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==Data from publications== | ==Data from publications== | ||
- | 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 July | + | 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 July 24, 2016. |
#Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." <i>Infect Immun</i> <b>57</b>(3):999–1001; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2645217 2645217]; GPMDB: [http://gpmdb.org/data/keyword/2645217 66]. | #Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." <i>Infect Immun</i> <b>57</b>(3):999–1001; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2645217 2645217]; GPMDB: [http://gpmdb.org/data/keyword/2645217 66]. | ||
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#Kieselbach T, Zijnge V, Granström E, Oscarsson J, (2015) "Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles." <i>PLoS One</i> <b>10</b>(9):e0138591; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26381655 26381655]; doi: [https://dx.doi.org/10.1371/journal.pone.0138591 10.1371/journal.pone.0138591]; GPMDB: [http://gpmdb.org/data/keyword/26381655 5]. | #Kieselbach T, Zijnge V, Granström E, Oscarsson J, (2015) "Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles." <i>PLoS One</i> <b>10</b>(9):e0138591; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26381655 26381655]; doi: [https://dx.doi.org/10.1371/journal.pone.0138591 10.1371/journal.pone.0138591]; GPMDB: [http://gpmdb.org/data/keyword/26381655 5]. | ||
#Goris T, Schiffmann CL, Gadkari J, Schubert T, Seifert J, Jehmlich N, von Bergen M, Diekert G, (2015) "Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates." <i>Sci Rep</i> <b>5</b>:13794; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26387727 26387727]; doi: [https://dx.doi.org/10.1038/srep13794 10.1038/srep13794]; GPMDB: [http://gpmdb.org/data/keyword/26387727 36]. | #Goris T, Schiffmann CL, Gadkari J, Schubert T, Seifert J, Jehmlich N, von Bergen M, Diekert G, (2015) "Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates." <i>Sci Rep</i> <b>5</b>:13794; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26387727 26387727]; doi: [https://dx.doi.org/10.1038/srep13794 10.1038/srep13794]; GPMDB: [http://gpmdb.org/data/keyword/26387727 36]. | ||
- | #Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R, (2015) "Kinome-wide decoding of network-attacking mutations rewiring cancer signaling." <i>Cell</i> <b>163</b>(1):202–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26388441 26388441]; doi: [https://dx.doi.org/10.1016/j.cell.2015.08.056 10.1016/j.cell.2015.08.056]; GPMDB: [http://gpmdb.org/data/keyword/26388441 | + | #Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R, (2015) "Kinome-wide decoding of network-attacking mutations rewiring cancer signaling." <i>Cell</i> <b>163</b>(1):202–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26388441 26388441]; doi: [https://dx.doi.org/10.1016/j.cell.2015.08.056 10.1016/j.cell.2015.08.056]; GPMDB: [http://gpmdb.org/data/keyword/26388441 8]. |
#Paulo JA, O'Connell JD, Gaun A, Gygi SP, (2015) "Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae." <i>Mol Biol Cell</i> <b>26</b>(22):4063–74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26399295 26399295]; doi: [https://dx.doi.org/10.1091/mbc.E15-07-0499 10.1091/mbc.E15-07-0499]; GPMDB: [http://gpmdb.org/data/keyword/26399295 1]. | #Paulo JA, O'Connell JD, Gaun A, Gygi SP, (2015) "Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae." <i>Mol Biol Cell</i> <b>26</b>(22):4063–74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26399295 26399295]; doi: [https://dx.doi.org/10.1091/mbc.E15-07-0499 10.1091/mbc.E15-07-0499]; GPMDB: [http://gpmdb.org/data/keyword/26399295 1]. | ||
#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 794]. |
