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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 February 24, 2018. |
#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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JD, Rajendran D, Couzens AL, Currie KW, Tkach JM, Cheung SW, Pelletier L, Gingras AC, (2016) "Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators." <i>Cell Rep</i> <b>17</b>(9):2488–2501; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27880917 27880917]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.10.078 10.1016/j.celrep.2016.10.078]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27880917 315]. | #St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JD, Rajendran D, Couzens AL, Currie KW, Tkach JM, Cheung SW, Pelletier L, Gingras AC, (2016) "Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators." <i>Cell Rep</i> <b>17</b>(9):2488–2501; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27880917 27880917]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.10.078 10.1016/j.celrep.2016.10.078]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27880917 315]. | ||
#Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." <i>Nat Commun</i> <b>7</b>:13595; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27882920 27882920]; doi: [https://dx.doi.org/10.1038/ncomms13595 10.1038/ncomms13595]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27882920 9]. | #Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." <i>Nat Commun</i> <b>7</b>:13595; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27882920 27882920]; doi: [https://dx.doi.org/10.1038/ncomms13595 10.1038/ncomms13595]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27882920 9]. | ||
+ | #Mossina A, Lukas C, Merl-Pham J, Uhl FE, Mutze K, Schamberger A, Staab-Weijnitz C, Jia J, Yildirim AÖ, Königshoff M, Hauck SM, Eickelberg O, Meiners S, (2017) "Cigarette smoke alters the secretome of lung epithelial cells." <i>Proteomics</i> <b>17</b>(1-2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27891773 27891773]; doi: [https://dx.doi.org/10.1002/pmic.201600243 10.1002/pmic.201600243]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27891773 24]. | ||
#Hurwitz SN, Rider MA, Bundy JL, Liu X, Singh RK, Meckes DG Jr, (2016) "Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers." <i>Oncotarget</i> <b>7</b>(52):86999–87015; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27894104 27894104]; doi: [https://dx.doi.org/10.18632/oncotarget.13569 10.18632/oncotarget.13569]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27894104 898]. | #Hurwitz SN, Rider MA, Bundy JL, Liu X, Singh RK, Meckes DG Jr, (2016) "Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers." <i>Oncotarget</i> <b>7</b>(52):86999–87015; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27894104 27894104]; doi: [https://dx.doi.org/10.18632/oncotarget.13569 10.18632/oncotarget.13569]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27894104 898]. | ||
#Gonneaud A, Jones C, Turgeon N, Lévesque D, Asselin C, Boudreau F, Boisvert FM, (2016) "A SILAC-Based Method for Quantitative Proteomic Analysis of Intestinal Organoids." <i>Sci Rep</i> <b>6</b>:38195; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27901089 27901089]; doi: [https://dx.doi.org/10.1038/srep38195 10.1038/srep38195]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27901089 38]. | #Gonneaud A, Jones C, Turgeon N, Lévesque D, Asselin C, Boudreau F, Boisvert FM, (2016) "A SILAC-Based Method for Quantitative Proteomic Analysis of Intestinal Organoids." <i>Sci Rep</i> <b>6</b>:38195; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27901089 27901089]; doi: [https://dx.doi.org/10.1038/srep38195 10.1038/srep38195]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27901089 38]. | ||
