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==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of | + | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of November 4, 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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#Bullen JW, Tchernyshyov I, Holewinski RJ, DeVine L, Wu F, Venkatraman V, Kass DL, Cole RN, Van Eyk J, Semenza GL, (2016) "Protein kinase A-dependent phosphorylation stimulates the transcriptional activity of hypoxia-inducible factor 1." <i>Sci Signal</i> <b>9</b>(430):ra56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27245613 27245613]; doi: [https://dx.doi.org/10.1126/scisignal.aaf0583 10.1126/scisignal.aaf0583]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27245613 14]. | #Bullen JW, Tchernyshyov I, Holewinski RJ, DeVine L, Wu F, Venkatraman V, Kass DL, Cole RN, Van Eyk J, Semenza GL, (2016) "Protein kinase A-dependent phosphorylation stimulates the transcriptional activity of hypoxia-inducible factor 1." <i>Sci Signal</i> <b>9</b>(430):ra56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27245613 27245613]; doi: [https://dx.doi.org/10.1126/scisignal.aaf0583 10.1126/scisignal.aaf0583]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27245613 14]. | ||
#Patella F, Neilson LJ, Athineos D, Erami Z, Anderson KI, Blyth K, Ryan KM, Zanivan S, (2016) "In-Depth Proteomics Identifies a Role for Autophagy in Controlling Reactive Oxygen Species Mediated Endothelial Permeability." <i>J Proteome Res</i> <b>15</b>(7):2187–97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27246970 27246970]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00166 10.1021/acs.jproteome.6b00166]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27246970 25]. | #Patella F, Neilson LJ, Athineos D, Erami Z, Anderson KI, Blyth K, Ryan KM, Zanivan S, (2016) "In-Depth Proteomics Identifies a Role for Autophagy in Controlling Reactive Oxygen Species Mediated Endothelial Permeability." <i>J Proteome Res</i> <b>15</b>(7):2187–97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27246970 27246970]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00166 10.1021/acs.jproteome.6b00166]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27246970 25]. | ||
+ | #Rai AN, Thornton JA, Stokes J, Sunesara I, Swiatlo E, Nanduri B, (2016) "Polyamine transporter in Streptococcus pneumoniae is essential for evading early innate immune responses in pneumococcal pneumonia." <i>Sci Rep</i> <b>6</b>:26964; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27247105 27247105]; doi: [https://dx.doi.org/10.1038/srep26964 10.1038/srep26964]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27247105 21]. | ||
#Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC., (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27251275 1265]. | #Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC., (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27251275 1265]. | ||
#Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(8):2671–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27259358 112]. | #Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(8):2671–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27259358 112]. | ||
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#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: [https://gpmdb.thegpm.org/data/keyword/28114419 24]. | #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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/28116781 41]. | #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: [https://gpmdb.thegpm.org/data/keyword/28116781 41]. | ||
+ | #Baker MS, Ahn SB, Mohamedali A, Islam MT, Cantor D, Verhaert PD, Fanayan S, Sharma S, Nice EC, Connor M, Ranganathan S, (2017) "Accelerating the search for the missing proteins in the human proteome." <i>Nat Commun</i> <b>8</b>:14271; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28117396 28117396]; doi: [https://dx.doi.org/10.1038/ncomms14271 10.1038/ncomms14271]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28117396 12]. | ||
