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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 February | + | 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 February 19, 2017. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | ||
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#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 844]. |
#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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#Rao SR, Flores-Rodriguez N, Page SL, Wong C, Robinson PJ, Chircop M, (2016) "The Clathrin-dependent Spindle Proteome." <i>Mol Cell Proteomics</i> <b>15</b>(8):2537–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27174698 27174698]; doi: [https://dx.doi.org/10.1074/mcp.M115.054809 10.1074/mcp.M115.054809]; GPMDB: [http://gpmdb.org/data/keyword/27174698 130]. | #Rao SR, Flores-Rodriguez N, Page SL, Wong C, Robinson PJ, Chircop M, (2016) "The Clathrin-dependent Spindle Proteome." <i>Mol Cell Proteomics</i> <b>15</b>(8):2537–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27174698 27174698]; doi: [https://dx.doi.org/10.1074/mcp.M115.054809 10.1074/mcp.M115.054809]; GPMDB: [http://gpmdb.org/data/keyword/27174698 130]. | ||
#Gupta I, Villanyi Z, Kassem S, Hughes C, Panasenko OO, Steinmetz LM, Collart MA, (2016) "Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex." <i>Cell Rep</i> <b>15</b>(8):1782–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27184853 27184853]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.04.055 10.1016/j.celrep.2016.04.055]; GPMDB: [http://gpmdb.org/data/keyword/27184853 4]. | #Gupta I, Villanyi Z, Kassem S, Hughes C, Panasenko OO, Steinmetz LM, Collart MA, (2016) "Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex." <i>Cell Rep</i> <b>15</b>(8):1782–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27184853 27184853]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.04.055 10.1016/j.celrep.2016.04.055]; GPMDB: [http://gpmdb.org/data/keyword/27184853 4]. | ||
+ | #Zvezdova E, Mikolajczak J, Garreau A, Marcellin M, Rigal L, Lee J, Choi S, Blaize G, Argenty J, Familiades J, Li L, Gonzalez de Peredo A, Burlet-Schiltz O, Love PE, Lesourne R, (2016) "Themis1 enhances T cell receptor signaling during thymocyte development by promoting Vav1 activity and Grb2 stability." <i>Sci Signal</i> <b>9</b>(428):ra51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27188442 27188442]; doi: [https://dx.doi.org/10.1126/scisignal.aad1576 10.1126/scisignal.aad1576]; GPMDB: [http://gpmdb.org/data/keyword/27188442 54]. | ||
#Kliuchnikova AA, Samokhina NI, Ilina IY, Karpov DS, Pyatnitskiy MA, Kuznetsova KG, Toropygin IY, Kochergin SA, Alekseev IB, Zgoda VG, Archakov AI, Moshkovskii SA, (2016) "Human aqueous humor proteome in cataract, glaucoma, and pseudoexfoliation syndrome." <i>Proteomics</i> <b>16</b>(13):1938–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193151 27193151]; doi: [https://dx.doi.org/10.1002/pmic.201500423 10.1002/pmic.201500423]; GPMDB: [http://gpmdb.org/data/keyword/27193151 86]. | #Kliuchnikova AA, Samokhina NI, Ilina IY, Karpov DS, Pyatnitskiy MA, Kuznetsova KG, Toropygin IY, Kochergin SA, Alekseev IB, Zgoda VG, Archakov AI, Moshkovskii SA, (2016) "Human aqueous humor proteome in cataract, glaucoma, and pseudoexfoliation syndrome." <i>Proteomics</i> <b>16</b>(13):1938–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193151 27193151]; doi: [https://dx.doi.org/10.1002/pmic.201500423 10.1002/pmic.201500423]; GPMDB: [http://gpmdb.org/data/keyword/27193151 86]. | ||
