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#Liu T, Tian CF, Chen WX, (2015) "Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase." <i>PLoS One</i> <b>10</b>(9):e0139143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26401955 26401955]; doi: [https://dx.doi.org/10.1371/journal.pone.0139143 10.1371/journal.pone.0139143]; GPMDB: [http://gpmdb.org/data/keyword/26401955 2]. | #Liu T, Tian CF, Chen WX, (2015) "Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase." <i>PLoS One</i> <b>10</b>(9):e0139143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26401955 26401955]; doi: [https://dx.doi.org/10.1371/journal.pone.0139143 10.1371/journal.pone.0139143]; GPMDB: [http://gpmdb.org/data/keyword/26401955 2]. | ||
#Li S, Dislich B, Brakebusch CH, Lichtenthaler SF, Brocker T, (2015) "Control of Homeostasis and Dendritic Cell Survival by the GTPase RhoA." <i>J Immunol</i> <b>195</b>(9):4244–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26408665 26408665]; doi: [https://dx.doi.org/10.4049/jimmunol.1500676 10.4049/jimmunol.1500676]; GPMDB: [http://gpmdb.org/data/keyword/26408665 60]. | #Li S, Dislich B, Brakebusch CH, Lichtenthaler SF, Brocker T, (2015) "Control of Homeostasis and Dendritic Cell Survival by the GTPase RhoA." <i>J Immunol</i> <b>195</b>(9):4244–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26408665 26408665]; doi: [https://dx.doi.org/10.4049/jimmunol.1500676 10.4049/jimmunol.1500676]; GPMDB: [http://gpmdb.org/data/keyword/26408665 60]. | ||
- | #Glatter T, Ahrné E, Schmidt A, (2015) "Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells." <i>J Proteome Res</i> <b>14</b>(11):4472–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412744 26412744]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00654 10.1021/acs.jproteome.5b00654]; GPMDB: [http://gpmdb.org/data/keyword/26412744 | + | #Glatter T, Ahrné E, Schmidt A, (2015) "Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells." <i>J Proteome Res</i> <b>14</b>(11):4472–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412744 26412744]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00654 10.1021/acs.jproteome.5b00654]; GPMDB: [http://gpmdb.org/data/keyword/26412744 678]. |
#Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A, (2015) "Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26418743 26418743]; doi: [https://dx.doi.org/10.7554/eLife.09579 10.7554/eLife.09579]; GPMDB: [http://gpmdb.org/data/keyword/26418743 12]. | #Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A, (2015) "Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26418743 26418743]; doi: [https://dx.doi.org/10.7554/eLife.09579 10.7554/eLife.09579]; GPMDB: [http://gpmdb.org/data/keyword/26418743 12]. | ||
#Gallart-Palau X, Serra A, Wong AS, Sandin S, Lai MK, Chen CP, Kon OL, Sze SK, (2015) "Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR)." <i>Sci Rep</i> <b>5</b>:14664; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26419333 26419333]; doi: [https://dx.doi.org/10.1038/srep14664 10.1038/srep14664]; GPMDB: [http://gpmdb.org/data/keyword/26419333 172]. | #Gallart-Palau X, Serra A, Wong AS, Sandin S, Lai MK, Chen CP, Kon OL, Sze SK, (2015) "Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR)." <i>Sci Rep</i> <b>5</b>:14664; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26419333 26419333]; doi: [https://dx.doi.org/10.1038/srep14664 10.1038/srep14664]; GPMDB: [http://gpmdb.org/data/keyword/26419333 172]. | ||