#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: [https://gpmdb.thegpm.org/data/keyword/28126900 60]. | #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: [https://gpmdb.thegpm.org/data/keyword/28126900 60]. | ||
#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: [https://gpmdb.thegpm.org/data/keyword/28129394 72]. | #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: [https://gpmdb.thegpm.org/data/keyword/28129394 72]. | ||
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#Lorenz C, Lesimple P, Bukowiecki R, Zink A, Inak G, Mlody B, Singh M, Semtner M, Mah N, Auré K, Leong M, Zabiegalov O, Lyras EM, Pfiffer V, Fauler B, Eichhorst J, Wiesner B, Huebner N, Priller J, Mielke T, Meierhofer D, Izsvák Z, Meier JC, Bouillaud F, Adjaye J, Schuelke M, Wanker EE, Lombès A, Prigione A, (2017) "Human iPSC-Derived Neural Progenitors Are an Effective Drug Discovery Model for Neurological mtDNA Disorders." <i>Cell Stem Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132834 28132834]; doi: [https://dx.doi.org/10.1016/j.stem.2016.12.013 10.1016/j.stem.2016.12.013]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28132834 14]. | #Lorenz C, Lesimple P, Bukowiecki R, Zink A, Inak G, Mlody B, Singh M, Semtner M, Mah N, Auré K, Leong M, Zabiegalov O, Lyras EM, Pfiffer V, Fauler B, Eichhorst J, Wiesner B, Huebner N, Priller J, Mielke T, Meierhofer D, Izsvák Z, Meier JC, Bouillaud F, Adjaye J, Schuelke M, Wanker EE, Lombès A, Prigione A, (2017) "Human iPSC-Derived Neural Progenitors Are an Effective Drug Discovery Model for Neurological mtDNA Disorders." <i>Cell Stem Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132834 28132834]; doi: [https://dx.doi.org/10.1016/j.stem.2016.12.013 10.1016/j.stem.2016.12.013]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28132834 14]. | ||
#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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/28132839 120]. | ||
+ | #Liu X, Zhao B, Sun L, Bhuripanyo K, Wang Y, Bi Y, Davuluri RV, Duong DM, Nanavati D, Yin J, Kiyokawa H, (2017) "Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes." <i>Nat Commun</i> <b>8</b>:14286; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28134249 28134249]; doi: [https://dx.doi.org/10.1038/ncomms14286 10.1038/ncomms14286]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28134249 5]. | ||
#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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/28135259 1095]. | ||
+ | #Zhang F, Xiao Y, Wang Y, (2017) "SILAC-Based Quantitative Proteomic Analysis Unveils Arsenite-Induced Perturbation of Multiple Pathways in Human Skin Fibroblast Cells." <i>Chem Res Toxicol</i> <b>30</b>(4):1006–1014; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28140569 28140569]; doi: [https://dx.doi.org/10.1021/acs.chemrestox.6b00416 10.1021/acs.chemrestox.6b00416]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28140569 66]. | ||
#Abe Y, Nagano M, Tada A, Adachi J, Tomonaga T, (2017) "Deep Phosphotyrosine Proteomics by Optimization of Phosphotyrosine Enrichment and MS/MS Parameters." <i>J Proteome Res</i> <b>16</b>(2):1077–1086; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28152594 28152594]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00576 10.1021/acs.jproteome.6b00576]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28152594 41]. | #Abe Y, Nagano M, Tada A, Adachi J, Tomonaga T, (2017) "Deep Phosphotyrosine Proteomics by Optimization of Phosphotyrosine Enrichment and MS/MS Parameters." <i>J Proteome Res</i> <b>16</b>(2):1077–1086; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28152594 28152594]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00576 10.1021/acs.jproteome.6b00576]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28152594 41]. | ||
#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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/28153913 610]. | ||
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#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: [https://gpmdb.thegpm.org/data/keyword/28164708 7]. | #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: [https://gpmdb.thegpm.org/data/keyword/28164708 7]. | ||