#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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#Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE, (2016) "miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells." <i>Cancer Cell</i> <b>29</b>(2):214–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832662 26832662]; doi: [https://dx.doi.org/10.1016/j.ccell.2015.12.011 10.1016/j.ccell.2015.12.011]; GPMDB: [http://gpmdb.org/data/keyword/26832662 72]. | #Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE, (2016) "miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells." <i>Cancer Cell</i> <b>29</b>(2):214–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832662 26832662]; doi: [https://dx.doi.org/10.1016/j.ccell.2015.12.011 10.1016/j.ccell.2015.12.011]; GPMDB: [http://gpmdb.org/data/keyword/26832662 72]. | ||
#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 | + | #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 180]. |
#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]. | #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]. | ||
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#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> <b>15</b>(6):2021–32; 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> <b>15</b>(6):2021–32; 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> <b>138</b>(1):124–38; 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]. | #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> <b>138</b>(1):124–38; 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]. | ||
+ | #Litholdo CG Jr, Parker BL, Eamens AL, Larsen MR, Cordwell SJ, Waterhouse PM, (2016) "Proteomic Identification of Putative MicroRNA394 Target Genes in Arabidopsis thaliana Identifies Major Latex Protein Family Members Critical for Normal Development." <i>Mol Cell Proteomics</i> <b>15</b>(6):2033–47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27067051 27067051]; doi: [https://dx.doi.org/10.1074/mcp.M115.053124 10.1074/mcp.M115.053124]; GPMDB: [http://gpmdb.org/data/keyword/27067051 21]. | ||
#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> <b>15</b>(6):1808–22; 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 134]. | #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> <b>15</b>(6):1808–22; 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 134]. | ||
#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> <b>15</b>(6):2093–107; 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]. | #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> <b>15</b>(6):2093–107; 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]. | ||
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#Liang W, Ward LJ, Karlsson H, Ljunggren SA, Li W, Lindahl M, Yuan XM, (2016) "Distinctive proteomic profiles among different regions of human carotid plaques in men and women." <i>Sci Rep</i> <b>6</b>:26231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27198765 27198765]; doi: [https://dx.doi.org/10.1038/srep26231 10.1038/srep26231]; GPMDB: [http://gpmdb.org/data/keyword/27198765 60]. | #Liang W, Ward LJ, Karlsson H, Ljunggren SA, Li W, Lindahl M, Yuan XM, (2016) "Distinctive proteomic profiles among different regions of human carotid plaques in men and women." <i>Sci Rep</i> <b>6</b>:26231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27198765 27198765]; doi: [https://dx.doi.org/10.1038/srep26231 10.1038/srep26231]; GPMDB: [http://gpmdb.org/data/keyword/27198765 60]. | ||
#Virant-Klun I, Leicht S, Hughes C, Krijgsveld J, (2016) "Identification of maturation-specific proteins by single-cell proteomics of human oocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27215607 27215607]; doi: [https://dx.doi.org/10.1074/mcp.M115.056887 10.1074/mcp.M115.056887]; GPMDB: [http://gpmdb.org/data/keyword/27215607 18]. | #Virant-Klun I, Leicht S, Hughes C, Krijgsveld J, (2016) "Identification of maturation-specific proteins by single-cell proteomics of human oocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27215607 27215607]; doi: [https://dx.doi.org/10.1074/mcp.M115.056887 10.1074/mcp.M115.056887]; GPMDB: [http://gpmdb.org/data/keyword/27215607 18]. | ||