#Heaven MR, Flint D, Randall SM, Sosunov AA, Wilson L, Barnes S, Goldman JE, Muddiman DC, Brenner M, (2016) "Composition of Rosenthal Fibers, the Protein Aggregate Hallmark of Alexander Disease." <i>J Proteome Res</i> <b>15</b>(7):2265–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193225 27193225]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00316 10.1021/acs.jproteome.6b00316]; GPMDB: [http://gpmdb.org/data/keyword/27193225 8]. | #Heaven MR, Flint D, Randall SM, Sosunov AA, Wilson L, Barnes S, Goldman JE, Muddiman DC, Brenner M, (2016) "Composition of Rosenthal Fibers, the Protein Aggregate Hallmark of Alexander Disease." <i>J Proteome Res</i> <b>15</b>(7):2265–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193225 27193225]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00316 10.1021/acs.jproteome.6b00316]; GPMDB: [http://gpmdb.org/data/keyword/27193225 8]. | ||
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#Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS, (2016) "Flexible Data Analysis Pipeline for High-Confidence Proteogenomics." <i>J Proteome Res</i> <b>15</b>(12):4686–4695; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27786492 27786492]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00765 10.1021/acs.jproteome.6b00765]; GPMDB: [http://gpmdb.org/data/keyword/27786492 35]. | #Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS, (2016) "Flexible Data Analysis Pipeline for High-Confidence Proteogenomics." <i>J Proteome Res</i> <b>15</b>(12):4686–4695; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27786492 27786492]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00765 10.1021/acs.jproteome.6b00765]; GPMDB: [http://gpmdb.org/data/keyword/27786492 35]. | ||
#Shishkova E, Hebert AS, Coon JJ, (2016) "Now, More Than Ever, Proteomics Needs Better Chromatography." <i>Cell Syst</i> <b>3</b>(4):321–324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27788355 27788355]; doi: [https://dx.doi.org/10.1016/j.cels.2016.10.007 10.1016/j.cels.2016.10.007]; GPMDB: [http://gpmdb.org/data/keyword/27788355 35]. | #Shishkova E, Hebert AS, Coon JJ, (2016) "Now, More Than Ever, Proteomics Needs Better Chromatography." <i>Cell Syst</i> <b>3</b>(4):321–324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27788355 27788355]; doi: [https://dx.doi.org/10.1016/j.cels.2016.10.007 10.1016/j.cels.2016.10.007]; GPMDB: [http://gpmdb.org/data/keyword/27788355 35]. | ||
+ | #Zhao M, Xu F, Wu F, Yu D, Su N, Zhang Y, Cheng L, Xu P, (2016) "iTRAQ-Based Membrane Proteomics Reveals Plasma Membrane Proteins Change During HepaRG Cell Differentiation." <i>J Proteome Res</i> <b>15</b>(12):4245–4257; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27790907 27790907]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00305 10.1021/acs.jproteome.6b00305]; GPMDB: [http://gpmdb.org/data/keyword/27790907 1]. | ||
#Lundquist PK, Mantegazza O, Stefanski A, Stühler K, Weber AP, (2016) "Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts." <i>Mol Plant</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27794502 27794502]; doi: [https://dx.doi.org/10.1016/j.molp.2016.10.011 10.1016/j.molp.2016.10.011]; GPMDB: [http://gpmdb.org/data/keyword/27794502 42]. | #Lundquist PK, Mantegazza O, Stefanski A, Stühler K, Weber AP, (2016) "Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts." <i>Mol Plant</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27794502 27794502]; doi: [https://dx.doi.org/10.1016/j.molp.2016.10.011 10.1016/j.molp.2016.10.011]; GPMDB: [http://gpmdb.org/data/keyword/27794502 42]. | ||