#Petrovic V, Olaisen C, Sharma A, Nepal A, Bugge S, Sundby E, Hoff BH, Slupphaug G, Otterlei M, (2017) "On-column trypsinization allows for re-use of matrix in modified multiplexed inhibitor beads assay." <i>Anal Biochem</i> <b>523</b>:10–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28167071 28167071]; doi: [https://dx.doi.org/10.1016/j.ab.2017.01.027 10.1016/j.ab.2017.01.027]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28167071 3]. | #Petrovic V, Olaisen C, Sharma A, Nepal A, Bugge S, Sundby E, Hoff BH, Slupphaug G, Otterlei M, (2017) "On-column trypsinization allows for re-use of matrix in modified multiplexed inhibitor beads assay." <i>Anal Biochem</i> <b>523</b>:10–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28167071 28167071]; doi: [https://dx.doi.org/10.1016/j.ab.2017.01.027 10.1016/j.ab.2017.01.027]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28167071 3]. | ||
+ | #Worthington J, Spain G, Timms JF, (2017) "Effects of ErbB2 Overexpression on the Proteome and ErbB Ligand-specific Phosphosignaling in Mammary Luminal Epithelial Cells." <i>Mol Cell Proteomics</i> <b>16</b>(4):608–621; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28174229 28174229]; doi: [https://dx.doi.org/10.1074/mcp.M116.061267 10.1074/mcp.M116.061267]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28174229 190]. | ||
#Li X, Gao M, Choi JM, Kim BJ, Zhou MT, Chen Z, Jain AN, Jung SY, Yuan J, Wang W, Wang Y, Chen J, (2017) "CRISPR/Cas9-Coupled Affinity Purification/Mass Spectrometry Analysis Revealed a Novel Role of Neurofibromin in mTOR Signaling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28174230 28174230]; doi: [https://dx.doi.org/10.1074/mcp.M116.064543 10.1074/mcp.M116.064543]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28174230 44]. | #Li X, Gao M, Choi JM, Kim BJ, Zhou MT, Chen Z, Jain AN, Jung SY, Yuan J, Wang W, Wang Y, Chen J, (2017) "CRISPR/Cas9-Coupled Affinity Purification/Mass Spectrometry Analysis Revealed a Novel Role of Neurofibromin in mTOR Signaling." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28174230 28174230]; doi: [https://dx.doi.org/10.1074/mcp.M116.064543 10.1074/mcp.M116.064543]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28174230 44]. | ||
#Kalkan T, Olova N, Roode M, Mulas C, Lee HJ, Nett I, Marks H, Walker R, Stunnenberg HG, Lilley KS, Nichols J, Reik W, Bertone P, Smith A, (2017) "Tracking the embryonic stem cell transition from ground state pluripotency." <i>Development</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28174249 28174249]; doi: [https://dx.doi.org/10.1242/dev.142711 10.1242/dev.142711]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28174249 24]. | #Kalkan T, Olova N, Roode M, Mulas C, Lee HJ, Nett I, Marks H, Walker R, Stunnenberg HG, Lilley KS, Nichols J, Reik W, Bertone P, Smith A, (2017) "Tracking the embryonic stem cell transition from ground state pluripotency." <i>Development</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28174249 28174249]; doi: [https://dx.doi.org/10.1242/dev.142711 10.1242/dev.142711]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28174249 24]. | ||
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#Perl K, Ushakov K, Pozniak Y, Yizhar-Barnea O, Bhonker Y, Shivatzki S, Geiger T, Avraham KB, Shamir R, (2017) "Reduced changes in protein compared to mRNA levels across non-proliferating tissues." <i>BMC Genomics</i> <b>18</b>(1):305; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28420336 28420336]; doi: [https://dx.doi.org/10.1186/s12864-017-3683-9 10.1186/s12864-017-3683-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28420336 6]. | #Perl K, Ushakov K, Pozniak Y, Yizhar-Barnea O, Bhonker Y, Shivatzki S, Geiger T, Avraham KB, Shamir R, (2017) "Reduced changes in protein compared to mRNA levels across non-proliferating tissues." <i>BMC Genomics</i> <b>18</b>(1):305; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28420336 28420336]; doi: [https://dx.doi.org/10.1186/s12864-017-3683-9 10.1186/s12864-017-3683-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28420336 6]. | ||
