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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 November 6, 2016. |
#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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#Li X, Tran KM, Aziz KE, Sorokin AV, Chen J, Wang W, (2016) "Defining the Protein-Protein Interaction Network of the Human Protein Tyrosine Phosphatase Family." <i>Mol Cell Proteomics</i> <b>15</b>(9):3030–44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432908 27432908]; doi: [https://dx.doi.org/10.1074/mcp.M116.060277 10.1074/mcp.M116.060277]; GPMDB: [http://gpmdb.org/data/keyword/27432908 88]. | #Li X, Tran KM, Aziz KE, Sorokin AV, Chen J, Wang W, (2016) "Defining the Protein-Protein Interaction Network of the Human Protein Tyrosine Phosphatase Family." <i>Mol Cell Proteomics</i> <b>15</b>(9):3030–44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432908 27432908]; doi: [https://dx.doi.org/10.1074/mcp.M116.060277 10.1074/mcp.M116.060277]; GPMDB: [http://gpmdb.org/data/keyword/27432908 88]. | ||
#Suárez-Cortés P, Sharma V, Bertuccini L, Costa G, Bannerman NL, Rosa Sannella A, Williamson K, Klemba M, Levashina EA, Lasonder E, Alano P, (2016) "Comparative Proteomics and Functional Analysis Reveal a Role of Plasmodium falciparum Osmiophilic Bodies in Malaria Parasite Transmission." <i>Mol Cell Proteomics</i> <b>15</b>(10):3243–3255; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432909 27432909]; doi: [https://dx.doi.org/10.1074/mcp.M116.060681 10.1074/mcp.M116.060681]; GPMDB: [http://gpmdb.org/data/keyword/27432909 162]. | #Suárez-Cortés P, Sharma V, Bertuccini L, Costa G, Bannerman NL, Rosa Sannella A, Williamson K, Klemba M, Levashina EA, Lasonder E, Alano P, (2016) "Comparative Proteomics and Functional Analysis Reveal a Role of Plasmodium falciparum Osmiophilic Bodies in Malaria Parasite Transmission." <i>Mol Cell Proteomics</i> <b>15</b>(10):3243–3255; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432909 27432909]; doi: [https://dx.doi.org/10.1074/mcp.M116.060681 10.1074/mcp.M116.060681]; GPMDB: [http://gpmdb.org/data/keyword/27432909 162]. | ||
- | #Vandenbrouck Y, Lane L, Carapito C, Duek P, Rondel K, Bruley C, Macron C, Gonzalez de Peredo A, Couté Y, Chaoui K, Com E, Gateau A, Hesse AM, Marcellin M, Méar L, Mouton-Barbosa E, Robin T, Burlet-Schiltz O, Cianferani S, Ferro M, Fréour T, Lindskog C, Garin J, Pineau C, (2016) "Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27444420 27444420]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00400 10.1021/acs.jproteome.6b00400]; GPMDB: [http://gpmdb.org/data/keyword/27444420 108]. | + | #Vandenbrouck Y, Lane L, Carapito C, Duek P, Rondel K, Bruley C, Macron C, Gonzalez de Peredo A, Couté Y, Chaoui K, Com E, Gateau A, Hesse AM, Marcellin M, Méar L, Mouton-Barbosa E, Robin T, Burlet-Schiltz O, Cianferani S, Ferro M, Fréour T, Lindskog C, Garin J, Pineau C, (2016) "Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update." <i>J Proteome Res</i> <b>15</b>(11):3998–4019; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27444420 27444420]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00400 10.1021/acs.jproteome.6b00400]; GPMDB: [http://gpmdb.org/data/keyword/27444420 108]. |
#Martinez-Val A, Garcia F, Ximénez-Embún P, Ibarz N, Zarzuela E, Ruppen I, Mohammed S, Munoz J, (2016) "On the Statistical Significance of Compressed Ratios in Isobaric Labeling: A Cross-Platform Comparison." <i>J Proteome Res</i> <b>15</b>(9):3029–38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27452035 27452035]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00151 10.1021/acs.jproteome.6b00151]; GPMDB: [http://gpmdb.org/data/keyword/27452035 18]. | #Martinez-Val A, Garcia F, Ximénez-Embún P, Ibarz N, Zarzuela E, Ruppen I, Mohammed S, Munoz J, (2016) "On the Statistical Significance of Compressed Ratios in Isobaric Labeling: A Cross-Platform Comparison." <i>J Proteome Res</i> <b>15</b>(9):3029–38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27452035 27452035]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00151 10.1021/acs.jproteome.6b00151]; GPMDB: [http://gpmdb.org/data/keyword/27452035 18]. | ||
