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==Data from publications== | ==Data from publications== | ||
- | The following is a data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of | + | The following is a data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of April 4, 2016. |
#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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#Cubeñas-Potts C, Srikumar T, Lee C, Osula O, Subramonian D, Zhang XD, Cotter RJ, Raught B, Matunis MJ, (2015) "Identification of SUMO-2/3-modified proteins associated with mitotic chromosomes." <i>Proteomics</i> <b>15</b>(4):763–72; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25367092 25367092]; doi: [https://dx.doi.org/10.1002/pmic.201400400 10.1002/pmic.201400400]; GPMDB: [http://gpmdb.org/data/keyword/25367092 8]. | #Cubeñas-Potts C, Srikumar T, Lee C, Osula O, Subramonian D, Zhang XD, Cotter RJ, Raught B, Matunis MJ, (2015) "Identification of SUMO-2/3-modified proteins associated with mitotic chromosomes." <i>Proteomics</i> <b>15</b>(4):763–72; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25367092 25367092]; doi: [https://dx.doi.org/10.1002/pmic.201400400 10.1002/pmic.201400400]; GPMDB: [http://gpmdb.org/data/keyword/25367092 8]. | ||
#Pfeiffer MJ, Taher L, Drexler H, Suzuki Y, Makałowski W, Schwarzer C, Wang B, Fuellen G, Boiani M, (2015) "Differences in embryo quality are associated with differences in oocyte composition: a proteomic study in inbred mice." <i>Proteomics</i> <b>15</b>(4):675–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25367296 25367296]; doi: [https://dx.doi.org/10.1002/pmic.201400334 10.1002/pmic.201400334]; GPMDB: [http://gpmdb.org/data/keyword/25367296 4]. | #Pfeiffer MJ, Taher L, Drexler H, Suzuki Y, Makałowski W, Schwarzer C, Wang B, Fuellen G, Boiani M, (2015) "Differences in embryo quality are associated with differences in oocyte composition: a proteomic study in inbred mice." <i>Proteomics</i> <b>15</b>(4):675–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25367296 25367296]; doi: [https://dx.doi.org/10.1002/pmic.201400334 10.1002/pmic.201400334]; GPMDB: [http://gpmdb.org/data/keyword/25367296 4]. | ||
+ | #Lamoliatte F, Caron D, Durette C, Mahrouche L, Maroui MA, Caron-Lizotte O, Bonneil E, Chelbi-Alix MK, Thibault P, (2014) "Large-scale analysis of lysine SUMOylation by SUMO remnant immunoaffinity profiling." <i>Nat Commun</i> <b>5</b>:5409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25391492 25391492]; doi: [https://dx.doi.org/10.1038/ncomms6409 10.1038/ncomms6409]; GPMDB: [http://gpmdb.org/data/keyword/25391492 6]. | ||
#Ruprecht B, Koch H, Medard G, Mundt M, Kuster B, Lemeer S, (2015) "Comprehensive and reproducible phosphopeptide enrichment using iron immobilized metal ion affinity chromatography (Fe-IMAC) columns." <i>Mol Cell Proteomics</i> <b>14</b>(1):205–15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25394399 25394399]; doi: [https://dx.doi.org/10.1074/mcp.M114.043109 10.1074/mcp.M114.043109]; GPMDB: [http://gpmdb.org/data/keyword/25394399 152]. | #Ruprecht B, Koch H, Medard G, Mundt M, Kuster B, Lemeer S, (2015) "Comprehensive and reproducible phosphopeptide enrichment using iron immobilized metal ion affinity chromatography (Fe-IMAC) columns." <i>Mol Cell Proteomics</i> <b>14</b>(1):205–15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25394399 25394399]; doi: [https://dx.doi.org/10.1074/mcp.M114.043109 10.1074/mcp.M114.043109]; GPMDB: [http://gpmdb.org/data/keyword/25394399 152]. | ||