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#Sun S, Shah P, Eshghi ST, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Höti N, Zhang Z, Chan DW, Zhang H, (2016) "Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides." <i>Nat Biotechnol</i> <b>34</b>(1):84–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26571101 26571101]; doi: [https://dx.doi.org/10.1038/nbt.3403 10.1038/nbt.3403]; GPMDB: [http://gpmdb.org/data/keyword/26571101 55]. | #Sun S, Shah P, Eshghi ST, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Höti N, Zhang Z, Chan DW, Zhang H, (2016) "Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides." <i>Nat Biotechnol</i> <b>34</b>(1):84–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26571101 26571101]; doi: [https://dx.doi.org/10.1038/nbt.3403 10.1038/nbt.3403]; GPMDB: [http://gpmdb.org/data/keyword/26571101 55]. | ||
#Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H, Beli P, (2016) "ATR inhibition rewires cellular signaling networks induced by replication stress." <i>Proteomics</i> <b>16</b>(3):402–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26572502 26572502]; doi: [https://dx.doi.org/10.1002/pmic.201500172 10.1002/pmic.201500172]; GPMDB: [http://gpmdb.org/data/keyword/26572502 20]. | #Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H, Beli P, (2016) "ATR inhibition rewires cellular signaling networks induced by replication stress." <i>Proteomics</i> <b>16</b>(3):402–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26572502 26572502]; doi: [https://dx.doi.org/10.1002/pmic.201500172 10.1002/pmic.201500172]; GPMDB: [http://gpmdb.org/data/keyword/26572502 20]. | ||
- | #Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE, ( | + | #Lichtman JS, Alsentzer E, Jaffe M, Sprockett D, Masutani E, Ikwa E, Fragiadakis GK, Clifford D, Huang BE, Sonnenburg JL, Huang KC, Elias JE, (2016) "The effect of microbial colonization on the host proteome varies by gastrointestinal location." <i>ISME J</i> <b>10</b>(5):1170–81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26574685 26574685]; doi: [https://dx.doi.org/10.1038/ismej.2015.187 10.1038/ismej.2015.187]; GPMDB: [http://gpmdb.org/data/keyword/26574685 45]. |
#Latos PA, Sienerth AR, Murray A, Senner CE, Muto M, Ikawa M, Oxley D, Burge S, Cox BJ, Hemberger M, (2015) "Elf5-centered transcription factor hub controls trophoblast stem cell self-renewal and differentiation through stoichiometry-sensitive shifts in target gene networks." <i>Genes Dev</i> <b>29</b>(23):2435–48; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26584622 26584622]; doi: [https://dx.doi.org/10.1101/gad.268821.115 10.1101/gad.268821.115]; GPMDB: [http://gpmdb.org/data/keyword/26584622 6]. | #Latos PA, Sienerth AR, Murray A, Senner CE, Muto M, Ikawa M, Oxley D, Burge S, Cox BJ, Hemberger M, (2015) "Elf5-centered transcription factor hub controls trophoblast stem cell self-renewal and differentiation through stoichiometry-sensitive shifts in target gene networks." <i>Genes Dev</i> <b>29</b>(23):2435–48; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26584622 26584622]; doi: [https://dx.doi.org/10.1101/gad.268821.115 10.1101/gad.268821.115]; GPMDB: [http://gpmdb.org/data/keyword/26584622 6]. | ||
#Cundiff JK, McConnell EJ, Lohe KJ, Maria SD, McMahon RJ, Zhang Q, (2016) "Sensing Small Changes in Protein Abundance: Stimulation of Caco-2 Cells by Human Whey Proteins." <i>J Proteome Res</i> <b>15</b>(1):125–43; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26586228 26586228]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00597 10.1021/acs.jproteome.5b00597]; GPMDB: [http://gpmdb.org/data/keyword/26586228 16]. | #Cundiff JK, McConnell EJ, Lohe KJ, Maria SD, McMahon RJ, Zhang Q, (2016) "Sensing Small Changes in Protein Abundance: Stimulation of Caco-2 Cells by Human Whey Proteins." <i>J Proteome Res</i> <b>15</b>(1):125–43; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26586228 26586228]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00597 10.1021/acs.jproteome.5b00597]; GPMDB: [http://gpmdb.org/data/keyword/26586228 16]. | ||