#Fournier M, Orpinell M, Grauffel C, Scheer E, Garnier JM, Ye T, Chavant V, Joint M, Esashi F, Dejaegere A, Gönczy P, Tora L, (2016) "KAT2A/KAT2B-targeted acetylome reveals a role for PLK4 acetylation in preventing centrosome amplification." <i>Nat Commun</i> <b>7</b>:13227; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27796307 27796307]; doi: [https://dx.doi.org/10.1038/ncomms13227 10.1038/ncomms13227]; GPMDB: [http://gpmdb.org/data/keyword/27796307 114]. | #Fournier M, Orpinell M, Grauffel C, Scheer E, Garnier JM, Ye T, Chavant V, Joint M, Esashi F, Dejaegere A, Gönczy P, Tora L, (2016) "KAT2A/KAT2B-targeted acetylome reveals a role for PLK4 acetylation in preventing centrosome amplification." <i>Nat Commun</i> <b>7</b>:13227; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27796307 27796307]; doi: [https://dx.doi.org/10.1038/ncomms13227 10.1038/ncomms13227]; GPMDB: [http://gpmdb.org/data/keyword/27796307 114]. | ||
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#Riesner K, Shi Y, Jacobi A, Kraeter M, Kalupa M, McGearey A, Mertlitz S, Cordes S, Schrezenmeier JF, Mengwasser J, Westphal S, Perez-Hernandez D, Schmitt C, Dittmar G, Guck J, Penack O, (2017) "Initiation of acute graft-versus-host disease by angiogenesis." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096092 28096092]; doi: [https://dx.doi.org/10.1182/blood-2016-08-736314 10.1182/blood-2016-08-736314]; GPMDB: [http://gpmdb.org/data/keyword/28096092 1]. | #Riesner K, Shi Y, Jacobi A, Kraeter M, Kalupa M, McGearey A, Mertlitz S, Cordes S, Schrezenmeier JF, Mengwasser J, Westphal S, Perez-Hernandez D, Schmitt C, Dittmar G, Guck J, Penack O, (2017) "Initiation of acute graft-versus-host disease by angiogenesis." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096092 28096092]; doi: [https://dx.doi.org/10.1182/blood-2016-08-736314 10.1182/blood-2016-08-736314]; GPMDB: [http://gpmdb.org/data/keyword/28096092 1]. | ||
#Princz LN, Wild P, Bittmann J, Aguado FJ, Blanco MG, Matos J, Pfander B, (2017) "Dbf4-dependent kinase and the Rtt107 scaffold promote Mus81-Mms4 resolvase activation during mitosis." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096179 28096179]; doi: [https://dx.doi.org/10.15252/embj.201694831 10.15252/embj.201694831]; GPMDB: [http://gpmdb.org/data/keyword/28096179 130]. | #Princz LN, Wild P, Bittmann J, Aguado FJ, Blanco MG, Matos J, Pfander B, (2017) "Dbf4-dependent kinase and the Rtt107 scaffold promote Mus81-Mms4 resolvase activation during mitosis." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096179 28096179]; doi: [https://dx.doi.org/10.15252/embj.201694831 10.15252/embj.201694831]; GPMDB: [http://gpmdb.org/data/keyword/28096179 130]. | ||
- | #Hendriks IA, Lyon D, Young C, Jensen LJ, Vertegaal AC, Nielsen ML, (2017) "Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation." <i>Nat Struct Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28112733 28112733]; doi: [https://dx.doi.org/10.1038/nsmb.3366 10.1038/nsmb.3366]; GPMDB: [http://gpmdb.org/data/keyword/28112733 | + | #Chymkowitch P, Nguéa P A, Aanes H, Robertson J, Klungland A, Enserink JM, (2017) "TORC1-dependent sumoylation of Rpc82 promotes RNA polymerase III assembly and activity." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(5):1039–1044; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096404 28096404]; doi: [https://dx.doi.org/10.1073/pnas.1615093114 10.1073/pnas.1615093114]; GPMDB: [http://gpmdb.org/data/keyword/28096404 21]. |
- | #Kulak NA, Geyer PE, Mann M, (2017) "Loss-less nano-fractionator for high sensitivity, high coverage proteomics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28126900 28126900]; doi: [https://dx.doi.org/10.1074/mcp.O116.065136 10.1074/mcp.O116.065136]; GPMDB: [http://gpmdb.org/data/keyword/28126900 | + | #Hendriks IA, Lyon D, Young C, Jensen LJ, Vertegaal AC, Nielsen ML, (2017) "Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation." <i>Nat Struct Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28112733 28112733]; doi: [https://dx.doi.org/10.1038/nsmb.3366 10.1038/nsmb.3366]; GPMDB: [http://gpmdb.org/data/keyword/28112733 311]. |