#Götzke H, Muheim C, Altelaar AF, Heck AJ, Maddalo G, Daley DO, (2015) "Identification of putative substrates for the periplasmic chaperone YfgM in Escherichia coli using quantitative proteomics." <i>Mol Cell Proteomics</i> <b>14</b>(1):216–26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25403562 25403562]; doi: [https://dx.doi.org/10.1074/mcp.M114.043216 10.1074/mcp.M114.043216]; GPMDB: [http://gpmdb.org/data/keyword/25403562 9]. | #Götzke H, Muheim C, Altelaar AF, Heck AJ, Maddalo G, Daley DO, (2015) "Identification of putative substrates for the periplasmic chaperone YfgM in Escherichia coli using quantitative proteomics." <i>Mol Cell Proteomics</i> <b>14</b>(1):216–26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25403562 25403562]; doi: [https://dx.doi.org/10.1074/mcp.M114.043216 10.1074/mcp.M114.043216]; GPMDB: [http://gpmdb.org/data/keyword/25403562 9]. | ||
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#Giguère SS, Guise AJ, Jean Beltran PM, Joshi PM, Greco TM, Quach OL, Kong J, Cristea IM, (2016) "The Proteomic Profile of Deleted in Breast Cancer 1 (DBC1) Interactions Points to a Multifaceted Regulation of Gene Expression." <i>Mol Cell Proteomics</i> <b>15</b>(3):791–809; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26657080 26657080]; doi: [https://dx.doi.org/10.1074/mcp.M115.054619 10.1074/mcp.M115.054619]; GPMDB: [http://gpmdb.org/data/keyword/26657080 109]. | #Giguère SS, Guise AJ, Jean Beltran PM, Joshi PM, Greco TM, Quach OL, Kong J, Cristea IM, (2016) "The Proteomic Profile of Deleted in Breast Cancer 1 (DBC1) Interactions Points to a Multifaceted Regulation of Gene Expression." <i>Mol Cell Proteomics</i> <b>15</b>(3):791–809; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26657080 26657080]; doi: [https://dx.doi.org/10.1074/mcp.M115.054619 10.1074/mcp.M115.054619]; GPMDB: [http://gpmdb.org/data/keyword/26657080 109]. | ||
#Su S, Zhu X, Lin L, Chen X, Wang Y, Zi J, Dong Y, Xie Y, Zhu Y, Zhang J, Zhu J, Xu D, Xu N, Lou X, Liu S, (2015) "Lowering endogenous cathepsin D abundance results in ROS accumulation and cell senescence." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26657266 26657266]; doi: [https://dx.doi.org/10.1074/mcp.M115.050179 10.1074/mcp.M115.050179]; GPMDB: [http://gpmdb.org/data/keyword/26657266 154]. | #Su S, Zhu X, Lin L, Chen X, Wang Y, Zi J, Dong Y, Xie Y, Zhu Y, Zhang J, Zhu J, Xu D, Xu N, Lou X, Liu S, (2015) "Lowering endogenous cathepsin D abundance results in ROS accumulation and cell senescence." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26657266 26657266]; doi: [https://dx.doi.org/10.1074/mcp.M115.050179 10.1074/mcp.M115.050179]; GPMDB: [http://gpmdb.org/data/keyword/26657266 154]. | ||
- | #Park JM, Park JH, Mun DG, Bae J, Jung JH, Back S, Lee H, Kim H, Jung HJ, Kim HK, Lee H, Kim KP, Hwang D, Lee SW, (2015) "Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks." <i>Sci Rep</i> <b>5</b>:18189; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26657352 26657352]; doi: [https://dx.doi.org/10.1038/srep18189 10.1038/srep18189]; GPMDB: [http://gpmdb.org/data/keyword/26657352 | + | #Park JM, Park JH, Mun DG, Bae J, Jung JH, Back S, Lee H, Kim H, Jung HJ, Kim HK, Lee H, Kim KP, Hwang D, Lee SW, (2015) "Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks." <i>Sci Rep</i> <b>5</b>:18189; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26657352 26657352]; doi: [https://dx.doi.org/10.1038/srep18189 10.1038/srep18189]; GPMDB: [http://gpmdb.org/data/keyword/26657352 144]. |
#Chen M, Hu Y, Liu J, Wu Q, Zhang C, Yu J, Xiao J, Wei F, Wu J, (2015) "Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome." <i>Sci Rep</i> <b>5</b>:18019; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26658305 26658305]; doi: [https://dx.doi.org/10.1038/srep18019 10.1038/srep18019]; GPMDB: [http://gpmdb.org/data/keyword/26658305 36]. | #Chen M, Hu Y, Liu J, Wu Q, Zhang C, Yu J, Xiao J, Wei F, Wu J, (2015) "Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome." <i>Sci Rep</i> <b>5</b>:18019; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26658305 26658305]; doi: [https://dx.doi.org/10.1038/srep18019 10.1038/srep18019]; GPMDB: [http://gpmdb.org/data/keyword/26658305 36]. | ||