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#Horton ER, Humphries JD, Stutchbury B, Jacquemet G, Ballestrem C, Barry ST, Humphries MJ, (2016) "Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition." <i>J Cell Biol</i> <b>212</b>(3):349–64; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26833789 26833789]; doi: [https://dx.doi.org/10.1083/jcb.201508080 10.1083/jcb.201508080]; GPMDB: [http://gpmdb.org/data/keyword/26833789 9]. | #Horton ER, Humphries JD, Stutchbury B, Jacquemet G, Ballestrem C, Barry ST, Humphries MJ, (2016) "Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition." <i>J Cell Biol</i> <b>212</b>(3):349–64; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26833789 26833789]; doi: [https://dx.doi.org/10.1083/jcb.201508080 10.1083/jcb.201508080]; GPMDB: [http://gpmdb.org/data/keyword/26833789 9]. | ||
#Zhang P, Kirby D, Dufresne C, Chen Y, Turner R, Ferri S, Edward DP, Van Eyk JE, Semba RD, (2016) "Defining the proteome of human iris, ciliary body, retinal pigment epithelium, and choroid." <i>Proteomics</i> <b>16</b>(7):1146–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26834087 26834087]; doi: [https://dx.doi.org/10.1002/pmic.201500188 10.1002/pmic.201500188]; GPMDB: [http://gpmdb.org/data/keyword/26834087 120]. | #Zhang P, Kirby D, Dufresne C, Chen Y, Turner R, Ferri S, Edward DP, Van Eyk JE, Semba RD, (2016) "Defining the proteome of human iris, ciliary body, retinal pigment epithelium, and choroid." <i>Proteomics</i> <b>16</b>(7):1146–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26834087 26834087]; doi: [https://dx.doi.org/10.1002/pmic.201500188 10.1002/pmic.201500188]; GPMDB: [http://gpmdb.org/data/keyword/26834087 120]. | ||
- | #Long B, Muhamad R, Yan G, Yu J, Fan Q, Wang Z, Li X, Purnomoadi A, Achmadi J, Yan X, (2016) "Quantitative proteomics analysis reveals glutamine deprivation activates fatty acid β-oxidation pathway in HepG2 cells." <i>Amino Acids</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26837383 26837383]; doi: [https://dx.doi.org/10.1007/s00726-016-2182-7 10.1007/s00726-016-2182-7]; GPMDB: [http://gpmdb.org/data/keyword/26837383 1]. | + | #Long B, Muhamad R, Yan G, Yu J, Fan Q, Wang Z, Li X, Purnomoadi A, Achmadi J, Yan X, (2016) "Quantitative proteomics analysis reveals glutamine deprivation activates fatty acid β-oxidation pathway in HepG2 cells." <i>Amino Acids</i> <b>48</b>(5):1297–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26837383 26837383]; doi: [https://dx.doi.org/10.1007/s00726-016-2182-7 10.1007/s00726-016-2182-7]; GPMDB: [http://gpmdb.org/data/keyword/26837383 1]. |
#Iwamoto N, D'Alessandro LA, Depner S, Hahn B, Kramer BA, Lucarelli P, Vlasov A, Stepath M, Böhm ME, Deharde D, Damm G, Seehofer D, Lehmann WD, Klingmüller U, Schilling M, (2016) "Context-specific flow through the MEK/ERK module produces cell- and ligand-specific patterns of ERK single and double phosphorylation." <i>Sci Signal</i> <b>9</b>(413):ra13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26838549 26838549]; doi: [https://dx.doi.org/10.1126/scisignal.aab1967 10.1126/scisignal.aab1967]; GPMDB: [http://gpmdb.org/data/keyword/26838549 66]. | #Iwamoto N, D'Alessandro LA, Depner S, Hahn B, Kramer BA, Lucarelli P, Vlasov A, Stepath M, Böhm ME, Deharde D, Damm G, Seehofer D, Lehmann WD, Klingmüller U, Schilling M, (2016) "Context-specific flow through the MEK/ERK module produces cell- and ligand-specific patterns of ERK single and double phosphorylation." <i>Sci Signal</i> <b>9</b>(413):ra13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26838549 26838549]; doi: [https://dx.doi.org/10.1126/scisignal.aab1967 10.1126/scisignal.aab1967]; GPMDB: [http://gpmdb.org/data/keyword/26838549 66]. | ||