#Mendoza-Viveros L, Chiang CK, Ong JLK, Hegazi S, Cheng AH, Bouchard-Cannon P, Fana M, Lowden C, Zhang P, Bothorel B, Michniewicz MG, Magill ST, Holmes MM, Goodman RH, Simonneaux V, Figeys D, Cheng HM, (2017) "miR-132/212 Modulates Seasonal Adaptation and Dendritic Morphology of the Central Circadian Clock." <i>Cell Rep</i> <b>19</b>(3):505–520; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28423315 28423315]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.03.057 10.1016/j.celrep.2017.03.057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28423315 128]. | #Mendoza-Viveros L, Chiang CK, Ong JLK, Hegazi S, Cheng AH, Bouchard-Cannon P, Fana M, Lowden C, Zhang P, Bothorel B, Michniewicz MG, Magill ST, Holmes MM, Goodman RH, Simonneaux V, Figeys D, Cheng HM, (2017) "miR-132/212 Modulates Seasonal Adaptation and Dendritic Morphology of the Central Circadian Clock." <i>Cell Rep</i> <b>19</b>(3):505–520; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28423315 28423315]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.03.057 10.1016/j.celrep.2017.03.057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28423315 128]. | ||
+ | #Maus RLG, Jakub JW, Nevala WK, Christensen TA, Noble-Orcutt K, Sachs Z, Hieken TJ, Markovic SN, (2017) "Human Melanoma-Derived Extracellular Vesicles Regulate Dendritic Cell Maturation." <i>Front Immunol</i> <b>8</b>:358; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28424693 28424693]; doi: [https://dx.doi.org/10.3389/fimmu.2017.00358 10.3389/fimmu.2017.00358]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28424693 18]. | ||
#Treiber T, Treiber N, Plessmann U, Harlander S, Daiß JL, Eichner N, Lehmann G, Schall K, Urlaub H, Meister G, (2017) "A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis." <i>Mol Cell</i> <b>66</b>(2):270–284.e13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28431233 28431233]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.03.014 10.1016/j.molcel.2017.03.014]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28431233 3033]. | #Treiber T, Treiber N, Plessmann U, Harlander S, Daiß JL, Eichner N, Lehmann G, Schall K, Urlaub H, Meister G, (2017) "A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis." <i>Mol Cell</i> <b>66</b>(2):270–284.e13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28431233 28431233]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.03.014 10.1016/j.molcel.2017.03.014]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28431233 3033]. | ||
#Beyene GT, Kalayou S, Riaz T, Tonjum T, (2017) "Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis." <i>BMC Microbiol</i> <b>17</b>(1):96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28431522 28431522]; doi: [https://dx.doi.org/10.1186/s12866-017-1004-8 10.1186/s12866-017-1004-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28431522 108]. | #Beyene GT, Kalayou S, Riaz T, Tonjum T, (2017) "Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis." <i>BMC Microbiol</i> <b>17</b>(1):96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28431522 28431522]; doi: [https://dx.doi.org/10.1186/s12866-017-1004-8 10.1186/s12866-017-1004-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28431522 108]. | ||
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#Sung E, Kwon OK, Lee JM, Lee S, (2017) "Proteomics approach to identify novel metastatic bone markers from the secretome of PC-3 prostate cancer cells." <i>Electrophoresis</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28627741 28627741]; doi: [https://dx.doi.org/10.1002/elps.201700052 10.1002/elps.201700052]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28627741 2]. | #Sung E, Kwon OK, Lee JM, Lee S, (2017) "Proteomics approach to identify novel metastatic bone markers from the secretome of PC-3 prostate cancer cells." <i>Electrophoresis</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28627741 28627741]; doi: [https://dx.doi.org/10.1002/elps.201700052 10.1002/elps.201700052]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28627741 2]. | ||
