann J, Aguado FJ, Blanco MG, Matos J, Pfander B, (2017) "Dbf4-dependent kinase and the Rtt107 scaffold promote Mus81-Mms4 resolvase activation during mitosis." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096179 28096179]; doi: [https://dx.doi.org/10.15252/embj.201694831 10.15252/embj.201694831]; GPMDB: [http://gpmdb.org/data/keyword/28096179 130]. | ||
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#Kulak NA, Geyer PE, Mann M, (2017) "Loss-less nano-fractionator for high sensitivity, high coverage proteomics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28126900 28126900]; doi: [https://dx.doi.org/10.1074/mcp.O116.065136 10.1074/mcp.O116.065136]; GPMDB: [http://gpmdb.org/data/keyword/28126900 60]. | #Kulak NA, Geyer PE, Mann M, (2017) "Loss-less nano-fractionator for high sensitivity, high coverage proteomics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28126900 28126900]; doi: [https://dx.doi.org/10.1074/mcp.O116.065136 10.1074/mcp.O116.065136]; GPMDB: [http://gpmdb.org/data/keyword/28126900 60]. | ||
#Yu Y, Kwon K, Tsitrin T, Bekele S, Sikorski P, Nelson KE, Pieper R, (2017) "Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections." <i>PLoS Pathog</i> <b>13</b>(1):e1006151; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28129394 28129394]; doi: [https://dx.doi.org/10.1371/journal.ppat.1006151 10.1371/journal.ppat.1006151]; GPMDB: [http://gpmdb.org/data/keyword/28129394 72]. | #Yu Y, Kwon K, Tsitrin T, Bekele S, Sikorski P, Nelson KE, Pieper R, (2017) "Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections." <i>PLoS Pathog</i> <b>13</b>(1):e1006151; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28129394 28129394]; doi: [https://dx.doi.org/10.1371/journal.ppat.1006151 10.1371/journal.ppat.1006151]; GPMDB: [http://gpmdb.org/data/keyword/28129394 72]. | ||
+ | #Lorenz C, Lesimple P, Bukowiecki R, Zink A, Inak G, Mlody B, Singh M, Semtner M, Mah N, Auré K, Leong M, Zabiegalov O, Lyras EM, Pfiffer V, Fauler B, Eichhorst J, Wiesner B, Huebner N, Priller J, Mielke T, Meierhofer D, Izsvák Z, Meier JC, Bouillaud F, Adjaye J, Schuelke M, Wanker EE, Lombès A, Prigione A, (2017) "Human iPSC-Derived Neural Progenitors Are an Effective Drug Discovery Model for Neurological mtDNA Disorders." <i>Cell Stem Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132834 28132834]; doi: [https://dx.doi.org/10.1016/j.stem.2016.12.013 10.1016/j.stem.2016.12.013]; GPMDB: [http://gpmdb.org/data/keyword/28132834 14]. | ||
#Godfrey M, Touati SA, Kataria M, Jones A, Snijders AP, Uhlmann F, (2017) "PP2A<sup>Cdc55</sup> Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation." <i>Mol Cell</i> <b>65</b>(3):393–402.e3; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132839 28132839]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.12.018 10.1016/j.molcel.2016.12.018]; GPMDB: [http://gpmdb.org/data/keyword/28132839 120]. | #Godfrey M, Touati SA, Kataria M, Jones A, Snijders AP, Uhlmann F, (2017) "PP2A<sup>Cdc55</sup> Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation." <i>Mol Cell</i> <b>65</b>(3):393–402.e3; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132839 28132839]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.12.018 10.1016/j.molcel.2016.12.018]; GPMDB: [http://gpmdb.org/data/keyword/28132839 120]. | ||
#Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B, (2017) "Building ProteomeTools based on a complete synthetic human proteome." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28135259 28135259]; doi: [https://dx.doi.org/10.1038/nmeth.4153 10.1038/nmeth.4153]; GPMDB: [http://gpmdb.org/data/keyword/28135259 1095]. | #Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B, (2017) "Building ProteomeTools based on a complete synthetic human proteome." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28135259 28135259]; doi: [https://dx.doi.org/10.1038/nmeth.4153 10.1038/nmeth.4153]; GPMDB: [http://gpmdb.org/data/keyword/28135259 1095]. | ||