#Huang H, Yoo CY, Bindbeutel R, Goldsworthy J, Tielking A, Alvarez S, Naldrett MJ, Evans BS, Chen M, Nusinow DA, (2016) "PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26839287 26839287]; doi: [https://dx.doi.org/10.7554/eLife.13292 10.7554/eLife.13292]; GPMDB: [http://gpmdb.org/data/keyword/26839287 9]. | #Huang H, Yoo CY, Bindbeutel R, Goldsworthy J, Tielking A, Alvarez S, Naldrett MJ, Evans BS, Chen M, Nusinow DA, (2016) "PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26839287 26839287]; doi: [https://dx.doi.org/10.7554/eLife.13292 10.7554/eLife.13292]; GPMDB: [http://gpmdb.org/data/keyword/26839287 9]. | ||
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#Zilkenat S, Franz-Wachtel M, Stierhof YD, Galan JE, Macek B, Wagner S, (2016) "Determination of the stoichiometry of the complete bacterial type III secretion needle complex using a combined quantitative proteomic approach." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26900162 26900162]; doi: [https://dx.doi.org/10.1074/mcp.M115.056598 10.1074/mcp.M115.056598]; GPMDB: [http://gpmdb.org/data/keyword/26900162 18]. | #Zilkenat S, Franz-Wachtel M, Stierhof YD, Galan JE, Macek B, Wagner S, (2016) "Determination of the stoichiometry of the complete bacterial type III secretion needle complex using a combined quantitative proteomic approach." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26900162 26900162]; doi: [https://dx.doi.org/10.1074/mcp.M115.056598 10.1074/mcp.M115.056598]; GPMDB: [http://gpmdb.org/data/keyword/26900162 18]. | ||
#Zhao L, Chen Y, Bajaj AO, Eblimit A, Xu M, Soens ZT, Wang F, Ge Z, Jung SY, He F, Li Y, Wensel TG, Qin J, Chen R, (2016) "Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes." <i>Genome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912414 26912414]; doi: [https://dx.doi.org/10.1101/gr.198911.115 10.1101/gr.198911.115]; GPMDB: [http://gpmdb.org/data/keyword/26912414 26]. | #Zhao L, Chen Y, Bajaj AO, Eblimit A, Xu M, Soens ZT, Wang F, Ge Z, Jung SY, He F, Li Y, Wensel TG, Qin J, Chen R, (2016) "Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes." <i>Genome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912414 26912414]; doi: [https://dx.doi.org/10.1101/gr.198911.115 10.1101/gr.198911.115]; GPMDB: [http://gpmdb.org/data/keyword/26912414 26]. | ||
- | #Abelin JG, Patel J, Lu X, Feeney CM, Fagbami L, Creech AL, Hu R, Lam D, Davison D, Pino L, Qiao JW, Kuhn E, Officer A, Li J, Abbatiello S, Subramanian A, Sidman R, Snyder EY, Carr SA, Jaffe JD, (2016) "Reduced-representation phosphosignatures measured by quantitative targeted MS capture cellular states and enable large-scale comparison of drug-induced phenotypes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912667 26912667]; doi: [https://dx.doi.org/10.1074/mcp.M116.058354 10.1074/mcp.M116.058354]; GPMDB: [http://gpmdb.org/data/keyword/26912667 | + | #Abelin JG, Patel J, Lu X, Feeney CM, Fagbami L, Creech AL, Hu R, Lam D, Davison D, Pino L, Qiao JW, Kuhn E, Officer A, Li J, Abbatiello S, Subramanian A, Sidman R, Snyder EY, Carr SA, Jaffe JD, (2016) "Reduced-representation phosphosignatures measured by quantitative targeted MS capture cellular states and enable large-scale comparison of drug-induced phenotypes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912667 26912667]; doi: [https://dx.doi.org/10.1074/mcp.M116.058354 10.1074/mcp.M116.058354]; GPMDB: [http://gpmdb.org/data/keyword/26912667 4]. |