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#Kreutz D, Bileck A, Plessl K, Wolrab D, Groessl M, Keppler BK, Meier SM, Gerner C, (2016) "Response Profiling Using Shotgun Proteomics Enables Global Metallodrug Mechanisms of Action To Be Established." <i>Chemistry</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28071820 28071820]; doi: [https://dx.doi.org/10.1002/chem.201604516 10.1002/chem.201604516]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28071820 6]. | #Kreutz D, Bileck A, Plessl K, Wolrab D, Groessl M, Keppler BK, Meier SM, Gerner C, (2016) "Response Profiling Using Shotgun Proteomics Enables Global Metallodrug Mechanisms of Action To Be Established." <i>Chemistry</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28071820 28071820]; doi: [https://dx.doi.org/10.1002/chem.201604516 10.1002/chem.201604516]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28071820 6]. | ||
#Xing F, Luan Y, Cai J, Wu S, Mai J, Gu J, Zhang H, Li K, Lin Y, Xiao X, Liang J, Li Y, Chen W, Tan Y, Sheng L, Lu B, Lu W, Gao M, Qiu P, Su X, Yin W, Hu J, Chen Z, Sai K, Wang J, Chen F, Chen Y, Zhu S, Liu D, Cheng S, Xie Z, Zhu W, Yan G, (2017) "The Anti-Warburg Effect Elicited by the cAMP-PGC1α Pathway Drives Differentiation of Glioblastoma Cells into Astrocytes." <i>Cell Rep</i> <b>18</b>(2):468–481; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28076790 28076790]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.037 10.1016/j.celrep.2016.12.037]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28076790 60]. | #Xing F, Luan Y, Cai J, Wu S, Mai J, Gu J, Zhang H, Li K, Lin Y, Xiao X, Liang J, Li Y, Chen W, Tan Y, Sheng L, Lu B, Lu W, Gao M, Qiu P, Su X, Yin W, Hu J, Chen Z, Sai K, Wang J, Chen F, Chen Y, Zhu S, Liu D, Cheng S, Xie Z, Zhu W, Yan G, (2017) "The Anti-Warburg Effect Elicited by the cAMP-PGC1α Pathway Drives Differentiation of Glioblastoma Cells into Astrocytes." <i>Cell Rep</i> <b>18</b>(2):468–481; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28076790 28076790]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.037 10.1016/j.celrep.2016.12.037]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28076790 60]. | ||
+ | #Loroch S, Trabold K, Gambaryan S, Reiß C, Schwierczek K, Fleming I, Sickmann A, Behnisch W, Zieger B, Zahedi RP, Walter U, Jurk K, (2017) "Alterations of the platelet proteome in type I Glanzmann thrombasthenia caused by different homozygous delG frameshift mutations in ITGA2B." <i>Thromb Haemost</i> <b>117</b>(3):556–569; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28078347 28078347]; doi: [https://dx.doi.org/10.1160/TH16-07-0515 10.1160/TH16-07-0515]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28078347 20]. | ||
#Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ, (2017) "Interactome disassembly during apoptosis occurs independent of caspase cleavage." <i>Mol Syst Biol</i> <b>13</b>(1):906; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28082348 28082348]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28082348 521]. | #Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ, (2017) "Interactome disassembly during apoptosis occurs independent of caspase cleavage." <i>Mol Syst Biol</i> <b>13</b>(1):906; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28082348 28082348]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28082348 521]. | ||
#Emmott E, Sorgeloos F, Caddy SL, Vashist S, Sosnovtsev S, Lloyd R, Heesom K, Locker N, Goodfellow I, (2017) "Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087593 28087593]; doi: [https://dx.doi.org/10.1074/mcp.M116.062448 10.1074/mcp.M116.062448]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28087593 3]. | #Emmott E, Sorgeloos F, Caddy SL, Vashist S, Sosnovtsev S, Lloyd R, Heesom K, Locker N, Goodfellow I, (2017) "Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087593 28087593]; doi: [https://dx.doi.org/10.1074/mcp.M116.062448 10.1074/mcp.M116.062448]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28087593 3]. | ||
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#Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | #Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | ||
#Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | #Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | ||