- | #Yu J, Storer BE, Kushekhar K, Abu Zaid M, Zhang Q, Gafken PR, Ogata Y, Martin PJ, Flowers ME, Hansen JA, Arora M, Cutler C, Jagasia M, Pidala J, Hamilton BK, Chen GL, Pusic I, Lee SJ, Paczesny S, (2016) "Biomarker Panel for Chronic Graft-Versus-Host Disease." <i>J Clin Oncol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27217465 27217465]; doi: [https://dx.doi.org/10.1200/JCO.2015.65.9615 10.1200/JCO.2015.65.9615]; GPMDB: [http://gpmdb.org/data/keyword/27217465 3]. | + | #Yu J, Storer BE, Kushekhar K, Abu Zaid M, Zhang Q, Gafken PR, Ogata Y, Martin PJ, Flowers ME, Hansen JA, Arora M, Cutler C, Jagasia M, Pidala J, Hamilton BK, Chen GL, Pusic I, Lee SJ, Paczesny S, (2016) "Biomarker Panel for Chronic Graft-Versus-Host Disease." <i>J Clin Oncol</i> <b>34</b>(22):2583–90; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27217465 27217465]; doi: [https://dx.doi.org/10.1200/JCO.2015.65.9615 10.1200/JCO.2015.65.9615]; GPMDB: [http://gpmdb.org/data/keyword/27217465 3]. |
#Wang B, Pfeiffer MJ, Drexler HC, Fuellen G, Boiani M, (2016) "Proteomic Analysis of Mouse Oocytes Identifies PRMT7 as a Reprogramming Factor that Replaces SOX2 in the Induction of Pluripotent Stem Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27225728 27225728]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01083 10.1021/acs.jproteome.5b01083]; GPMDB: [http://gpmdb.org/data/keyword/27225728 14]. | #Wang B, Pfeiffer MJ, Drexler HC, Fuellen G, Boiani M, (2016) "Proteomic Analysis of Mouse Oocytes Identifies PRMT7 as a Reprogramming Factor that Replaces SOX2 in the Induction of Pluripotent Stem Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27225728 27225728]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01083 10.1021/acs.jproteome.5b01083]; GPMDB: [http://gpmdb.org/data/keyword/27225728 14]. | ||
#Lodrini M, Poschmann G, Schmidt V, Wünschel J, Dreidax D, Witt O, Höfer T, Meyer HE, Stühler K, Eggert A, Deubzer HE, (2016) "Minichromosome Maintenance Complex Is a Critical Node in the miR-183 Signaling Network of MYCN-Amplified Neuroblastoma Cells." <i>J Proteome Res</i> <b>15</b>(7):2178–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27239679 27239679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00134 10.1021/acs.jproteome.6b00134]; GPMDB: [http://gpmdb.org/data/keyword/27239679 12]. | #Lodrini M, Poschmann G, Schmidt V, Wünschel J, Dreidax D, Witt O, Höfer T, Meyer HE, Stühler K, Eggert A, Deubzer HE, (2016) "Minichromosome Maintenance Complex Is a Critical Node in the miR-183 Signaling Network of MYCN-Amplified Neuroblastoma Cells." <i>J Proteome Res</i> <b>15</b>(7):2178–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27239679 27239679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00134 10.1021/acs.jproteome.6b00134]; GPMDB: [http://gpmdb.org/data/keyword/27239679 12]. | ||
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#Prendergast L, Müller S, Liu Y, Huang H, Dingli F, Loew D, Vassias I, Patel DJ, Sullivan KF, Almouzni G, (2016) "The CENP-T/-W complex is a binding partner of the histone chaperone FACT." <i>Genes Dev</i> <b>30</b>(11):1313–26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27284163 27284163]; doi: [https://dx.doi.org/10.1101/gad.275073.115 10.1101/gad.275073.115]; GPMDB: [http://gpmdb.org/data/keyword/27284163 47]. | #Prendergast L, Müller S, Liu Y, Huang H, Dingli F, Loew D, Vassias I, Patel DJ, Sullivan KF, Almouzni G, (2016) "The CENP-T/-W complex is a binding partner of the histone chaperone FACT." <i>Genes Dev</i> <b>30</b>(11):1313–26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27284163 27284163]; doi: [https://dx.doi.org/10.1101/gad.275073.115 10.1101/gad.275073.115]; GPMDB: [http://gpmdb.org/data/keyword/27284163 47]. | ||