+ | #Badalato N, Guillot A, Sabarly V, Dubois M, Pourette N, Pontoire B, Robert P, Bridier A, Monnet V, Sousa DZ, Durand S, Mazéas L, Buléon A, Bouchez T, Mortha G, Bize A, (2017) "Whole Proteome Analyses on Ruminiclostridium cellulolyticum Show a Modulation of the Cellulolysis Machinery in Response to Cellulosic Materials with Subtle Differences in Chemical and Structural Properties." <i>PLoS One</i> <b>12</b>(1):e0170524; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28114419 28114419]; doi: [https://dx.doi.org/10.1371/journal.pone.0170524 10.1371/journal.pone.0170524]; GPMDB: [http://gpmdb.org/data/keyword/28114419 24]. | ||
+ | #Glisovic-Aplenc T, Gill S, Spruce LA, Smith IR, Fazelinia H, Shestova O, Ding H, Tasian SK, Aplenc R, Seeholzer SH, (2017) "Improved plasma membrane proteome coverage with a label-free non-affinity-purified workflow." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28116781 28116781]; doi: [https://dx.doi.org/10.1002/pmic.201600344 10.1002/pmic.201600344]; GPMDB: [http://gpmdb.org/data/keyword/28116781 41]. | ||
+ | #Kulak NA, Geyer PE, Mann M, (2017) "Loss-less nano-fractionator for high sensitivity, high coverage proteomics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28126900 28126900]; doi: [https://dx.doi.org/10.1074/mcp.O116.065136 10.1074/mcp.O116.065136]; GPMDB: [http://gpmdb.org/data/keyword/28126900 28]. | ||
+ | #Yu Y, Kwon K, Tsitrin T, Bekele S, Sikorski P, Nelson KE, Pieper R, (2017) "Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections." <i>PLoS Pathog</i> <b>13</b>(1):e1006151; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28129394 28129394]; doi: [https://dx.doi.org/10.1371/journal.ppat.1006151 10.1371/journal.ppat.1006151]; GPMDB: [http://gpmdb.org/data/keyword/28129394 72]. | ||
#Godfrey M, Touati SA, Kataria M, Jones A, Snijders AP, Uhlmann F, (2017) "PP2A<sup>Cdc55</sup> Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation." <i>Mol Cell</i> <b>65</b>(3):393–402.e3; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132839 28132839]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.12.018 10.1016/j.molcel.2016.12.018]; GPMDB: [http://gpmdb.org/data/keyword/28132839 120]. | #Godfrey M, Touati SA, Kataria M, Jones A, Snijders AP, Uhlmann F, (2017) "PP2A<sup>Cdc55</sup> Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation." <i>Mol Cell</i> <b>65</b>(3):393–402.e3; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132839 28132839]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.12.018 10.1016/j.molcel.2016.12.018]; GPMDB: [http://gpmdb.org/data/keyword/28132839 120]. | ||
#Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B, (2017) "Building ProteomeTools based on a complete synthetic human proteome." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28135259 28135259]; doi: [https://dx.doi.org/10.1038/nmeth.4153 10.1038/nmeth.4153]; GPMDB: [http://gpmdb.org/data/keyword/28135259 1095]. | #Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B, (2017) "Building ProteomeTools based on a complete synthetic human proteome." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28135259 28135259]; doi: [https://dx.doi.org/10.1038/nmeth.4153 10.1038/nmeth.4153]; GPMDB: [http://gpmdb.org/data/keyword/28135259 1095]. | ||
#Jung SY, Choi JM, Rousseaux MW, Malovannaya A, Kim JJ, Kutzera J, Wang Y, Huang Y, Zhu W, Maity S, Zoghbi HY, Qin J, (2017) "An anatomically resolved mouse brain proteome reveals Parkinson disease-relevant pathways." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28153913 28153913]; doi: [https://dx.doi.org/10.1074/mcp.M116.061440 10.1074/mcp.M116.061440]; GPMDB: [http://gpmdb.org/data/keyword/28153913 610]. | #Jung SY, Choi JM, Rousseaux MW, Malovannaya A, Kim JJ, Kutzera J, Wang Y, Huang Y, Zhu W, Maity S, Zoghbi HY, Qin J, (2017) "An anatomically resolved mouse brain proteome reveals Parkinson disease-relevant pathways." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28153913 28153913]; doi: [https://dx.doi.org/10.1074/mcp.M116.061440 10.1074/mcp.M116.061440]; GPMDB: [http://gpmdb.org/data/keyword/28153913 610]. | ||