+ | #Finamore F, Reny JL, Malacarne S, Fontana P, Sanchez JC, (2018) "A high glucose level is associated with decreased aspirin-mediated acetylation of platelet cyclooxygenase (COX)-1 at serine 529: A pilot study." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30240925 30240925]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.09.007 10.1016/j.jprot.2018.09.007]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30240925 18]. | ||
#Sun J, Shi J, Wang Y, Chen Y, Li Y, Kong D, Chang L, Liu F, Lv Z, Zhou Y, He F, Zhang Y, Xu P, (2018) "Multiproteases Combined with High-pH Reverse-Phase Separation Strategy Verified Fourteen Missing Proteins in Human Testis Tissue." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30280576 30280576]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00397 10.1021/acs.jproteome.8b00397]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30280576 108]. | #Sun J, Shi J, Wang Y, Chen Y, Li Y, Kong D, Chang L, Liu F, Lv Z, Zhou Y, He F, Zhang Y, Xu P, (2018) "Multiproteases Combined with High-pH Reverse-Phase Separation Strategy Verified Fourteen Missing Proteins in Human Testis Tissue." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30280576 30280576]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00397 10.1021/acs.jproteome.8b00397]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30280576 108]. | ||
+ | #Sepil I, Hopkins BR, Dean R, Thézénas ML, Charles PD, Konietzny R, Fischer R, Kessler B, Wigby S, (2018) "Quantitative proteomics identification of seminal fluid proteins in male <i>Drosophila melanogaster</i>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30287546 30287546]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000831 10.1074/mcp.RA118.000831]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30287546 87]. | ||
#Erdmann J, Preusse M, Khaledi A, Pich A, Häussler S, (2018) "Environment-driven changes of mRNA and protein levels in Pseudomonas aeruginosa." <i>Environ Microbiol</i> <b>20</b>(11):3952–3963; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30346651 30346651]; doi: [https://dx.doi.org/10.1111/1462-2920.14419 10.1111/1462-2920.14419]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30346651 253]. | #Erdmann J, Preusse M, Khaledi A, Pich A, Häussler S, (2018) "Environment-driven changes of mRNA and protein levels in Pseudomonas aeruginosa." <i>Environ Microbiol</i> <b>20</b>(11):3952–3963; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30346651 30346651]; doi: [https://dx.doi.org/10.1111/1462-2920.14419 10.1111/1462-2920.14419]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30346651 253]. | ||
#Krahmer N, Najafi B, Schueder F, Quagliarini F, Steger M, Seitz S, Kasper R, Salinas F, Cox J, Uhlenhaut NH, Walther TC, Jungmann R, Zeigerer A, Borner GHH, Mann M, (2018) "Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis." <i>Dev Cell</i> <b>47</b>(2):205–221.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352176 30352176]; doi: [https://dx.doi.org/10.1016/j.devcel.2018.09.017 10.1016/j.devcel.2018.09.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352176 134]. | #Krahmer N, Najafi B, Schueder F, Quagliarini F, Steger M, Seitz S, Kasper R, Salinas F, Cox J, Uhlenhaut NH, Walther TC, Jungmann R, Zeigerer A, Borner GHH, Mann M, (2018) "Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis." <i>Dev Cell</i> <b>47</b>(2):205–221.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352176 30352176]; doi: [https://dx.doi.org/10.1016/j.devcel.2018.09.017 10.1016/j.devcel.2018.09.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352176 134]. | ||
#van Mierlo G, Wester RA, Marks H, (2018) "Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in the pluripotent ground state." <i>Stem Cell Res</i> <b>33</b>:135–145; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352361 30352361]; doi: [https://dx.doi.org/10.1016/j.scr.2018.09.017 10.1016/j.scr.2018.09.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352361 6]. | #van Mierlo G, Wester RA, Marks H, (2018) "Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in the pluripotent ground state." <i>Stem Cell Res</i> <b>33</b>:135–145; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352361 30352361]; doi: [https://dx.doi.org/10.1016/j.scr.2018.09.017 10.1016/j.scr.2018.09.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352361 6]. | ||