#Wiśniewski JR, Mann M, (2016) "A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting." <i>J Proteome Res</i> <b>15</b>(7):2321–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27297043 27297043]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00403 10.1021/acs.jproteome.6b00403]; GPMDB: [http://gpmdb.org/data/keyword/27297043 64]. | #Wiśniewski JR, Mann M, (2016) "A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting." <i>J Proteome Res</i> <b>15</b>(7):2321–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27297043 27297043]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00403 10.1021/acs.jproteome.6b00403]; GPMDB: [http://gpmdb.org/data/keyword/27297043 64]. | ||
+ | #Narasimhan PB, Bennuru S, Meng Z, Cotton RN, Elliott KR, Ganesan S, McDonald-Fleming R, Veenstra TD, Nutman TB, Semnani RT, (2016) "Microfilariae of Brugia malayi inhibit the mTOR pathway and induce autophagy in human dendritic cells." <i>Infect Immun</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27297394 27297394]; doi: [https://dx.doi.org/10.1128/IAI.00174-16 10.1128/IAI.00174-16]; GPMDB: [http://gpmdb.org/data/keyword/27297394 233]. | ||
#Rakus D, Gizak A, Wiśniewski JR, (2016) "Proteomics Unveils Fibroblast-Cardiomyocyte Lactate Shuttle and Hexokinase Paradox in Mouse Muscles." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27302655 27302655]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01149 10.1021/acs.jproteome.5b01149]; GPMDB: [http://gpmdb.org/data/keyword/27302655 60]. | #Rakus D, Gizak A, Wiśniewski JR, (2016) "Proteomics Unveils Fibroblast-Cardiomyocyte Lactate Shuttle and Hexokinase Paradox in Mouse Muscles." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27302655 27302655]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01149 10.1021/acs.jproteome.5b01149]; GPMDB: [http://gpmdb.org/data/keyword/27302655 60]. | ||
#Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SP, (2016) "Defining the consequences of genetic variation on a proteome-wide scale." <i>Nature</i> <b>534</b>(7608):500–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27309819 27309819]; doi: [https://dx.doi.org/10.1038/nature18270 10.1038/nature18270]; GPMDB: [http://gpmdb.org/data/keyword/27309819 27]. | #Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SP, (2016) "Defining the consequences of genetic variation on a proteome-wide scale." <i>Nature</i> <b>534</b>(7608):500–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27309819 27309819]; doi: [https://dx.doi.org/10.1038/nature18270 10.1038/nature18270]; GPMDB: [http://gpmdb.org/data/keyword/27309819 27]. | ||
+ | #Madeira JP, Omer H, Alpha-Bazin B, Armengaud J, Duport C, (2016) "Deciphering the interactions between the Bacillus cereus linear plasmid, pBClin15, and its host by high-throughput comparative proteomics." <i>J Proteomics</i> <b>146</b>:25–33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27321915 27321915]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.06.022 10.1016/j.jprot.2016.06.022]; GPMDB: [http://gpmdb.org/data/keyword/27321915 26]. | ||
#Szklanna PB, Foy M, Wynne K, Byrne D, Maguire PB, (2016) "Analysis of the proteins associated with platelet detergent resistant membranes." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27329341 27329341]; doi: [https://dx.doi.org/10.1002/pmic.201500309 10.1002/pmic.201500309]; GPMDB: [http://gpmdb.org/data/keyword/27329341 18]. | #Szklanna PB, Foy M, Wynne K, Byrne D, Maguire PB, (2016) "Analysis of the proteins associated with platelet detergent resistant membranes." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27329341 27329341]; doi: [https://dx.doi.org/10.1002/pmic.201500309 10.1002/pmic.201500309]; GPMDB: [http://gpmdb.org/data/keyword/27329341 18]. | ||
#Ahrné E, Glatter T, Viganò C, Schubert CV, Nigg EA, Schmidt A, (2016) "Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27345528 27345528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00066 10.1021/acs.jproteome.6b00066]; GPMDB: [http://gpmdb.org/data/keyword/27345528 41]. | #Ahrné E, Glatter T, Viganò C, Schubert CV, Nigg EA, Schmidt A, (2016) "Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27345528 27345528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00066 10.1021/acs.jproteome.6b00066]; GPMDB: [http://gpmdb.org/data/keyword/27345528 41]. | ||