#Mizuno Y, Nagano-Shoji M, Kubo S, Kawamura Y, Yoshida A, Kawasaki H, Nishiyama M, Yoshida M, Kosono S, (2016) "Altered acetylation and succinylation profiles in Corynebacterium glutamicum in response to conditions inducing glutamate overproduction." <i>Microbiologyopen</i> <b>5</b>(1):152–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26663479 26663479]; doi: [https://dx.doi.org/10.1002/mbo3.320 10.1002/mbo3.320]; GPMDB: [http://gpmdb.org/data/keyword/26663479 10]. | #Mizuno Y, Nagano-Shoji M, Kubo S, Kawamura Y, Yoshida A, Kawasaki H, Nishiyama M, Yoshida M, Kosono S, (2016) "Altered acetylation and succinylation profiles in Corynebacterium glutamicum in response to conditions inducing glutamate overproduction." <i>Microbiologyopen</i> <b>5</b>(1):152–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26663479 26663479]; doi: [https://dx.doi.org/10.1002/mbo3.320 10.1002/mbo3.320]; GPMDB: [http://gpmdb.org/data/keyword/26663479 10]. | ||
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#Cheng Z, Teo G, Krueger S, Rock TM, Koh HW, Choi H, Vogel C, (2016) "Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress." <i>Mol Syst Biol</i> <b>12</b>(1):855; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26792871 26792871]; GPMDB: [http://gpmdb.org/data/keyword/26792871 138]. | #Cheng Z, Teo G, Krueger S, Rock TM, Koh HW, Choi H, Vogel C, (2016) "Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress." <i>Mol Syst Biol</i> <b>12</b>(1):855; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26792871 26792871]; GPMDB: [http://gpmdb.org/data/keyword/26792871 138]. | ||
#Vincent D, Ezernieks V, Elkins A, Nguyen N, Moate PJ, Cocks BG, Rochfort S, (2015) "Milk Bottom-Up Proteomics: Method Optimization." <i>Front Genet</i> <b>6</b>:360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26793233 26793233]; doi: [https://dx.doi.org/10.3389/fgene.2015.00360 10.3389/fgene.2015.00360]; GPMDB: [http://gpmdb.org/data/keyword/26793233 262]. | #Vincent D, Ezernieks V, Elkins A, Nguyen N, Moate PJ, Cocks BG, Rochfort S, (2015) "Milk Bottom-Up Proteomics: Method Optimization." <i>Front Genet</i> <b>6</b>:360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26793233 26793233]; doi: [https://dx.doi.org/10.3389/fgene.2015.00360 10.3389/fgene.2015.00360]; GPMDB: [http://gpmdb.org/data/keyword/26793233 262]. | ||
- | #Li Q, Lex RK, Chung H, Giovanetti SM, Ji Z, Ji H, Person MD, Kim J, Vokes SA, (2016) "NANOG | + | #Li Q, Lex RK, Chung H, Giovanetti SM, Ji Z, Ji H, Person MD, Kim J, Vokes SA, (2016) "The Pluripotency Factor NANOG Binds to GLI Proteins and Represses Hedgehog-mediated Transcription." <i>J Biol Chem</i> <b>291</b>(13):7171–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26797124 26797124]; doi: [https://dx.doi.org/10.1074/jbc.M116.714857 10.1074/jbc.M116.714857]; GPMDB: [http://gpmdb.org/data/keyword/26797124 10]. |
#Schüller R, Forné I, Straub T, Schreieck A, Texier Y, Shah N, Decker TM, Cramer P, Imhof A, Eick D, (2016) "Heptad-Specific Phosphorylation of RNA Polymerase II CTD." <i>Mol Cell</i> <b>61</b>(2):305–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26799765 26799765]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.12.003 10.1016/j.molcel.2015.12.003]; GPMDB: [http://gpmdb.org/data/keyword/26799765 209]. | #Schüller R, Forné I, Straub T, Schreieck A, Texier Y, Shah N, Decker TM, Cramer P, Imhof A, Eick D, (2016) "Heptad-Specific Phosphorylation of RNA Polymerase II CTD." <i>Mol Cell</i> <b>61</b>(2):305–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26799765 26799765]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.12.003 10.1016/j.molcel.2015.12.003]; GPMDB: [http://gpmdb.org/data/keyword/26799765 209]. | ||