+ | #El-Rami FE, Zielke RA, Wi T, Sikora AE, Unemo M, (2018) "Quantitative proteomics of the 2016 WHO <i>Neisseria gonorrhoeae</i> reference strains surveys vaccine candidates and antimicrobial resistance determinants." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352803 30352803]; doi: [https://dx.doi.org/10.1074/mcp.RA118.001125 10.1074/mcp.RA118.001125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352803 8]. | ||
#Serra A, Gallart-Palau X, Park JE, Lim GGY, Lim KL, Ho HH, Tam JP, Sze SK, (2018) "Vascular Bed Molecular Profiling by Differential Systemic Decellularization In Vivo." <i>Arterioscler Thromb Vasc Biol</i> <b>38</b>(10):2396–2409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30354219 30354219]; doi: [https://dx.doi.org/10.1161/ATVBAHA.118.311552 10.1161/ATVBAHA.118.311552]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30354219 16]. | #Serra A, Gallart-Palau X, Park JE, Lim GGY, Lim KL, Ho HH, Tam JP, Sze SK, (2018) "Vascular Bed Molecular Profiling by Differential Systemic Decellularization In Vivo." <i>Arterioscler Thromb Vasc Biol</i> <b>38</b>(10):2396–2409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30354219 30354219]; doi: [https://dx.doi.org/10.1161/ATVBAHA.118.311552 10.1161/ATVBAHA.118.311552]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30354219 16]. | ||
#Magagnotti C, Zerbini G, Fermo I, Carletti RM, Bonfanti R, Vallone F, Andolfo A, (2018) "Identification of nephropathy predictors in urine from children with a recent diagnosis of type 1 diabetes." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30366120 30366120]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.10.010 10.1016/j.jprot.2018.10.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30366120 51]. | #Magagnotti C, Zerbini G, Fermo I, Carletti RM, Bonfanti R, Vallone F, Andolfo A, (2018) "Identification of nephropathy predictors in urine from children with a recent diagnosis of type 1 diabetes." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30366120 30366120]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.10.010 10.1016/j.jprot.2018.10.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30366120 51]. | ||
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#Wolf A, Liesinger L, Spoerk S, Schittmayer M, Lang-Loidolt D, Birner-Gruenberger R, Tomazic PV, (2018) "Olfactory cleft proteome does not reflect olfactory performance in patients with idiopathic and postinfectious olfactory disorder: A pilot study." <i>Sci Rep</i> <b>8</b>(1):17554; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30510230 30510230]; doi: [https://dx.doi.org/10.1038/s41598-018-35776-8 10.1038/s41598-018-35776-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30510230 21]. | #Wolf A, Liesinger L, Spoerk S, Schittmayer M, Lang-Loidolt D, Birner-Gruenberger R, Tomazic PV, (2018) "Olfactory cleft proteome does not reflect olfactory performance in patients with idiopathic and postinfectious olfactory disorder: A pilot study." <i>Sci Rep</i> <b>8</b>(1):17554; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30510230 30510230]; doi: [https://dx.doi.org/10.1038/s41598-018-35776-8 10.1038/s41598-018-35776-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30510230 21]. | ||