#Loke I, Østergaard O, Heegaard NHH, Packer NH, Thaysen-Andersen M, (2017) "Paucimannose-Rich <i>N</i>-glycosylation of Spatiotemporally Regulated Human Neutrophil Elastase Modulates Its Immune Functions." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28630087 28630087]; doi: [https://dx.doi.org/10.1074/mcp.M116.066746 10.1074/mcp.M116.066746]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28630087 118]. | #Loke I, Østergaard O, Heegaard NHH, Packer NH, Thaysen-Andersen M, (2017) "Paucimannose-Rich <i>N</i>-glycosylation of Spatiotemporally Regulated Human Neutrophil Elastase Modulates Its Immune Functions." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28630087 28630087]; doi: [https://dx.doi.org/10.1074/mcp.M116.066746 10.1074/mcp.M116.066746]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28630087 118]. | ||
+ | #Ahsan N, Belmont J, Chen Z, Clifton JG, Salomon AR, (2017) "Highly reproducible improved label-free quantitative analysis of cellular phosphoproteome by optimization of LC-MS/MS gradient and analytical column construction." <i>J Proteomics</i> <b>165</b>:69–74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28634120 28634120]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.06.013 10.1016/j.jprot.2017.06.013]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28634120 30]. | ||
#Feil G, Horres R, Schulte J, Mack AF, Petzoldt S, Arnold C, Meng C, Jost L, Boxleitner J, Kiessling-Wolf N, Serbest E, Helm D, Kuster B, Hartmann I, Korff T, Hahne H, (2017) "Bacterial cellulose shifts transcriptome and proteome of cultured endothelial cells towards native differentiation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28637836 28637836]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000001 10.1074/mcp.RA117.000001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28637836 2]. | #Feil G, Horres R, Schulte J, Mack AF, Petzoldt S, Arnold C, Meng C, Jost L, Boxleitner J, Kiessling-Wolf N, Serbest E, Helm D, Kuster B, Hartmann I, Korff T, Hahne H, (2017) "Bacterial cellulose shifts transcriptome and proteome of cultured endothelial cells towards native differentiation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28637836 28637836]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000001 10.1074/mcp.RA117.000001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28637836 2]. | ||
#Cosme J, Guo H, Hadipour-Lakmehsari S, Emili A, Gramolini AO, (2017) "Hypoxia-Induced Changes in the Fibroblast Secretome, Exosome, and Whole-Cell Proteome Using Cultured, Cardiac-Derived Cells Isolated from Neonatal Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28641008 28641008]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00144 10.1021/acs.jproteome.7b00144]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28641008 39]. | #Cosme J, Guo H, Hadipour-Lakmehsari S, Emili A, Gramolini AO, (2017) "Hypoxia-Induced Changes in the Fibroblast Secretome, Exosome, and Whole-Cell Proteome Using Cultured, Cardiac-Derived Cells Isolated from Neonatal Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28641008 28641008]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00144 10.1021/acs.jproteome.7b00144]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28641008 39]. | ||
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#Karg E, Smets M, Ryan J, Forné I, Qin W, Mulholland CB, Kalideris G, Imhof A, Bultmann S, Leonhardt H, (2017) "Ubiquitome analysis reveals PCNA-associated factor 15 (PAF15) as a specific ubiquitination target of UHRF1 in embryonic stem cells." <i>J Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29055779 29055779]; doi: [https://dx.doi.org/10.1016/j.jmb.2017.10.014 10.1016/j.jmb.2017.10.014]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29055779 32]. | #Karg E, Smets M, Ryan J, Forné I, Qin W, Mulholland CB, Kalideris G, Imhof A, Bultmann S, Leonhardt H, (2017) "Ubiquitome analysis reveals PCNA-associated factor 15 (PAF15) as a specific ubiquitination target of UHRF1 in embryonic stem cells." <i>J Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29055779 29055779]; doi: [https://dx.doi.org/10.1016/j.jmb.2017.10.014 10.1016/j.jmb.2017.10.014]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29055779 32]. | ||