#Wojtuszkiewicz A, Schuurhuis GJ, Kessler FL, Piersma SR, Knol JC, Pham TV, Jansen G, Musters RJ, van Meerloo J, Assaraf YG, Kaspers GJ, Zweegman S, Cloos J, Jimenez CR, (2016) "Exosomes secreted by apoptosis-resistant AML blasts harbor regulatory network proteins potentially involved in antagonism of apoptosis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26801919 26801919]; doi: [https://dx.doi.org/10.1074/mcp.M115.052944 10.1074/mcp.M115.052944]; GPMDB: [http://gpmdb.org/data/keyword/26801919 271]. | #Wojtuszkiewicz A, Schuurhuis GJ, Kessler FL, Piersma SR, Knol JC, Pham TV, Jansen G, Musters RJ, van Meerloo J, Assaraf YG, Kaspers GJ, Zweegman S, Cloos J, Jimenez CR, (2016) "Exosomes secreted by apoptosis-resistant AML blasts harbor regulatory network proteins potentially involved in antagonism of apoptosis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26801919 26801919]; doi: [https://dx.doi.org/10.1074/mcp.M115.052944 10.1074/mcp.M115.052944]; GPMDB: [http://gpmdb.org/data/keyword/26801919 271]. | ||
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#Coman C, Solari FA, Hentschel A, Sickmann A, Zahedi RP, Ahrends R, (2016) "SIMPLEX: a combinatorial multimolecular omics approach for systems biology." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26814187 26814187]; doi: [https://dx.doi.org/10.1074/mcp.M115.053702 10.1074/mcp.M115.053702]; GPMDB: [http://gpmdb.org/data/keyword/26814187 68]. | #Coman C, Solari FA, Hentschel A, Sickmann A, Zahedi RP, Ahrends R, (2016) "SIMPLEX: a combinatorial multimolecular omics approach for systems biology." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26814187 26814187]; doi: [https://dx.doi.org/10.1074/mcp.M115.053702 10.1074/mcp.M115.053702]; GPMDB: [http://gpmdb.org/data/keyword/26814187 68]. | ||
#Bigaud E, Corrales FJ, (2016) "Methylthioadenosine regulates liver cells proteome and methylproteome. Implications in liver biology and disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26819315 26819315]; doi: [https://dx.doi.org/10.1074/mcp.M115.055772 10.1074/mcp.M115.055772]; GPMDB: [http://gpmdb.org/data/keyword/26819315 3]. | #Bigaud E, Corrales FJ, (2016) "Methylthioadenosine regulates liver cells proteome and methylproteome. Implications in liver biology and disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26819315 26819315]; doi: [https://dx.doi.org/10.1074/mcp.M115.055772 10.1074/mcp.M115.055772]; GPMDB: [http://gpmdb.org/data/keyword/26819315 3]. | ||
- | #Kristensen TN, Kjeldal H, Schou MF, Nielsen JL, (2016) "Proteomic data | + | #Kristensen TN, Kjeldal H, Schou MF, Nielsen JL, (2016) "Proteomic data reveal a physiological basis for costs and benefits associated with thermal acclimation." <i>J Exp Biol</i> <b>219</b>(Pt 7):969–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26823104 26823104]; doi: [https://dx.doi.org/10.1242/jeb.132696 10.1242/jeb.132696]; GPMDB: [http://gpmdb.org/data/keyword/26823104 9]. |
#Steger M, Tonelli F, Ito G, Davies P, Trost M, Vetter M, Wachter S, Lorentzen E, Duddy G, Wilson S, Baptista MA, Fiske BK, Fell MJ, Morrow JA, Reith AD, Alessi DR, Mann M, (2016) "Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26824392 26824392]; doi: [https://dx.doi.org/10.7554/eLife.12813 10.7554/eLife.12813]; GPMDB: [http://gpmdb.org/data/keyword/26824392 216]. | #Steger M, Tonelli F, Ito G, Davies P, Trost M, Vetter M, Wachter S, Lorentzen E, Duddy G, Wilson S, Baptista MA, Fiske BK, Fell MJ, Morrow JA, Reith AD, Alessi DR, Mann M, (2016) "Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26824392 26824392]; doi: [https://dx.doi.org/10.7554/eLife.12813 10.7554/eLife.12813]; GPMDB: [http://gpmdb.org/data/keyword/26824392 216]. | ||