#Chen JX, Cipriani PG, Mecenas D, Polanowska J, Piano F, Gunsalus KC, Selbach M, (2016) "In vivo interaction proteomics in C. elegans embryos provides new insights into P granule dynamics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912668 26912668]; doi: [https://dx.doi.org/10.1074/mcp.M115.053975 10.1074/mcp.M115.053975]; GPMDB: [http://gpmdb.org/data/keyword/26912668 66]. | #Chen JX, Cipriani PG, Mecenas D, Polanowska J, Piano F, Gunsalus KC, Selbach M, (2016) "In vivo interaction proteomics in C. elegans embryos provides new insights into P granule dynamics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26912668 26912668]; doi: [https://dx.doi.org/10.1074/mcp.M115.053975 10.1074/mcp.M115.053975]; GPMDB: [http://gpmdb.org/data/keyword/26912668 66]. | ||
#Mostafa I, Zhu N, Yoo MJ, Balmant KM, Misra BB, Dufresne C, Abou-Hashem M, Chen S, El-Domiaty M, (2016) "New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants." <i>J Proteomics</i> <b>138</b>:1–19; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26915584 26915584]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.012 10.1016/j.jprot.2016.02.012]; GPMDB: [http://gpmdb.org/data/keyword/26915584 24]. | #Mostafa I, Zhu N, Yoo MJ, Balmant KM, Misra BB, Dufresne C, Abou-Hashem M, Chen S, El-Domiaty M, (2016) "New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants." <i>J Proteomics</i> <b>138</b>:1–19; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26915584 26915584]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.012 10.1016/j.jprot.2016.02.012]; GPMDB: [http://gpmdb.org/data/keyword/26915584 24]. | ||
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#Xu G, Pattamatta A, Hildago R, Pace MC, Brown H, Borchelt DR, (2016) "Vulnerability of newly synthesized proteins to proteostasis stress." <i>J Cell Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27026526 27026526]; doi: [https://dx.doi.org/10.1242/jcs.176479 10.1242/jcs.176479]; GPMDB: [http://gpmdb.org/data/keyword/27026526 55]. | #Xu G, Pattamatta A, Hildago R, Pace MC, Brown H, Borchelt DR, (2016) "Vulnerability of newly synthesized proteins to proteostasis stress." <i>J Cell Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27026526 27026526]; doi: [https://dx.doi.org/10.1242/jcs.176479 10.1242/jcs.176479]; GPMDB: [http://gpmdb.org/data/keyword/27026526 55]. | ||
#Goldman-Pinkovich A, Balno C, Strasser R, Zeituni-Molad M, Bendelak K, Rentsch D, Ephros M, Wiese M, Jardim A, Myler PJ, Zilberstein D, (2016) "An Arginine Deprivation Response Pathway Is Induced in Leishmania during Macrophage Invasion." <i>PLoS Pathog</i> <b>12</b>(4):e1005494; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27043018 27043018]; doi: [https://dx.doi.org/10.1371/journal.ppat.1005494 10.1371/journal.ppat.1005494]; GPMDB: [http://gpmdb.org/data/keyword/27043018 8]. | #Goldman-Pinkovich A, Balno C, Strasser R, Zeituni-Molad M, Bendelak K, Rentsch D, Ephros M, Wiese M, Jardim A, Myler PJ, Zilberstein D, (2016) "An Arginine Deprivation Response Pathway Is Induced in Leishmania during Macrophage Invasion." <i>PLoS Pathog</i> <b>12</b>(4):e1005494; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27043018 27043018]; doi: [https://dx.doi.org/10.1371/journal.ppat.1005494 10.1371/journal.ppat.1005494]; GPMDB: [http://gpmdb.org/data/keyword/27043018 8]. | ||