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#Park YJ, Koh J, Kwon JT, Park YS, Yang L, Cha S, (2017) "Uncovering stem cell differentiation factors for salivary gland regeneration by quantitative analysis of differential proteomes." <i>PLoS One</i> <b>12</b>(2):e0169677; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28158262 28158262]; doi: [https://dx.doi.org/10.1371/journal.pone.0169677 10.1371/journal.pone.0169677]; GPMDB: [http://gpmdb.org/data/keyword/28158262 2]. | #Park YJ, Koh J, Kwon JT, Park YS, Yang L, Cha S, (2017) "Uncovering stem cell differentiation factors for salivary gland regeneration by quantitative analysis of differential proteomes." <i>PLoS One</i> <b>12</b>(2):e0169677; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28158262 28158262]; doi: [https://dx.doi.org/10.1371/journal.pone.0169677 10.1371/journal.pone.0169677]; GPMDB: [http://gpmdb.org/data/keyword/28158262 2]. | ||
#Davis S, Charles PD, He L, Mowlds P, Kessler BM, Fischer R, (2017) "Expanding proteome coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) combined with broad specificity proteolysis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28164708 28164708]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00915 10.1021/acs.jproteome.6b00915]; GPMDB: [http://gpmdb.org/data/keyword/28164708 7]. | #Davis S, Charles PD, He L, Mowlds P, Kessler BM, Fischer R, (2017) "Expanding proteome coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) combined with broad specificity proteolysis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28164708 28164708]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00915 10.1021/acs.jproteome.6b00915]; GPMDB: [http://gpmdb.org/data/keyword/28164708 7]. | ||
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+ | #Kalkan T, Olova N, Roode M, Mulas C, Lee HJ, Nett I, Marks H, Walker R, Stunnenberg HG, Lilley KS, Nichols J, Reik W, Bertone P, Smith A, (2017) "Tracking the embryonic stem cell transition from ground state pluripotency." <i>Development</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28174249 28174249]; doi: [https://dx.doi.org/10.1242/dev.142711 10.1242/dev.142711]; GPMDB: [http://gpmdb.org/data/keyword/28174249 23]. | ||
+ | #Cantù C, Pagella P, Shajiei TD, Zimmerli D, Valenta T, Hausmann G, Basler K, Mitsiadis TA, (2017) "A cytoplasmic role of Wnt/β-catenin transcriptional cofactors Bcl9, Bcl9l, and Pygopus in tooth enamel formation." <i>Sci Signal</i> <b>10</b>(465):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28174279 28174279]; doi: [https://dx.doi.org/10.1126/scisignal.aah4598 10.1126/scisignal.aah4598]; GPMDB: [http://gpmdb.org/data/keyword/28174279 3]. | ||
#Massafra V, Milona A, Vos HR, Burgering BM, van Mil SW, (2017) "Quantitative liver proteomics identifies FGF19 targets that couple metabolism and proliferation." <i>PLoS One</i> <b>12</b>(2):e0171185; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28178326 28178326]; doi: [https://dx.doi.org/10.1371/journal.pone.0171185 10.1371/journal.pone.0171185]; GPMDB: [http://gpmdb.org/data/keyword/28178326 9]. | #Massafra V, Milona A, Vos HR, Burgering BM, van Mil SW, (2017) "Quantitative liver proteomics identifies FGF19 targets that couple metabolism and proliferation." <i>PLoS One</i> <b>12</b>(2):e0171185; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28178326 28178326]; doi: [https://dx.doi.org/10.1371/journal.pone.0171185 10.1371/journal.pone.0171185]; GPMDB: [http://gpmdb.org/data/keyword/28178326 9]. | ||
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#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]. | ||
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#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]. | ||
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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.
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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 5, 2017.