#Gautier EF, Ducamp S, Leduc M, Salnot V, Guillonneau F, Dussiot M, Hale J, Giarratana MC, Raimbault A, Douay L, Lacombe C, Mohandas N, Verdier F, Zermati Y, Mayeux P, (2016) "Comprehensive Proteomic Analysis of Human Erythropoiesis." <i>Cell Rep</i> <b>16</b>(5):1470–84; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27452463 27452463]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.06.085 10.1016/j.celrep.2016.06.085]; GPMDB: [http://gpmdb.org/data/keyword/27452463 235]. | #Gautier EF, Ducamp S, Leduc M, Salnot V, Guillonneau F, Dussiot M, Hale J, Giarratana MC, Raimbault A, Douay L, Lacombe C, Mohandas N, Verdier F, Zermati Y, Mayeux P, (2016) "Comprehensive Proteomic Analysis of Human Erythropoiesis." <i>Cell Rep</i> <b>16</b>(5):1470–84; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27452463 27452463]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.06.085 10.1016/j.celrep.2016.06.085]; GPMDB: [http://gpmdb.org/data/keyword/27452463 235]. | ||
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#Dobó J, Szakács D, Oroszlán G, Kortvely E, Kiss B, Boros E, Szász R, Závodszky P, Gál P, Pál G, (2016) "MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked." <i>Sci Rep</i> <b>6</b>:31877; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535802 27535802]; doi: [https://dx.doi.org/10.1038/srep31877 10.1038/srep31877]; GPMDB: [http://gpmdb.org/data/keyword/27535802 6]. | #Dobó J, Szakács D, Oroszlán G, Kortvely E, Kiss B, Boros E, Szász R, Závodszky P, Gál P, Pál G, (2016) "MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked." <i>Sci Rep</i> <b>6</b>:31877; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535802 27535802]; doi: [https://dx.doi.org/10.1038/srep31877 10.1038/srep31877]; GPMDB: [http://gpmdb.org/data/keyword/27535802 6]. | ||
#Zhang P, Karani R, Turner RL, Dufresne C, Ferri S, Van Eyk JE, Semba RD, (2016) "The proteome of normal human retrobulbar optic nerve and sclera." <i>Proteomics</i> <b>16</b>(19):2592–2596; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27538499 27538499]; doi: [https://dx.doi.org/10.1002/pmic.201600229 10.1002/pmic.201600229]; GPMDB: [http://gpmdb.org/data/keyword/27538499 60]. | #Zhang P, Karani R, Turner RL, Dufresne C, Ferri S, Van Eyk JE, Semba RD, (2016) "The proteome of normal human retrobulbar optic nerve and sclera." <i>Proteomics</i> <b>16</b>(19):2592–2596; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27538499 27538499]; doi: [https://dx.doi.org/10.1002/pmic.201600229 10.1002/pmic.201600229]; GPMDB: [http://gpmdb.org/data/keyword/27538499 60]. | ||
- | #Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP, (2016) "Integration of omic networks in a developmental atlas of maize." <i>Science</i> <b>353</b>(6301):814–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27540173 27540173]; doi: [https://dx.doi.org/10.1126/science.aag1125 10.1126/science.aag1125]; GPMDB: [http://gpmdb.org/data/keyword/27540173 | + | #Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP, (2016) "Integration of omic networks in a developmental atlas of maize." <i>Science</i> <b>353</b>(6301):814–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27540173 27540173]; doi: [https://dx.doi.org/10.1126/science.aag1125 10.1126/science.aag1125]; GPMDB: [http://gpmdb.org/data/keyword/27540173 10122]. |