#Hartl M, Füßl M, Boersema PJ, Jost JO, Kramer K, Bakirbas A, Sindlinger J, Plöchinger M, Leister D, Uhrig G, Moorhead GB, Cox J, Salvucci ME, Schwarzer D, Mann M, Finkemeier I, (2017) "Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in <i>Arabidopsis</i>." <i>Mol Syst Biol</i> <b>13</b>(10):949; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29061669 29061669]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29061669 44]. | #Hartl M, Füßl M, Boersema PJ, Jost JO, Kramer K, Bakirbas A, Sindlinger J, Plöchinger M, Leister D, Uhrig G, Moorhead GB, Cox J, Salvucci ME, Schwarzer D, Mann M, Finkemeier I, (2017) "Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in <i>Arabidopsis</i>." <i>Mol Syst Biol</i> <b>13</b>(10):949; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29061669 29061669]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29061669 44]. | ||
+ | #Graham LC, Eaton SL, Brunton PJ, Atrih A, Smith C, Lamont DJ, Gillingwater TH, Pennetta G, Skehel P, Wishart TM, (2017) "Proteomic profiling of neuronal mitochondria reveals modulators of synaptic architecture." <i>Mol Neurodegener</i> <b>12</b>(1):77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29078798 29078798]; doi: [https://dx.doi.org/10.1186/s13024-017-0221-9 10.1186/s13024-017-0221-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29078798 6]. | ||
#Pan D, Gao J, Zeng X, Ma G, Li N, Huang X, Du X, Miao Q, Lian J, Xu L, Zhou H, Chen S, (2017) "Quantitative proteomic Analysis Reveals up-regulation of caveolin-1 in FOXP3-overexpressed human gastric cancer cells." <i>Sci Rep</i> <b>7</b>(1):14460; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29089565 29089565]; doi: [https://dx.doi.org/10.1038/s41598-017-14453-2 10.1038/s41598-017-14453-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29089565 10]. | #Pan D, Gao J, Zeng X, Ma G, Li N, Huang X, Du X, Miao Q, Lian J, Xu L, Zhou H, Chen S, (2017) "Quantitative proteomic Analysis Reveals up-regulation of caveolin-1 in FOXP3-overexpressed human gastric cancer cells." <i>Sci Rep</i> <b>7</b>(1):14460; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29089565 29089565]; doi: [https://dx.doi.org/10.1038/s41598-017-14453-2 10.1038/s41598-017-14453-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29089565 10]. | ||
#Schuster H, Peper JK, Bösmüller HC, Röhle K, Backert L, Bilich T, Ney B, Löffler MW, Kowalewski DJ, Trautwein N, Rabsteyn A, Engler T, Braun S, Haen SP, Walz JS, Schmid-Horch B, Brucker SY, Wallwiener D, Kohlbacher O, Fend F, Rammensee HG, Stevanović S, Staebler A, Wagner P, (2017) "The immunopeptidomic landscape of ovarian carcinomas." <i>Proc Natl Acad Sci U S A</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29093164 29093164]; doi: [https://dx.doi.org/10.1073/pnas.1707658114 10.1073/pnas.1707658114]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29093164 275]. | #Schuster H, Peper JK, Bösmüller HC, Röhle K, Backert L, Bilich T, Ney B, Löffler MW, Kowalewski DJ, Trautwein N, Rabsteyn A, Engler T, Braun S, Haen SP, Walz JS, Schmid-Horch B, Brucker SY, Wallwiener D, Kohlbacher O, Fend F, Rammensee HG, Stevanović S, Staebler A, Wagner P, (2017) "The immunopeptidomic landscape of ovarian carcinomas." <i>Proc Natl Acad Sci U S A</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29093164 29093164]; doi: [https://dx.doi.org/10.1073/pnas.1707658114 10.1073/pnas.1707658114]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29093164 275]. | ||
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#Chen JT, Liu CC, Yu JS, Li HH, Lai MC, (2018) "Integrated omics profiling identifies hypoxia-regulated genes in HCT116 colon cancer cells." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29524648 29524648]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.02.031 10.1016/j.jprot.2018.02.031]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29524648 4]. | #Chen JT, Liu CC, Yu JS, Li HH, Lai MC, (2018) "Integrated omics profiling identifies hypoxia-regulated genes in HCT116 colon cancer cells." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29524648 29524648]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.02.031 10.1016/j.jprot.2018.02.031]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29524648 4]. | ||