- | #Salvetti A, Couté Y, Epstein A, Arata L, Kraut A, Navratil V, Bouvet P, Greco A, (2016) "Nuclear | + | #Salvetti A, Couté Y, Epstein A, Arata L, Kraut A, Navratil V, Bouvet P, Greco A, (2016) "Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27049334 27049334]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00126 10.1021/acs.jproteome.6b00126]; GPMDB: [http://gpmdb.org/data/keyword/27049334 7]. |
#Slomnicki L, Malinowska A, Kistowski M, Palusinski A, Zheng JJ, Sepp M, Timmusk T, Dadlez M, Hetman M, (2016) "Nucleolar enrichment of brain proteins with critical roles in human neurodevelopment." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27053602 27053602]; doi: [https://dx.doi.org/10.1074/mcp.M115.051920 10.1074/mcp.M115.051920]; GPMDB: [http://gpmdb.org/data/keyword/27053602 18]. | #Slomnicki L, Malinowska A, Kistowski M, Palusinski A, Zheng JJ, Sepp M, Timmusk T, Dadlez M, Hetman M, (2016) "Nucleolar enrichment of brain proteins with critical roles in human neurodevelopment." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27053602 27053602]; doi: [https://dx.doi.org/10.1074/mcp.M115.051920 10.1074/mcp.M115.051920]; GPMDB: [http://gpmdb.org/data/keyword/27053602 18]. | ||
#Liberton M, Saha R, Jacobs JM, Nguyen AY, Gritsenko MA, Smith RD, Koppenaal DW, Pakrasi HB, (2016) "Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27056914 27056914]; doi: [https://dx.doi.org/10.1074/mcp.M115.057240 10.1074/mcp.M115.057240]; GPMDB: [http://gpmdb.org/data/keyword/27056914 2]. | #Liberton M, Saha R, Jacobs JM, Nguyen AY, Gritsenko MA, Smith RD, Koppenaal DW, Pakrasi HB, (2016) "Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27056914 27056914]; doi: [https://dx.doi.org/10.1074/mcp.M115.057240 10.1074/mcp.M115.057240]; GPMDB: [http://gpmdb.org/data/keyword/27056914 2]. | ||
- | #Kähne T, Richter S, Kolodziej A, Smalla KH, Pielot R, Engler A, Ohl FW, Dieterich DC, Seidenbecher C, Tischmeyer W, Naumann M, Gundelfinger ED, (2016) "Proteome rearrangements after auditory learning: high-resolution profiling of synapse-enriched protein fractions from mouse brain." <i>J Neurochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27062398 27062398]; doi: [https://dx.doi.org/10.1111/jnc.13636 10.1111/jnc.13636]; GPMDB: [http://gpmdb.org/data/keyword/27062398 | + | #Kähne T, Richter S, Kolodziej A, Smalla KH, Pielot R, Engler A, Ohl FW, Dieterich DC, Seidenbecher C, Tischmeyer W, Naumann M, Gundelfinger ED, (2016) "Proteome rearrangements after auditory learning: high-resolution profiling of synapse-enriched protein fractions from mouse brain." <i>J Neurochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27062398 27062398]; doi: [https://dx.doi.org/10.1111/jnc.13636 10.1111/jnc.13636]; GPMDB: [http://gpmdb.org/data/keyword/27062398 15]. |
- | #Drabovich AP, Pavlou MP, Schiza C, Diamandis EP, (2016) "Dynamics of protein expression reveals primary targets and secondary messengers of estrogen receptor alpha signaling in MCF-7 breast cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067054 27067054]; doi: [https://dx.doi.org/10.1074/mcp.M115.057257 10.1074/mcp.M115.057257]; GPMDB: [http://gpmdb.org/data/keyword/27067054 | + | #Hoernstein SN, Mueller SJ, Fiedler K, Schuelke M, Vanselow JT, Schuessele C, Lang D, Nitschke R, Igloi GL, Schlosser A, Reski R, (2016) "Identification of targets and interaction partners of arginyl-tRNA protein transferase in the moss Physcomitrella patens." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067052 27067052]; doi: [https://dx.doi.org/10.1074/mcp.M115.057190 10.1074/mcp.M115.057190]; GPMDB: [http://gpmdb.org/data/keyword/27067052 90]. |