#Xie Y, Wang J, Zhang Y, Liu X, Wang X, Liu K, Huang X, Wang Y, (2016) "Quantitative profiling of spreading-coupled protein tyrosine phosphorylation in migratory cells." <i>Sci Rep</i> <b>6</b>:31811; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554326 27554326]; doi: [https://dx.doi.org/10.1038/srep31811 10.1038/srep31811]; GPMDB: [http://gpmdb.org/data/keyword/27554326 6]. | #Xie Y, Wang J, Zhang Y, Liu X, Wang X, Liu K, Huang X, Wang Y, (2016) "Quantitative profiling of spreading-coupled protein tyrosine phosphorylation in migratory cells." <i>Sci Rep</i> <b>6</b>:31811; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554326 27554326]; doi: [https://dx.doi.org/10.1038/srep31811 10.1038/srep31811]; GPMDB: [http://gpmdb.org/data/keyword/27554326 6]. | ||
#He PH, Dong WX, Chu XL, Feng MG, Ying SH, (2016) "The cellular proteome is affected by a gelsolin (BbGEL1) during morphological transitions in aerobic surface versus liquid growth in the entomopathogenic fungus Beauveria bassiana." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554994 27554994]; doi: [https://dx.doi.org/10.1111/1462-2920.13500 10.1111/1462-2920.13500]; GPMDB: [http://gpmdb.org/data/keyword/27554994 34]. | #He PH, Dong WX, Chu XL, Feng MG, Ying SH, (2016) "The cellular proteome is affected by a gelsolin (BbGEL1) during morphological transitions in aerobic surface versus liquid growth in the entomopathogenic fungus Beauveria bassiana." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554994 27554994]; doi: [https://dx.doi.org/10.1111/1462-2920.13500 10.1111/1462-2920.13500]; GPMDB: [http://gpmdb.org/data/keyword/27554994 34]. | ||
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#Cassidy L, Prasse D, Linke D, Schmitz RA, Tholey A, (2016) "Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei." <i>J Proteome Res</i> <b>15</b>(10):3773–3783; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27557128 27557128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00569 10.1021/acs.jproteome.6b00569]; GPMDB: [http://gpmdb.org/data/keyword/27557128 6]. | #Cassidy L, Prasse D, Linke D, Schmitz RA, Tholey A, (2016) "Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei." <i>J Proteome Res</i> <b>15</b>(10):3773–3783; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27557128 27557128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00569 10.1021/acs.jproteome.6b00569]; GPMDB: [http://gpmdb.org/data/keyword/27557128 6]. | ||
#Häupl B, Ihling CH, Sinz A, (2016) "Protein Interaction Network of Human Protein Kinase D2 Revealed by Chemical Cross-Linking/Mass Spectrometry." <i>J Proteome Res</i> <b>15</b>(10):3686–3699; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27559607 27559607]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00513 10.1021/acs.jproteome.6b00513]; GPMDB: [http://gpmdb.org/data/keyword/27559607 81]. | #Häupl B, Ihling CH, Sinz A, (2016) "Protein Interaction Network of Human Protein Kinase D2 Revealed by Chemical Cross-Linking/Mass Spectrometry." <i>J Proteome Res</i> <b>15</b>(10):3686–3699; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27559607 27559607]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00513 10.1021/acs.jproteome.6b00513]; GPMDB: [http://gpmdb.org/data/keyword/27559607 81]. | ||
- | #Jiang Y, Lee J, Lee JH, Lee JW, Kim JH, Choi WH, Yoo YD, Cha-Molstad H, Kim BY, Kwon YT, Noh SA, Kim KP, Lee MJ, (2016) "The arginylation branch of the N-end rule pathway positively regulates cellular autophagic flux and clearance of proteotoxic proteins." <i>Autophagy</i> <b></b>: | + | #Jiang Y, Lee J, Lee JH, Lee JW, Kim JH, Choi WH, Yoo YD, Cha-Molstad H, Kim BY, Kwon YT, Noh SA, Kim KP, Lee MJ, (2016) "The arginylation branch of the N-end rule pathway positively regulates cellular autophagic flux and clearance of proteotoxic proteins." <i>Autophagy</i> <b>12</b>(11):2197–2212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27560450 27560450]; doi: [https://dx.doi.org/10.1080/15548627.2016.1222991 10.1080/15548627.2016.1222991]; GPMDB: [http://gpmdb.org/data/keyword/27560450 2]. |