#Tascher G, Gerbaix M, Maes P, Chazarin B, Ghislin S, Antropova E, Vassilieva G, Ouzren-Zarhloul N, Gauquelin-Koch G, Vico L, Frippiat JP, Bertile F, (2018) "Analysis of femurs from mice embarked on board BION-M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth." <i>FASEB J</i> <b></b>:fj201801463R; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30521760 30521760]; doi: [https://dx.doi.org/10.1096/fj.201801463R 10.1096/fj.201801463R]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30521760 36]. | #Tascher G, Gerbaix M, Maes P, Chazarin B, Ghislin S, Antropova E, Vassilieva G, Ouzren-Zarhloul N, Gauquelin-Koch G, Vico L, Frippiat JP, Bertile F, (2018) "Analysis of femurs from mice embarked on board BION-M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth." <i>FASEB J</i> <b></b>:fj201801463R; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30521760 30521760]; doi: [https://dx.doi.org/10.1096/fj.201801463R 10.1096/fj.201801463R]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30521760 36]. | ||
+ | #Cann ML, Herring LE, Haar L, Gilbert TSK, Goldfarb D, Richards KL, Graves LM, Lawrence DS, (2018) "Dasatinib is preferentially active in the activated B-cell subtype of diffuse large B-cell lymphoma." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30540191 30540191]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00841 10.1021/acs.jproteome.8b00841]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30540191 24]. | ||
+ | #Khodadoust MS, Olsson N, Chen B, Sworder B, Shree T, Liu CL, Zhang L, Czerwinski DK, Davis MM, Levy R, Elias JE, Alizadeh AA, (2018) "B cell lymphomas present immunoglobulin neoantigens." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30545830 30545830]; doi: [https://dx.doi.org/10.1182/blood-2018-06-845156 10.1182/blood-2018-06-845156]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30545830 52]. | ||
+ | #Roustan V, Weckwerth W, (2018) "Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in <i>Chlamydomonas reinhardtii</i>." <i>Front Plant Sci</i> <b>9</b>:1590; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30546371 30546371]; doi: [https://dx.doi.org/10.3389/fpls.2018.01590 10.3389/fpls.2018.01590]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30546371 54]. | ||
+ | #Yao Z, Jia X, Megger DA, Chen J, Liu Y, Li J, Sitek B, Yuan Z, (2018) "Label-free Proteomic Analysis of Exosomes Secreted from THP-1-derived Macrophages Treated with IFN-α Identifies Antiviral Proteins Enriched in Exosomes." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30550287 30550287]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00514 10.1021/acs.jproteome.8b00514]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30550287 23]. | ||
+ | #Yelamanchi SD, Tyagi A, Mohanty V, Dutta P, Korbonits M, Chavan S, Advani J, Madugundu AK, Dey G, Datta KK, Rajyalakshmi M, Sahasrabuddhe NA, Chaturvedi A, Kumar A, Das AA, Ghosh D, Jogdand GM, Nair HH, Saini K, Panchal M, Sarvaiya MA, Mohanraj SS, Sengupta N, Saxena P, Subramani PA, Kumar P, Akkali R, Reshma SV, Santhosh RS, Rastogi S, Kumar S, Ghosh SK, Irlapati VK, Srinivasan A, Radotra BD, Mathur PP, Wong GW, Satishchandra P, Chatterjee A, Gowda H, Bhansali A, Pandey A, Shankar SK, Mahadevan A, Prasad TSK, (2018) "Proteomic Analysis of the Human Anterior Pituitary Gland." <i>OMICS</i> <b>22</b>(12):759–769; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30571610 30571610]; doi: [https://dx.doi.org/10.1089/omi.2018.0160 10.1089/omi.2018.0160]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30571610 3]. | ||
+ | #Nanaware PP, Jurewicz MM, Leszyk J, Shaffer SA, Stern LJ, (2018) "HLA-DO modulates the diversity of the MHC-II self-peptidome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30573663 30573663]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000956 10.1074/mcp.RA118.000956]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30573663 26]. | ||
+ | #Aloui C, Barlier C, Claverol S, Fagan J, Awounou D, Tavernier E, Guyotat D, Hamzeh-Cognasse H, Cognasse F, Garraud O, Laradi S, (2019) "Differential protein expression of blood platelet components associated with adverse transfusion reactions." <i>J Proteomics</i> <b>194</b>:25–36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30590131 30590131]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.12.019 10.1016/j.jprot.2018.12.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30590131 48]. | ||