- | #Sarhan AR, Patel TR, Creese AJ, Tomlinson MG, Hellberg C, Heath JK, Hotchin NA, Cunningham DL, (2016) "Regulation of platelet derived growth factor signalling by LAR protein tyrosine phosphatase: a quantitative phosphoproteomics study." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27074791 27074791]; doi: [https://dx.doi.org/10.1074/mcp.M115.053652 10.1074/mcp.M115.053652]; GPMDB: [http://gpmdb.org/data/keyword/27074791 | + | #Drabovich AP, Pavlou MP, Schiza C, Diamandis EP, (2016) "Dynamics of protein expression reveals primary targets and secondary messengers of estrogen receptor alpha signaling in MCF-7 breast cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067054 27067054]; doi: [https://dx.doi.org/10.1074/mcp.M115.057257 10.1074/mcp.M115.057257]; GPMDB: [http://gpmdb.org/data/keyword/27067054 12]. |
+ | #Osinalde N, Mitxelena J, Sanchez-Quiles V, Akimov V, Aloria K, Arizmendi JM, Zubiaga AM, Blagoev B, Kratchmarova I, (2016) "Nuclear phosphoproteomic screen uncovers ACLY as mediator of IL-2-induced proliferation of CD4+ T-lymphocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067055 27067055]; doi: [https://dx.doi.org/10.1074/mcp.M115.057158 10.1074/mcp.M115.057158]; GPMDB: [http://gpmdb.org/data/keyword/27067055 18]. | ||
+ | #Xu B, Tian R, Wang X, Zhan S, Wang R, Guo Y, Ge W, (2016) "Protein profile changes in the frontotemporal lobes in human severe traumatic brain injury." <i>Brain Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067185 27067185]; doi: [https://dx.doi.org/10.1016/j.brainres.2016.04.008 10.1016/j.brainres.2016.04.008]; GPMDB: [http://gpmdb.org/data/keyword/27067185 20]. | ||
+ | #Rider MA, Hurwitz SN, Meckes DG Jr, (2016) "ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles." <i>Sci Rep</i> <b>6</b>:23978; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27068479 27068479]; doi: [https://dx.doi.org/10.1038/srep23978 10.1038/srep23978]; GPMDB: [http://gpmdb.org/data/keyword/27068479 3]. | ||
+ | #Sarhan AR, Patel TR, Creese AJ, Tomlinson MG, Hellberg C, Heath JK, Hotchin NA, Cunningham DL, (2016) "Regulation of platelet derived growth factor signalling by LAR protein tyrosine phosphatase: a quantitative phosphoproteomics study." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27074791 27074791]; doi: [https://dx.doi.org/10.1074/mcp.M115.053652 10.1074/mcp.M115.053652]; GPMDB: [http://gpmdb.org/data/keyword/27074791 17]. | ||
+ | #Arts IS, Vertommen D, Baldin F, Laloux G, Collet JF, (2016) "Comprehensively characterizing the thioredoxin interactome in vivo highlights the central role played by this ubiquitous oxidoreductase in redox control." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27081212 27081212]; doi: [https://dx.doi.org/10.1074/mcp.M115.056440 10.1074/mcp.M115.056440]; GPMDB: [http://gpmdb.org/data/keyword/27081212 103]. | ||
+ | #Tape CJ, Ling S, Dimitriadi M, McMahon KM, Worboys JD, Leong HS, Norrie IC, Miller CJ, Poulogiannis G, Lauffenburger DA, Jørgensen C, (2016) "Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation." <i>Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27087446 27087446]; doi: [https://dx.doi.org/10.1016/j.cell.2016.03.029 10.1016/j.cell.2016.03.029]; GPMDB: [http://gpmdb.org/data/keyword/27087446 274]. |
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 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 18, 2016.