#Ross SH, Rollings C, Anderson KE, Hawkins PT, Stephens LR, Cantrell DA, (2016) "Phosphoproteomic Analyses of Interleukin 2 Signaling Reveal Integrated JAK Kinase-Dependent and -Independent Networks in CD8(+) T Cells." <i>Immunity</i> <b>45</b>(3):685–700; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27566939 27566939]; doi: [https://dx.doi.org/10.1016/j.immuni.2016.07.022 10.1016/j.immuni.2016.07.022]; GPMDB: [http://gpmdb.org/data/keyword/27566939 208]. | #Ross SH, Rollings C, Anderson KE, Hawkins PT, Stephens LR, Cantrell DA, (2016) "Phosphoproteomic Analyses of Interleukin 2 Signaling Reveal Integrated JAK Kinase-Dependent and -Independent Networks in CD8(+) T Cells." <i>Immunity</i> <b>45</b>(3):685–700; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27566939 27566939]; doi: [https://dx.doi.org/10.1016/j.immuni.2016.07.022 10.1016/j.immuni.2016.07.022]; GPMDB: [http://gpmdb.org/data/keyword/27566939 208]. | ||
#Larsen SC, Sylvestersen KB, Mund A, Lyon D, Mullari M, Madsen MV, Daniel JA, Jensen LJ, Nielsen ML, (2016) "Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells." <i>Sci Signal</i> <b>9</b>(443):rs9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27577262 27577262]; doi: [https://dx.doi.org/10.1126/scisignal.aaf7329 10.1126/scisignal.aaf7329]; GPMDB: [http://gpmdb.org/data/keyword/27577262 10]. | #Larsen SC, Sylvestersen KB, Mund A, Lyon D, Mullari M, Madsen MV, Daniel JA, Jensen LJ, Nielsen ML, (2016) "Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells." <i>Sci Signal</i> <b>9</b>(443):rs9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27577262 27577262]; doi: [https://dx.doi.org/10.1126/scisignal.aaf7329 10.1126/scisignal.aaf7329]; GPMDB: [http://gpmdb.org/data/keyword/27577262 10]. | ||
#Delaveau T, Davoine D, Jolly A, Vallot A, Rouvière JO, Gerber A, Brochet S, Plessis M, Roquigny R, Merhej J, Leger T, Garcia C, Lelandais G, Laine E, Palancade B, Devaux F, Garcia M, (2016) "Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae." <i>Nucleic Acids Res</i> <b>44</b>(18):8826–8841; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27580715 27580715]; doi: [https://dx.doi.org/10.1093/nar/gkw732 10.1093/nar/gkw732]; GPMDB: [http://gpmdb.org/data/keyword/27580715 19]. | #Delaveau T, Davoine D, Jolly A, Vallot A, Rouvière JO, Gerber A, Brochet S, Plessis M, Roquigny R, Merhej J, Leger T, Garcia C, Lelandais G, Laine E, Palancade B, Devaux F, Garcia M, (2016) "Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae." <i>Nucleic Acids Res</i> <b>44</b>(18):8826–8841; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27580715 27580715]; doi: [https://dx.doi.org/10.1093/nar/gkw732 10.1093/nar/gkw732]; GPMDB: [http://gpmdb.org/data/keyword/27580715 19]. | ||
- | #Lee H, Chae S, Park J, Bae J, Go EB, Kim SJ, Kim H, Hwang D, Lee SW, Lee SY, (2016) "Comprehensive | + | #Lee H, Chae S, Park J, Bae J, Go EB, Kim SJ, Kim H, Hwang D, Lee SW, Lee SY, (2016) "Comprehensive Proteome Profiling of Platelet Identified a Protein Profile Predictive of Responses to An Antiplatelet Agent Sarpogrelate." <i>Mol Cell Proteomics</i> <b>15</b>(11):3461–3472; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27601597 27601597]; doi: [https://dx.doi.org/10.1074/mcp.M116.059154 10.1074/mcp.M116.059154]; GPMDB: [http://gpmdb.org/data/keyword/27601597 96]. |
- | #Treitz C, Enjalbert B, Portais JC, Letisse F, Tholey A, (2016) "Differential quantitative proteome analysis of Escherichia coli grown on acetate versus glucose." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27604403 27604403]; doi: [https://dx.doi.org/10.1002/pmic.201600303 10.1002/pmic.201600303]; GPMDB: [http://gpmdb.org/data/keyword/27604403 42]. | + | #Treitz C, Enjalbert B, Portais JC, Letisse F, Tholey A, (2016) "Differential quantitative proteome analysis of Escherichia coli grown on acetate versus glucose." <i>Proteomics</i> <b>16</b>(21):2742–2746; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27604403 27604403]; doi: [https://dx.doi.org/10.1002/pmic.201600303 10.1002/pmic.201600303]; GPMDB: [http://gpmdb.org/data/keyword/27604403 42]. |