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#Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsveld J, Hentze MW, Castello A, Ephrussi A, (2016) "Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila." <i>Nat Commun</i> <b>7</b>:12128; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27378189 27378189]; doi: [https://dx.doi.org/10.1038/ncomms12128 10.1038/ncomms12128]; GPMDB: [http://gpmdb.org/data/keyword/27378189 25]. | #Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsveld J, Hentze MW, Castello A, Ephrussi A, (2016) "Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila." <i>Nat Commun</i> <b>7</b>:12128; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27378189 27378189]; doi: [https://dx.doi.org/10.1038/ncomms12128 10.1038/ncomms12128]; GPMDB: [http://gpmdb.org/data/keyword/27378189 25]. | ||
#Ashford P, Hernandez A, Greco TM, Buch A, Sodeik B, Cristea IM, Grunewald K, Shepherd A, Topf M, (2016) "HVint: A strategy for identifying novel protein-protein interactions in herpes simplex virus type 1." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27384951 27384951]; doi: [https://dx.doi.org/10.1074/mcp.M116.058552 10.1074/mcp.M116.058552]; GPMDB: [http://gpmdb.org/data/keyword/27384951 19]. | #Ashford P, Hernandez A, Greco TM, Buch A, Sodeik B, Cristea IM, Grunewald K, Shepherd A, Topf M, (2016) "HVint: A strategy for identifying novel protein-protein interactions in herpes simplex virus type 1." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27384951 27384951]; doi: [https://dx.doi.org/10.1074/mcp.M116.058552 10.1074/mcp.M116.058552]; GPMDB: [http://gpmdb.org/data/keyword/27384951 19]. | ||
+ | #Picariello G, Addeo F, Ferranti P, Nocerino R, Paparo L, Passariello A, Dallas DC, Robinson RC, Barile D, Canani RB, (2016) "Antibody-independent identification of bovine milk-derived peptides in breast-milk." <i>Food Funct</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27396729 27396729]; doi: [https://dx.doi.org/10.1039/c6fo00731g 10.1039/c6fo00731g]; GPMDB: [http://gpmdb.org/data/keyword/27396729 12]. | ||
#Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M, (2016) "Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development." <i>Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27397507 27397507]; doi: [https://dx.doi.org/10.1016/j.cell.2016.06.015 10.1016/j.cell.2016.06.015]; GPMDB: [http://gpmdb.org/data/keyword/27397507 18]. | #Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M, (2016) "Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development." <i>Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27397507 27397507]; doi: [https://dx.doi.org/10.1016/j.cell.2016.06.015 10.1016/j.cell.2016.06.015]; GPMDB: [http://gpmdb.org/data/keyword/27397507 18]. | ||
+ | #Shraibman B, Melamed Kadosh D, Barnea E, Admon A, (2016) "HLA peptides derived from tumor antigens induced by inhibition of DNA methylation for development of drug-facilitated immunotherapy." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27412690 27412690]; doi: [https://dx.doi.org/10.1074/mcp.M116.060350 10.1074/mcp.M116.060350]; GPMDB: [http://gpmdb.org/data/keyword/27412690 11]. | ||
+ | #Müller S, Balaz M, Stefanicka P, Varga L, Amri EZ, Ukropec J, Wollscheid B, Wolfrum C, (2016) "Proteomic Analysis of Human Brown Adipose Tissue Reveals Utilization of Coupled and Uncoupled Energy Expenditure Pathways." <i>Sci Rep</i> <b>6</b>:30030; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418403 27418403]; doi: [https://dx.doi.org/10.1038/srep30030 10.1038/srep30030]; GPMDB: [http://gpmdb.org/data/keyword/27418403 32]. |
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 July 24, 2016.