- | #Davis S, Charles PD, He L, Mowlds P, Kessler BM, Fischer R, (2017) "Expanding proteome coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) combined with broad specificity proteolysis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28164708 28164708]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00915 10.1021/acs.jproteome.6b00915]; GPMDB: [http://gpmdb.org/data/keyword/28164708 | + | #Diering GH, Nirujogi RS, Roth RH, Worley PF, Pandey A, Huganir RL, (2017) "Homer1a drives homeostatic scaling-down of excitatory synapses during sleep." <i>Science</i> <b>355</b>(6324):511–515; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28154077 28154077]; doi: [https://dx.doi.org/10.1126/science.aai8355 10.1126/science.aai8355]; GPMDB: [http://gpmdb.org/data/keyword/28154077 25]. |
+ | #Nuzzo D, Inguglia L, Walters J, Picone P, Di Carlo M, (2017) "A Shotgun Proteomics Approach Reveals a New Toxic Role For Alzheimer's Disease Aβ Peptide: Spliceosome Impairment." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28157316 28157316]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00925 10.1021/acs.jproteome.6b00925]; GPMDB: [http://gpmdb.org/data/keyword/28157316 8]. | ||
+ | #Park YJ, Koh J, Kwon JT, Park YS, Yang L, Cha S, (2017) "Uncovering stem cell differentiation factors for salivary gland regeneration by quantitative analysis of differential proteomes." <i>PLoS One</i> <b>12</b>(2):e0169677; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28158262 28158262]; doi: [https://dx.doi.org/10.1371/journal.pone.0169677 10.1371/journal.pone.0169677]; GPMDB: [http://gpmdb.org/data/keyword/28158262 2]. | ||
+ | #Davis S, Charles PD, He L, Mowlds P, Kessler BM, Fischer R, (2017) "Expanding proteome coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) combined with broad specificity proteolysis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28164708 28164708]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00915 10.1021/acs.jproteome.6b00915]; GPMDB: [http://gpmdb.org/data/keyword/28164708 7]. | ||
+ | #Schm Oumllders J, Manske C, Otto A, Hoffmann C, Steiner B, Welin A, Becher DO, Hilbi H, (2017) "Comparative proteomics of purified pathogen vacuoles correlates intracellular replication of <i>Legionella pneumophila</i> with the small GTPase Rap1." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28183814 28183814]; doi: [https://dx.doi.org/10.1074/mcp.M116.063453 10.1074/mcp.M116.063453]; GPMDB: [http://gpmdb.org/data/keyword/28183814 118]. | ||
+ | #Fielding CA, Weekes MP, Nobre LV, Ruckova E, Wilkie GS, Paulo JA, Chang C, Suárez NM, Davies JA, Antrobus R, Stanton RJ, Aicheler RJ, Nichols H, Vojtesek B, Trowsdale J, Davison AJ, Gygi SP, Tomasec P, Lehner PJ, Wilkinson GW, (2017) "Control of immune ligands by members of a cytomegalovirus gene expansion suppresses natural killer cell activation." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28186488 28186488]; doi: [https://dx.doi.org/10.7554/eLife.22206 10.7554/eLife.22206]; GPMDB: [http://gpmdb.org/data/keyword/28186488 3]. | ||
+ | #Barnea E, Melamed Kadosh D, Haimovich Y, Satumtira N, Dorris ML, Nguyen MT, Hammer RE, Tran TM, Colbert RA, Taurog JD, Admon A, (2017) "The HLA-B27 peptidome in vivo in spondyloarthritis-susceptible HLA-B27 transgenic rats and the effect of ERAP1 deletion." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28188227 28188227]; doi: [https://dx.doi.org/10.1074/mcp.M116.066241 10.1074/mcp.M116.066241]; GPMDB: [http://gpmdb.org/data/keyword/28188227 26]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of February 19, 2017.