#Mauri M, Kirchner M, Aharoni R, Ciolli Mattioli C, van den Bruck D, Gutkovitch N, Modepalli V, Selbach M, Moran Y, Chekulaeva M, (2016) "Conservation of miRNA-mediated silencing mechanisms across 600 million years of animal evolution." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27604873 27604873]; doi: [https://dx.doi.org/10.1093/nar/gkw792 10.1093/nar/gkw792]; GPMDB: [http://gpmdb.org/data/keyword/27604873 35]. | #Mauri M, Kirchner M, Aharoni R, Ciolli Mattioli C, van den Bruck D, Gutkovitch N, Modepalli V, Selbach M, Moran Y, Chekulaeva M, (2016) "Conservation of miRNA-mediated silencing mechanisms across 600 million years of animal evolution." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27604873 27604873]; doi: [https://dx.doi.org/10.1093/nar/gkw792 10.1093/nar/gkw792]; GPMDB: [http://gpmdb.org/data/keyword/27604873 35]. | ||
#Lee J, McKinney KQ, Pavlopoulos AJ, Han MH, Kim SH, Kim HJ, Hwang S, (2016) "Exosomal proteome analysis of cerebrospinal fluid detects biosignatures of neuromyelitis optica and multiple sclerosis." <i>Clin Chim Acta</i> <b>462</b>:118–126; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27609124 27609124]; doi: [https://dx.doi.org/10.1016/j.cca.2016.09.001 10.1016/j.cca.2016.09.001]; GPMDB: [http://gpmdb.org/data/keyword/27609124 24]. | #Lee J, McKinney KQ, Pavlopoulos AJ, Han MH, Kim SH, Kim HJ, Hwang S, (2016) "Exosomal proteome analysis of cerebrospinal fluid detects biosignatures of neuromyelitis optica and multiple sclerosis." <i>Clin Chim Acta</i> <b>462</b>:118–126; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27609124 27609124]; doi: [https://dx.doi.org/10.1016/j.cca.2016.09.001 10.1016/j.cca.2016.09.001]; GPMDB: [http://gpmdb.org/data/keyword/27609124 24]. | ||
#Subramanian S, Souleimanov A, Smith DL, (2016) "Proteomic Studies on the Effects of Lipo-Chitooligosaccharide and Thuricin 17 under Unstressed and Salt Stressed Conditions in Arabidopsis thaliana." <i>Front Plant Sci</i> <b>7</b>:1314; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27625672 27625672]; doi: [https://dx.doi.org/10.3389/fpls.2016.01314 10.3389/fpls.2016.01314]; GPMDB: [http://gpmdb.org/data/keyword/27625672 36]. | #Subramanian S, Souleimanov A, Smith DL, (2016) "Proteomic Studies on the Effects of Lipo-Chitooligosaccharide and Thuricin 17 under Unstressed and Salt Stressed Conditions in Arabidopsis thaliana." <i>Front Plant Sci</i> <b>7</b>:1314; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27625672 27625672]; doi: [https://dx.doi.org/10.3389/fpls.2016.01314 10.3389/fpls.2016.01314]; GPMDB: [http://gpmdb.org/data/keyword/27625672 36]. | ||
- | #Stroud DA, Surgenor EE, Formosa LE, Reljic B, Frazier AE, Dibley MG, Osellame LD, Stait T, Beilharz TH, Thorburn DR, Salim A, Ryan MT, (2016) "Accessory subunits are integral for assembly and function of human mitochondrial complex I." <i>Nature</i> <b>538</b>(7623):123–126; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27626371 27626371]; doi: [https://dx.doi.org/10.1038/nature19754 10.1038/nature19754]; GPMDB: [http://gpmdb.org/data/keyword/27626371 | + | #Stroud DA, Surgenor EE, Formosa LE, Reljic B, Frazier AE, Dibley MG, Osellame LD, Stait T, Beilharz TH, Thorburn DR, Salim A, Ryan MT, (2016) "Accessory subunits are integral for assembly and function of human mitochondrial complex I." <i>Nature</i> <b>538</b>(7623):123–126; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27626371 27626371]; doi: [https://dx.doi.org/10.1038/nature19754 10.1038/nature19754]; GPMDB: [http://gpmdb.org/data/keyword/27626371 10]. |