#Chen Z, Tran M, Tang M, Wang W, Gong Z, Chen J, (2016) "Proteomic Analysis Reveals a Novel MutS Partner Involved in Mismatch Repair Pathway." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26828036 26828036]; doi: [https://dx.doi.org/10.1074/mcp.M115.056093 10.1074/mcp.M115.056093]; GPMDB: [http://gpmdb.org/data/keyword/26828036 22]. | #Chen Z, Tran M, Tang M, Wang W, Gong Z, Chen J, (2016) "Proteomic Analysis Reveals a Novel MutS Partner Involved in Mismatch Repair Pathway." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26828036 26828036]; doi: [https://dx.doi.org/10.1074/mcp.M115.056093 10.1074/mcp.M115.056093]; GPMDB: [http://gpmdb.org/data/keyword/26828036 22]. | ||
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#Kowal J, Arras G, Colombo M, Jouve M, Morath JP, Primdal-Bengtson B, Dingli F, Loew D, Tkach M, Théry C, (2016) "Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes." <i>Proc Natl Acad Sci U S A</i> <b>113</b>(8):E968–77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26858453 26858453]; doi: [https://dx.doi.org/10.1073/pnas.1521230113 10.1073/pnas.1521230113]; GPMDB: [http://gpmdb.org/data/keyword/26858453 56]. | #Kowal J, Arras G, Colombo M, Jouve M, Morath JP, Primdal-Bengtson B, Dingli F, Loew D, Tkach M, Théry C, (2016) "Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes." <i>Proc Natl Acad Sci U S A</i> <b>113</b>(8):E968–77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26858453 26858453]; doi: [https://dx.doi.org/10.1073/pnas.1521230113 10.1073/pnas.1521230113]; GPMDB: [http://gpmdb.org/data/keyword/26858453 56]. | ||
#Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C, (2016) "Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration." <i>Sci Signal</i> <b>9</b>(414):ra15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861043 26861043]; doi: [https://dx.doi.org/10.1126/scisignal.aac5820 10.1126/scisignal.aac5820]; GPMDB: [http://gpmdb.org/data/keyword/26861043 76]. | #Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C, (2016) "Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration." <i>Sci Signal</i> <b>9</b>(414):ra15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861043 26861043]; doi: [https://dx.doi.org/10.1126/scisignal.aac5820 10.1126/scisignal.aac5820]; GPMDB: [http://gpmdb.org/data/keyword/26861043 76]. | ||
- | #Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-Dürr P, Shah AM, Brandes RP, (2016) "The | + | #Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-Dürr P, Shah AM, Brandes RP, (2016) "The Endoplasmic Reticulum Chaperone Calnexin Is a NADPH Oxidase NOX4 Interacting Protein." <i>J Biol Chem</i> <b>291</b>(13):7045–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861875 26861875]; doi: [https://dx.doi.org/10.1074/jbc.M115.710772 10.1074/jbc.M115.710772]; GPMDB: [http://gpmdb.org/data/keyword/26861875 80]. |
#Lamberti Y, Cafiero JH, Surmann K, Valdez H, Holubova J, Večerek B, Sebo P, Schmidt F, Völker U, Rodriguez ME, (2016) "Proteome analysis of Bordetella pertussis isolated from human macrophages." <i>J Proteomics</i> <b>136</b>:55–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26873878 26873878]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.002 10.1016/j.jprot.2016.02.002]; GPMDB: [http://gpmdb.org/data/keyword/26873878 9]. | #Lamberti Y, Cafiero JH, Surmann K, Valdez H, Holubova J, Večerek B, Sebo P, Schmidt F, Völker U, Rodriguez ME, (2016) "Proteome analysis of Bordetella pertussis isolated from human macrophages." <i>J Proteomics</i> <b>136</b>:55–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26873878 26873878]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.002 10.1016/j.jprot.2016.02.002]; GPMDB: [http://gpmdb.org/data/keyword/26873878 9]. | ||