+ | #Zhou Z, Chen Y, Jin M, He J, Guli A, Yan C, Ding S, (2018) "Comprehensive analysis of lysine acetylome reveals a site-specific pattern in rapamycin-induced autophagy." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30592415 30592415]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00533 10.1021/acs.jproteome.8b00533]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30592415 6]. | ||
+ | #Dunn J, Ferluga S, Sharma V, Futschik M, Hilton DA, Adams CL, Lasonder E, Hannemann OC, (2018) "Proteomic analysis discovers the differential expression of novel proteins and phosphoproteins in meningioma including NEK9, HK2 and SET and deregulation of RNA metabolism." <i>EBioMedicine</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30594554 30594554]; doi: [https://dx.doi.org/10.1016/j.ebiom.2018.12.048 10.1016/j.ebiom.2018.12.048]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30594554 78]. | ||
+ | #Żylicz JJ, Bousard A, Žumer K, Dossin F, Mohammad E, da Rocha ST, Schwalb B, Syx L, Dingli F, Loew D, Cramer P, Heard E, (2019) "The Implication of Early Chromatin Changes in X Chromosome Inactivation." <i>Cell</i> <b>176</b>(1-2):182–197.e23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30595450 30595450]; doi: [https://dx.doi.org/10.1016/j.cell.2018.11.041 10.1016/j.cell.2018.11.041]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30595450 10]. | ||
+ | #Queiroz RML, Smith T, Villanueva E, Marti-Solano M, Monti M, Pizzinga M, Mirea DM, Ramakrishna M, Harvey RF, Dezi V, Thomas GH, Willis AE, Lilley KS, (2019) "Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS)." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30607034 30607034]; doi: [https://dx.doi.org/10.1038/s41587-018-0001-2 10.1038/s41587-018-0001-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30607034 106]. | ||
+ | #Orre LM, Vesterlund M, Pan Y, Arslan T, Zhu Y, Fernandez Woodbridge A, Frings O, Fredlund E, Lehtiö J, (2019) "SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization." <i>Mol Cell</i> <b>73</b>(1):166–182.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30609389 30609389]; doi: [https://dx.doi.org/10.1016/j.molcel.2018.11.035 10.1016/j.molcel.2018.11.035]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30609389 18]. | ||
+ | #Landsberg CD, Megger DA, Hotter D, Rückborn MU, Eilbrecht M, Rashidi-Alavijeh J, Howe S, Heinrichs S, Sauter D, Sitek B, Le-Trilling VTK, Trilling M, (2018) "A Mass Spectrometry-Based Profiling of Interactomes of Viral DDB1- and Cullin Ubiquitin Ligase-Binding Proteins Reveals NF-κB Inhibitory Activity of the HIV-2-Encoded Vpx." <i>Front Immunol</i> <b>9</b>:2978; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30619335 30619335]; doi: [https://dx.doi.org/10.3389/fimmu.2018.02978 10.3389/fimmu.2018.02978]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30619335 48]. | ||
+ | #Yang H, Li Y, Zhao M, Wu F, Wang X, Xiao W, Wang Y, Zhang J, Wang F, Xu F, Zeng WF, Overall CM, He SM, Chi H, Xu P, (2019) "Precision <i>de novo</i> peptide sequencing using mirror proteases of Ac-LysargiNase and trypsin for large-scale proteomics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30622160 30622160]; doi: [https://dx.doi.org/10.1074/mcp.TIR118.000918 10.1074/mcp.TIR118.000918]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30622160 2]. | ||
+ | #Chen D, Ludwig K, Krokhin OV, Spicer V, Yang Z, Shen X, Hummon AB, Sun L, (2019) "Capillary zone electrophoresis-tandem mass spectrometry for large-scale phosphoproteomics with the production of over 11000 phosphopeptides from the colon carcinoma HCT116 cell line." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30624053 30624053]; doi: [https://dx.doi.org/10.1021/acs.analchem.8b04770 10.1021/acs.analchem.8b04770]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30624053 40]. | ||
+ | #Chen Z, Lei C, Wang C, Li N, Srivastava M, Tang M, Zhang H, Choi JM, Jung SY, Qin J, Chen J, (2019) "Global phosphoproteomic analysis reveals ARMC10 as an AMPK substrate that regulates mitochondrial dynamics." <i>Nat Commun</i> <b>10</b>(1):104; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30631047 30631047]; doi: [https://dx.doi.org/10.1038/s41467-018-08004-0 10.1038/s41467-018-08004-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30631047 30]. | ||