#Worah K, Mathan TS, Vu Manh TP, Keerthikumar S, Schreibelt G, Tel J, Duiveman-de Boer T, Sköld AE, van Spriel AB, de Vries IJ, Huynen MA, Wessels HJ, Gloerich J, Dalod M, Lasonder E, Figdor CG, Buschow SI, (2016) "Proteomics of Human Dendritic Cell Subsets Reveals Subset-Specific Surface Markers and Differential Inflammasome Function." <i>Cell Rep</i> <b>16</b>(11):2953–66; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27626665 27626665]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.08.023 10.1016/j.celrep.2016.08.023]; GPMDB: [http://gpmdb.org/data/keyword/27626665 719]. | #Worah K, Mathan TS, Vu Manh TP, Keerthikumar S, Schreibelt G, Tel J, Duiveman-de Boer T, Sköld AE, van Spriel AB, de Vries IJ, Huynen MA, Wessels HJ, Gloerich J, Dalod M, Lasonder E, Figdor CG, Buschow SI, (2016) "Proteomics of Human Dendritic Cell Subsets Reveals Subset-Specific Surface Markers and Differential Inflammasome Function." <i>Cell Rep</i> <b>16</b>(11):2953–66; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27626665 27626665]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.08.023 10.1016/j.celrep.2016.08.023]; GPMDB: [http://gpmdb.org/data/keyword/27626665 719]. | ||
#Bennike TB, Ellingsen T, Glerup H, Bonderup OK, Carlsen TG, Meyer MK, Bøgsted M, Christiansen G, Birkelund S, Andersen V, Stensballe A, (2016) "Proteome Analysis of Rheumatoid Arthritis Gut Mucosa." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27627584 27627584]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00598 10.1021/acs.jproteome.6b00598]; GPMDB: [http://gpmdb.org/data/keyword/27627584 33]. | #Bennike TB, Ellingsen T, Glerup H, Bonderup OK, Carlsen TG, Meyer MK, Bøgsted M, Christiansen G, Birkelund S, Andersen V, Stensballe A, (2016) "Proteome Analysis of Rheumatoid Arthritis Gut Mucosa." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27627584 27627584]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00598 10.1021/acs.jproteome.6b00598]; GPMDB: [http://gpmdb.org/data/keyword/27627584 33]. | ||
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#Athanason MG, Stevens SM Jr, Burkhardt BR, (2016) "Hepatic SILAC proteomic data from PANDER transgenic model." <i>Data Brief</i> <b>9</b>:159–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27642623 27642623]; doi: [https://dx.doi.org/10.1016/j.dib.2016.08.017 10.1016/j.dib.2016.08.017]; GPMDB: [http://gpmdb.org/data/keyword/27642623 18]. | #Athanason MG, Stevens SM Jr, Burkhardt BR, (2016) "Hepatic SILAC proteomic data from PANDER transgenic model." <i>Data Brief</i> <b>9</b>:159–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27642623 27642623]; doi: [https://dx.doi.org/10.1016/j.dib.2016.08.017 10.1016/j.dib.2016.08.017]; GPMDB: [http://gpmdb.org/data/keyword/27642623 18]. | ||
#Kubicek-Sutherland JZ, Lofton H, Vestergaard M, Hjort K, Ingmer H, Andersson DI, (2016) "Antimicrobial peptide exposure selects for Staphylococcus aureus resistance to human defence peptides." <i>J Antimicrob Chemother</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27650186 27650186]; doi: [https://dx.doi.org/10.1093/jac/dkw381 10.1093/jac/dkw381]; GPMDB: [http://gpmdb.org/data/keyword/27650186 42]. | #Kubicek-Sutherland JZ, Lofton H, Vestergaard M, Hjort K, Ingmer H, Andersson DI, (2016) "Antimicrobial peptide exposure selects for Staphylococcus aureus resistance to human defence peptides." <i>J Antimicrob Chemother</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27650186 27650186]; doi: [https://dx.doi.org/10.1093/jac/dkw381 10.1093/jac/dkw381]; GPMDB: [http://gpmdb.org/data/keyword/27650186 42]. | ||
- | #Goldman AR, Bitler BG, Schug Z, Conejo-Garcia JR, Zhang R, Speicher DW, (2016) "The Primary Effect on the Proteome of ARID1A- | + | #Goldman AR, Bitler BG, Schug Z, Conejo-Garcia JR, Zhang R, Speicher DW, (2016) "The Primary Effect on the Proteome of ARID1A-mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post-transcriptional Level." <i>Mol Cell Proteomics</i> <b>15</b>(11):3348–3360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27654507 27654507]; doi: [https://dx.doi.org/10.1074/mcp.M116.062539 10.1074/mcp.M116.062539]; GPMDB: [http://gpmdb.org/data/keyword/27654507 12]. |