#Knöppel A, Näsvall J, Andersson DI, (2016) "Compensating the Fitness Costs of Synonymous Mutations." <i>Mol Biol Evol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26882986 26882986]; doi: [https://dx.doi.org/10.1093/molbev/msw028 10.1093/molbev/msw028]; GPMDB: [http://gpmdb.org/data/keyword/26882986 72]. | #Knöppel A, Näsvall J, Andersson DI, (2016) "Compensating the Fitness Costs of Synonymous Mutations." <i>Mol Biol Evol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26882986 26882986]; doi: [https://dx.doi.org/10.1093/molbev/msw028 10.1093/molbev/msw028]; GPMDB: [http://gpmdb.org/data/keyword/26882986 72]. | ||
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#Zufferey A, Ibberson M, Reny JL, Nolli S, Schvartz D, Docquier M, Xenarios I, Sanchez JC, Fontana P, (2016) "New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach." <i>Hum Genet</i> <b>135</b>(4):403–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26883867 26883867]; doi: [https://dx.doi.org/10.1007/s00439-016-1642-1 10.1007/s00439-016-1642-1]; GPMDB: [http://gpmdb.org/data/keyword/26883867 13]. | #Zufferey A, Ibberson M, Reny JL, Nolli S, Schvartz D, Docquier M, Xenarios I, Sanchez JC, Fontana P, (2016) "New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach." <i>Hum Genet</i> <b>135</b>(4):403–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26883867 26883867]; doi: [https://dx.doi.org/10.1007/s00439-016-1642-1 10.1007/s00439-016-1642-1]; GPMDB: [http://gpmdb.org/data/keyword/26883867 13]. | ||
#Huebner AR, Cheng L, Somparn P, Knepper MA, Fenton RA, Pisitkun T, (2016) "Deubiquitylation of protein cargo is not an essential step in exosome formation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26884507 26884507]; doi: [https://dx.doi.org/10.1074/mcp.M115.054965 10.1074/mcp.M115.054965]; GPMDB: [http://gpmdb.org/data/keyword/26884507 64]. | #Huebner AR, Cheng L, Somparn P, Knepper MA, Fenton RA, Pisitkun T, (2016) "Deubiquitylation of protein cargo is not an essential step in exosome formation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26884507 26884507]; doi: [https://dx.doi.org/10.1074/mcp.M115.054965 10.1074/mcp.M115.054965]; GPMDB: [http://gpmdb.org/data/keyword/26884507 64]. | ||
+ | #Ramallo Guevara C, Philipp O, Hamann A, Werner A, Osiewacz H, Rexroth S, Rögner M, Poetsch A, (2016) "Global protein oxidation profiling suggests efficient mitochondrial proteome homeostasis during ageing." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26884511 26884511]; doi: [https://dx.doi.org/10.1074/mcp.M115.055616 10.1074/mcp.M115.055616]; GPMDB: [http://gpmdb.org/data/keyword/26884511 17]. | ||
#Lee HL, Chiang IC, Liang SY, Lee DY, Chang GD, Wang KY, Lin SY, Shih YL, (2016) "Quantitative proteomics analysis reveals the Min system of Escherichia coli modulates reversible protein association with the inner membrane." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26889046 26889046]; doi: [https://dx.doi.org/10.1074/mcp.M115.053603 10.1074/mcp.M115.053603]; GPMDB: [http://gpmdb.org/data/keyword/26889046 4]. | #Lee HL, Chiang IC, Liang SY, Lee DY, Chang GD, Wang KY, Lin SY, Shih YL, (2016) "Quantitative proteomics analysis reveals the Min system of Escherichia coli modulates reversible protein association with the inner membrane." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26889046 26889046]; doi: [https://dx.doi.org/10.1074/mcp.M115.053603 10.1074/mcp.M115.053603]; GPMDB: [http://gpmdb.org/data/keyword/26889046 4]. | ||
#Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE, (2016) "Proteomic analysis reveals branch-specific regulation of the unfolded protein response by nonsense-mediated mRNA decay." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26896796 26896796]; doi: [https://dx.doi.org/10.1074/mcp.M115.054056 10.1074/mcp.M115.054056]; GPMDB: [http://gpmdb.org/data/keyword/26896796 4]. | #Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE, (2016) "Proteomic analysis reveals branch-specific regulation of the unfolded protein response by nonsense-mediated mRNA decay." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26896796 26896796]; doi: [https://dx.doi.org/10.1074/mcp.M115.054056 10.1074/mcp.M115.054056]; GPMDB: [http://gpmdb.org/data/keyword/26896796 4]. | ||
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#Lai ZW, Bolm L, Fuellgraf H, Biniossek ML, Makowiec F, Hopt UT, Werner M, Keck T, Bausch D, Sorio C, Scarpa A, Schilling O, Bronsert P, Wellner UF, (2016) "Characterization of various cell lines from different ampullary cancer subtypes and cancer associated fibroblast-mediated responses." <i>BMC Cancer</i> <b>16</b>(1):195; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26951071 26951071]; doi: [https://dx.doi.org/10.1186/s12885-016-2193-5 10.1186/s12885-016-2193-5]; GPMDB: [http://gpmdb.org/data/keyword/26951071 5]. | #Lai ZW, Bolm L, Fuellgraf H, Biniossek ML, Makowiec F, Hopt UT, Werner M, Keck T, Bausch D, Sorio C, Scarpa A, Schilling O, Bronsert P, Wellner UF, (2016) "Characterization of various cell lines from different ampullary cancer subtypes and cancer associated fibroblast-mediated responses." <i>BMC Cancer</i> <b>16</b>(1):195; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26951071 26951071]; doi: [https://dx.doi.org/10.1186/s12885-016-2193-5 10.1186/s12885-016-2193-5]; GPMDB: [http://gpmdb.org/data/keyword/26951071 5]. | ||
#Bonn F, Pané-Farré J, Schlüter R, Schaffer M, Fuchs S, Bernhardt J, Riedel K, Otto A, Völker U, van Dijl JM, Hecker M, Mäder U, Becher D, (2016) "Global analysis of the impact of linezolid onto virulence factor production in S. aureus USA300." <i>Int J Med Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26996810 26996810]; doi: [https://dx.doi.org/10.1016/j.ijmm.2016.02.004 10.1016/j.ijmm.2016.02.004]; GPMDB: [http://gpmdb.org/data/keyword/26996810 300]. | #Bonn F, Pané-Farré J, Schlüter R, Schaffer M, Fuchs S, Bernhardt J, Riedel K, Otto A, Völker U, van Dijl JM, Hecker M, Mäder U, Becher D, (2016) "Global analysis of the impact of linezolid onto virulence factor production in S. aureus USA300." <i>Int J Med Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26996810 26996810]; doi: [https://dx.doi.org/10.1016/j.ijmm.2016.02.004 10.1016/j.ijmm.2016.02.004]; GPMDB: [http://gpmdb.org/data/keyword/26996810 300]. | ||
- | #Wilkerson EM, Johansson MW, Hebert AS, Westphall MS, Mathur SK, Jarjour NN, Schwantes EA, Mosher | + | #He JJ, Ma J, Elsheikha HM, Song HQ, Zhou DH, Zhu XQ, (2016) "Proteomic Profiling of Mouse Liver following Acute Toxoplasma gondii Infection." <i>PLoS One</i> <b>11</b>(3):e0152022; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27003162 27003162]; doi: [https://dx.doi.org/10.1371/journal.pone.0152022 10.1371/journal.pone.0152022]; GPMDB: [http://gpmdb.org/data/keyword/27003162 1]. |
+ | #Wilkerson EM, Johansson MW, Hebert AS, Westphall MS, Mathur SK, Jarjour NN, Schwantes EA, Mosher DF, Coon JJ, (2016) "The Peripheral Blood Eosinophil Proteome." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27005946 27005946]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00006 10.1021/acs.jproteome.6b00006]; GPMDB: [http://gpmdb.org/data/keyword/27005946 45]. | ||
+ | #Lawrence RT, Searle BC, Llovet A, Villén J, (2016) "Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27018578 27018578]; doi: [https://dx.doi.org/10.1038/nmeth.3811 10.1038/nmeth.3811]; GPMDB: [http://gpmdb.org/data/keyword/27018578 6]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of April 4, 2016.