+ | #Hansen M, Peltier J, Killy B, Amin B, Bodendorfer B, Härtlova A, Uebel S, Bosmann M, Hofmann J, Büttner C, Ekici AB, Kuttke M, Franzyk H, Foged C, Beer-Hammer S, Schabbauer G, Trost M, Lang R, (2019) "Macrophage phosphoproteome analysis reveals MINCLE-dependent and -independent mycobacterial cord factor signaling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30635358 30635358]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000929 10.1074/mcp.RA118.000929]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30635358 72]. | ||
+ | #Tripathi SK, Välikangas T, Shetty A, Khan MM, Moulder R, Bhosale SD, Komsi E, Salo V, De Albuquerque RS, Rasool O, Galande S, Elo LL, Lahesmaa R, (2019) "Quantitative Proteomics Reveals the Dynamic Protein Landscape during Initiation of Human Th17 Cell Polarization." <i>iScience</i> <b>11</b>:334–355; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30641411 30641411]; doi: [https://dx.doi.org/10.1016/j.isci.2018.12.020 10.1016/j.isci.2018.12.020]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30641411 75]. | ||
+ | #Pfaff F, Hägglund S, Zoli M, Blaise-Boisseau S, Laloy E, Koethe S, Zühlke D, Riedel K, Zientara S, Bakkali-Kassimi L, Valarcher JF, Höper D, Beer M, Eschbaumer M, (2019) "Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus." <i>Viruses</i> <b>11</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30642035 30642035]; doi: [https://dx.doi.org/10.3390/v11010053 10.3390/v11010053]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30642035 110]. | ||
+ | #Kosack L, Wingelhofer B, Popa A, Orlova A, Agerer B, Vilagos B, Majek P, Parapatics K, Lercher A, Ringler A, Klughammer J, Smyth M, Khamina K, Baazim H, de Araujo ED, Rosa DA, Park J, Tin G, Ahmar S, Gunning PT, Bock C, Siddle HV, Woods GM, Kubicek S, Murchison EP, Bennett KL, Moriggl R, Bergthaler A, (2019) "The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease." <i>Cancer Cell</i> <b>35</b>(1):125–139.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30645971 30645971]; doi: [https://dx.doi.org/10.1016/j.ccell.2018.11.018 10.1016/j.ccell.2018.11.018]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30645971 20]. | ||
+ | #van Oorschot R, Hansen M, Koornneef JM, Marneth AE, Bergevoet SM, van Bergen MGJM, van Alphen FPJ, van der Zwaan C, Martens JHA, Vermeulen M, Jansen PWTC, Baltissen MPA, Laros-van Gorkom BAP, Janssen H, Jansen JH, von Lindern M, Meijer AB, van den Akker E, van der Reijden BA, (2019) "Molecular mechanisms of bleeding disorder-associated GFI1BQ287* mutation and its affected pathways in megakaryocytes and platelets." <i>Haematologica</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30655368 30655368]; doi: [https://dx.doi.org/10.3324/haematol.2018.194555 10.3324/haematol.2018.194555]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30655368 63]. | ||
+ | #Gärtner SMK, Hundertmark T, Nolte H, Theofel I, Eren-Ghiani Z, Tetzner C, Duchow TB, Rathke C, Krüger M, Renkawitz-Pohl R, (2019) "Stage-specific testes proteomics of Drosophila melanogaster identifies essential proteins for male fertility." <i>Eur J Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30679029 30679029]; doi: [https://dx.doi.org/10.1016/j.ejcb.2019.01.001 10.1016/j.ejcb.2019.01.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30679029 180]. | ||
+ | #McKetney J, Runde RM, Hebert AS, Salamat S, Roy S, Coon JJ, (2019) "Proteomic Atlas of the Human Brain in Alzheimer's Disease." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30735395 30735395]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00004 10.1021/acs.jproteome.9b00004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30735395 12]. |
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.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
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 24, 2018.