#Radzikowski JL, Vedelaar S, Siegel D, Ortega ÁD, Schmidt A, Heinemann M, (2016) "Bacterial persistence is an active σS stress response to metabolic flux limitation." <i>Mol Syst Biol</i> <b>12</b>(9):882; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27655400 27655400]; GPMDB: [http://gpmdb.org/data/keyword/27655400 30]. | #Radzikowski JL, Vedelaar S, Siegel D, Ortega ÁD, Schmidt A, Heinemann M, (2016) "Bacterial persistence is an active σS stress response to metabolic flux limitation." <i>Mol Syst Biol</i> <b>12</b>(9):882; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27655400 27655400]; GPMDB: [http://gpmdb.org/data/keyword/27655400 30]. | ||
#Rose CM, Isasa M, Ordureau A, Prado MA, Beausoleil SA, Jedrychowski MP, Finley DJ, Harper JW, Gygi SP, (2016) "Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes." <i>Cell Syst</i> <b>3</b>(4):395–403.e4; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27667366 27667366]; doi: [https://dx.doi.org/10.1016/j.cels.2016.08.009 10.1016/j.cels.2016.08.009]; GPMDB: [http://gpmdb.org/data/keyword/27667366 26]. | #Rose CM, Isasa M, Ordureau A, Prado MA, Beausoleil SA, Jedrychowski MP, Finley DJ, Harper JW, Gygi SP, (2016) "Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes." <i>Cell Syst</i> <b>3</b>(4):395–403.e4; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27667366 27667366]; doi: [https://dx.doi.org/10.1016/j.cels.2016.08.009 10.1016/j.cels.2016.08.009]; GPMDB: [http://gpmdb.org/data/keyword/27667366 26]. | ||
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#Greenwood EJ, Matheson NJ, Wals K, van den Boomen DJ, Antrobus R, Williamson JC, Lehner PJ, (2016) "Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27690223 27690223]; doi: [https://dx.doi.org/10.7554/eLife.18296 10.7554/eLife.18296]; GPMDB: [http://gpmdb.org/data/keyword/27690223 10]. | #Greenwood EJ, Matheson NJ, Wals K, van den Boomen DJ, Antrobus R, Williamson JC, Lehner PJ, (2016) "Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27690223 27690223]; doi: [https://dx.doi.org/10.7554/eLife.18296 10.7554/eLife.18296]; GPMDB: [http://gpmdb.org/data/keyword/27690223 10]. | ||
#Gautier V, Cayrol C, Farache D, Roga S, Monsarrat B, Burlet-Schiltz O, Gonzalez de Peredo A, Girard JP, (2016) "Extracellular IL-33 cytokine, but not endogenous nuclear IL-33, regulates protein expression in endothelial cells." <i>Sci Rep</i> <b>6</b>:34255; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27694941 27694941]; doi: [https://dx.doi.org/10.1038/srep34255 10.1038/srep34255]; GPMDB: [http://gpmdb.org/data/keyword/27694941 252]. | #Gautier V, Cayrol C, Farache D, Roga S, Monsarrat B, Burlet-Schiltz O, Gonzalez de Peredo A, Girard JP, (2016) "Extracellular IL-33 cytokine, but not endogenous nuclear IL-33, regulates protein expression in endothelial cells." <i>Sci Rep</i> <b>6</b>:34255; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27694941 27694941]; doi: [https://dx.doi.org/10.1038/srep34255 10.1038/srep34255]; GPMDB: [http://gpmdb.org/data/keyword/27694941 252]. | ||
- | #Kwon OK, Kim | + | #Kwon OK, Kim S, Lee S, (2016) "Global proteomic analysis of lysine acetylation in zebrafish (Danio rerio) embryos." <i>Electrophoresis</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27696471 27696471]; doi: [https://dx.doi.org/10.1002/elps.201600210 10.1002/elps.201600210]; GPMDB: [http://gpmdb.org/data/keyword/27696471 2]. |
#Witzke KE, Rosowski K, Müller C, Ahrens M, Eisenacher M, Megger DA, Knobloch J, Koch AR, Bracht T, Sitek B, (2016) "Quantitative Secretome Analysis of Activated Jurkat Cells using Click Chemistry-Based Enrichment of Secreted Glycoproteins." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27696881 27696881]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00575 10.1021/acs.jproteome.6b00575]; GPMDB: [http://gpmdb.org/data/keyword/27696881 82]. | #Witzke KE, Rosowski K, Müller C, Ahrens M, Eisenacher M, Megger DA, Knobloch J, Koch AR, Bracht T, Sitek B, (2016) "Quantitative Secretome Analysis of Activated Jurkat Cells using Click Chemistry-Based Enrichment of Secreted Glycoproteins." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27696881 27696881]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00575 10.1021/acs.jproteome.6b00575]; GPMDB: [http://gpmdb.org/data/keyword/27696881 82]. | ||