#Deeke SA, Starr AE, Ning Z, Ahmadi S, Zhang X, Mayne J, Chiang CK, Singleton R, Benchimol EI, Mack DR, Stintzi A, Figeys D, (2018) "Mucosal-luminal interface proteomics reveals biomarkers of pediatric inflammatory bowel disease-associated colitis." <i>Am J Gastroenterol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29531307 29531307]; doi: [https://dx.doi.org/10.1038/s41395-018-0024-9 10.1038/s41395-018-0024-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29531307 112]. | #Deeke SA, Starr AE, Ning Z, Ahmadi S, Zhang X, Mayne J, Chiang CK, Singleton R, Benchimol EI, Mack DR, Stintzi A, Figeys D, (2018) "Mucosal-luminal interface proteomics reveals biomarkers of pediatric inflammatory bowel disease-associated colitis." <i>Am J Gastroenterol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29531307 29531307]; doi: [https://dx.doi.org/10.1038/s41395-018-0024-9 10.1038/s41395-018-0024-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29531307 112]. | ||
+ | #Costanza B, Turtoi A, Bellahcène A, Hirano T, Peulen O, Blomme A, Hennequière V, Mutijima E, Boniver J, Meuwis MA, Josse C, Koopmansch B, Segers K, Yokobori T, Fahmy K, Thiry M, Coimbra C, Garbacki N, Colige A, Baiwir D, Bours V, Louis E, Detry O, Delvenne P, Nishiyama M, Castronovo V, (2018) "Innovative methodology for the identification of soluble biomarkers in fresh tissues." <i>Oncotarget</i> <b>9</b>(12):10665–10680; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29535834 29535834]; doi: [https://dx.doi.org/10.18632/oncotarget.24366 10.18632/oncotarget.24366]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29535834 15]. | ||
#Zila N, Bileck A, Muqaku B, Janker L, Eichhoff OM, Cheng PF, Dummer R, Levesque MP, Gerner C, Paulitschke V, (2018) "Proteomics-based insights into mitogen-activated protein kinase inhibitor resistance of cerebral melanoma metastases." <i>Clin Proteomics</i> <b>15</b>:13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29541007 29541007]; doi: [https://dx.doi.org/10.1186/s12014-018-9189-x 10.1186/s12014-018-9189-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29541007 36]. | #Zila N, Bileck A, Muqaku B, Janker L, Eichhoff OM, Cheng PF, Dummer R, Levesque MP, Gerner C, Paulitschke V, (2018) "Proteomics-based insights into mitogen-activated protein kinase inhibitor resistance of cerebral melanoma metastases." <i>Clin Proteomics</i> <b>15</b>:13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29541007 29541007]; doi: [https://dx.doi.org/10.1186/s12014-018-9189-x 10.1186/s12014-018-9189-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29541007 36]. | ||
#Savitski MM, Zinn N, Faelth-Savitski M, Poeckel D, Gade S, Becher I, Muelbaier M, Wagner AJ, Strohmer K, Werner T, Melchert S, Petretich M, Rutkowska A, Vappiani J, Franken H, Steidel M, Sweetman GM, Gilan O, Lam EYN, Dawson MA, Prinjha RK, Grandi P, Bergamini G, Bantscheff M, (2018) "Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis." <i>Cell</i> <b>173</b>(1):260–274.e25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29551266 29551266]; doi: [https://dx.doi.org/10.1016/j.cell.2018.02.030 10.1016/j.cell.2018.02.030]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29551266 5]. | #Savitski MM, Zinn N, Faelth-Savitski M, Poeckel D, Gade S, Becher I, Muelbaier M, Wagner AJ, Strohmer K, Werner T, Melchert S, Petretich M, Rutkowska A, Vappiani J, Franken H, Steidel M, Sweetman GM, Gilan O, Lam EYN, Dawson MA, Prinjha RK, Grandi P, Bergamini G, Bantscheff M, (2018) "Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis." <i>Cell</i> <b>173</b>(1):260–274.e25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29551266 29551266]; doi: [https://dx.doi.org/10.1016/j.cell.2018.02.030 10.1016/j.cell.2018.02.030]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29551266 5]. | ||
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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]. | ||
- | #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 | + | #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]. |
+ | #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 10]. |
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 November 4, 2018.