#Baas R, Sijm A, van Teeffelen HA, van Es R, Vos HR, Timmers HT, (2016) "Quantitative Proteomics of the SMAD (Suppressor of Mothers Against Decapentaplegic) Transcription Factor Family Identifies Importin 5 as a Bone Morphogenic Protein Receptor-SMAD specific Importin." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27703004 27703004]; doi: [https://dx.doi.org/10.1074/jbc.M116.748582 10.1074/jbc.M116.748582]; GPMDB: [http://gpmdb.org/data/keyword/27703004 108]. | #Baas R, Sijm A, van Teeffelen HA, van Es R, Vos HR, Timmers HT, (2016) "Quantitative Proteomics of the SMAD (Suppressor of Mothers Against Decapentaplegic) Transcription Factor Family Identifies Importin 5 as a Bone Morphogenic Protein Receptor-SMAD specific Importin." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27703004 27703004]; doi: [https://dx.doi.org/10.1074/jbc.M116.748582 10.1074/jbc.M116.748582]; GPMDB: [http://gpmdb.org/data/keyword/27703004 108]. | ||
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#Sivadasan R, Hornburg D, Drepper C, Frank N, Jablonka S, Hansel A, Lojewski X, Sterneckert J, Hermann A, Shaw PJ, Ince PG, Mann M, Meissner F, Sendtner M, (2016) "C9ORF72 interaction with cofilin modulates actin dynamics in motor neurons." <i>Nat Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27723745 27723745]; doi: [https://dx.doi.org/10.1038/nn.4407 10.1038/nn.4407]; GPMDB: [http://gpmdb.org/data/keyword/27723745 6]. | #Sivadasan R, Hornburg D, Drepper C, Frank N, Jablonka S, Hansel A, Lojewski X, Sterneckert J, Hermann A, Shaw PJ, Ince PG, Mann M, Meissner F, Sendtner M, (2016) "C9ORF72 interaction with cofilin modulates actin dynamics in motor neurons." <i>Nat Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27723745 27723745]; doi: [https://dx.doi.org/10.1038/nn.4407 10.1038/nn.4407]; GPMDB: [http://gpmdb.org/data/keyword/27723745 6]. | ||
#Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE, (2016) "Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27726376 27726376]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00386 10.1021/acs.jproteome.6b00386]; GPMDB: [http://gpmdb.org/data/keyword/27726376 61]. | #Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE, (2016) "Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27726376 27726376]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00386 10.1021/acs.jproteome.6b00386]; GPMDB: [http://gpmdb.org/data/keyword/27726376 61]. | ||
- | #Al-Daghri NM, Alokail MS, Manousopoulou A, Heinson A, Al-Attas O, Al-Saleh Y, Sabico S, Yakout S, Woelk CH, Chrousos GP, Garbis SD, (2016) "Sex specific vitamin D effects on blood coagulation among overweight adults." <i>Eur J Clin Invest</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27727459 27727459]; doi: [https://dx.doi.org/10.1111/eci.12688 10.1111/eci.12688]; GPMDB: [http://gpmdb.org/data/keyword/27727459 50]. | + | #Al-Daghri NM, Alokail MS, Manousopoulou A, Heinson A, Al-Attas O, Al-Saleh Y, Sabico S, Yakout S, Woelk CH, Chrousos GP, Garbis SD, (2016) "Sex-specific vitamin D effects on blood coagulation among overweight adults." <i>Eur J Clin Invest</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27727459 27727459]; doi: [https://dx.doi.org/10.1111/eci.12688 10.1111/eci.12688]; GPMDB: [http://gpmdb.org/data/keyword/27727459 50]. |
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 pass our internal automated quality control tests 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 November 6, 2016.