Line 24: | Line 24: | ||
==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 July 3, 2016. |
#Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." <i>Infect Immun</i> <b>57</b>(3):999–1001; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2645217 2645217]; GPMDB: [http://gpmdb.org/data/keyword/2645217 66]. | #Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." <i>Infect Immun</i> <b>57</b>(3):999–1001; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2645217 2645217]; GPMDB: [http://gpmdb.org/data/keyword/2645217 66]. | ||
Line 718: | Line 718: | ||
#Song Z, Chen L, Wang J, Lu Y, Jiang W, Zhang W, (2014) "A transcriptional regulator Sll0794 regulates tolerance to biofuel ethanol in photosynthetic Synechocystis sp. PCC 6803." <i>Mol Cell Proteomics</i> <b>13</b>(12):3519–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25239498 25239498]; doi: [https://dx.doi.org/10.1074/mcp.M113.035675 10.1074/mcp.M113.035675]; GPMDB: [http://gpmdb.org/data/keyword/25239498 21]. | #Song Z, Chen L, Wang J, Lu Y, Jiang W, Zhang W, (2014) "A transcriptional regulator Sll0794 regulates tolerance to biofuel ethanol in photosynthetic Synechocystis sp. PCC 6803." <i>Mol Cell Proteomics</i> <b>13</b>(12):3519–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25239498 25239498]; doi: [https://dx.doi.org/10.1074/mcp.M113.035675 10.1074/mcp.M113.035675]; GPMDB: [http://gpmdb.org/data/keyword/25239498 21]. | ||
#Wu X, Renuse S, Sahasrabuddhe NA, Zahari MS, Chaerkady R, Kim MS, Nirujogi RS, Mohseni M, Kumar P, Raju R, Zhong J, Yang J, Neiswinger J, Jeong JS, Newman R, Powers MA, Somani BL, Gabrielson E, Sukumar S, Stearns V, Qian J, Zhu H, Vogelstein B, Park BH, Pandey A, (2014) "Activation of diverse signalling pathways by oncogenic PIK3CA mutations." <i>Nat Commun</i> <b>5</b>:4961; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25247763 25247763]; doi: [https://dx.doi.org/10.1038/ncomms5961 10.1038/ncomms5961]; GPMDB: [http://gpmdb.org/data/keyword/25247763 91]. | #Wu X, Renuse S, Sahasrabuddhe NA, Zahari MS, Chaerkady R, Kim MS, Nirujogi RS, Mohseni M, Kumar P, Raju R, Zhong J, Yang J, Neiswinger J, Jeong JS, Newman R, Powers MA, Somani BL, Gabrielson E, Sukumar S, Stearns V, Qian J, Zhu H, Vogelstein B, Park BH, Pandey A, (2014) "Activation of diverse signalling pathways by oncogenic PIK3CA mutations." <i>Nat Commun</i> <b>5</b>:4961; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25247763 25247763]; doi: [https://dx.doi.org/10.1038/ncomms5961 10.1038/ncomms5961]; GPMDB: [http://gpmdb.org/data/keyword/25247763 91]. | ||
+ | #van der Lelij P, Stocsits RR, Ladurner R, Petzold G, Kreidl E, Koch B, Schmitz J, Neumann B, Ellenberg J, Peters JM, (2014) "SNW1 enables sister chromatid cohesion by mediating the splicing of sororin and APC2 pre-mRNAs." <i>EMBO J</i> <b>33</b>(22):2643–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25257309 25257309]; doi: [https://dx.doi.org/10.15252/embj.201488202 10.15252/embj.201488202]; GPMDB: [http://gpmdb.org/data/keyword/25257309 2]. | ||
#Zhong J, Martinez M, Sengupta S, Lee A, Wu X, Chaerkady R, Chatterjee A, O'Meally RN, Cole RN, Pandey A, Zachara NE, (2015) "Quantitative phosphoproteomics reveals crosstalk between phosphorylation and O-GlcNAc in the DNA damage response pathway." <i>Proteomics</i> <b>15</b>(2-3):591–607; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25263469 25263469]; doi: [https://dx.doi.org/10.1002/pmic.201400339 10.1002/pmic.201400339]; GPMDB: [http://gpmdb.org/data/keyword/25263469 6]. | #Zhong J, Martinez M, Sengupta S, Lee A, Wu X, Chaerkady R, Chatterjee A, O'Meally RN, Cole RN, Pandey A, Zachara NE, (2015) "Quantitative phosphoproteomics reveals crosstalk between phosphorylation and O-GlcNAc in the DNA damage response pathway." <i>Proteomics</i> <b>15</b>(2-3):591–607; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25263469 25263469]; doi: [https://dx.doi.org/10.1002/pmic.201400339 10.1002/pmic.201400339]; GPMDB: [http://gpmdb.org/data/keyword/25263469 6]. | ||
#Navarro MN, Goebel J, Hukelmann JL, Cantrell DA, (2014) "Quantitative phosphoproteomics of cytotoxic T cells to reveal protein kinase d 2 regulated networks." <i>Mol Cell Proteomics</i> <b>13</b>(12):3544–57; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25266776 25266776]; doi: [https://dx.doi.org/10.1074/mcp.M113.037242 10.1074/mcp.M113.037242]; GPMDB: [http://gpmdb.org/data/keyword/25266776 274]. | #Navarro MN, Goebel J, Hukelmann JL, Cantrell DA, (2014) "Quantitative phosphoproteomics of cytotoxic T cells to reveal protein kinase d 2 regulated networks." <i>Mol Cell Proteomics</i> <b>13</b>(12):3544–57; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25266776 25266776]; doi: [https://dx.doi.org/10.1074/mcp.M113.037242 10.1074/mcp.M113.037242]; GPMDB: [http://gpmdb.org/data/keyword/25266776 274]. | ||
Line 790: | Line 791: | ||
#Kasvandik S, Sillaste G, Velthut-Meikas A, Mikelsaar AV, Hallap T, Padrik P, Tenson T, Jaakma Ü, Kõks S, Salumets A, (2015) "Bovine sperm plasma membrane proteomics through biotinylation and subcellular enrichment." <i>Proteomics</i> <b>15</b>(11):1906–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25603787 25603787]; doi: [https://dx.doi.org/10.1002/pmic.201400297 10.1002/pmic.201400297]; GPMDB: [http://gpmdb.org/data/keyword/25603787 16]. | #Kasvandik S, Sillaste G, Velthut-Meikas A, Mikelsaar AV, Hallap T, Padrik P, Tenson T, Jaakma Ü, Kõks S, Salumets A, (2015) "Bovine sperm plasma membrane proteomics through biotinylation and subcellular enrichment." <i>Proteomics</i> <b>15</b>(11):1906–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25603787 25603787]; doi: [https://dx.doi.org/10.1002/pmic.201400297 10.1002/pmic.201400297]; GPMDB: [http://gpmdb.org/data/keyword/25603787 16]. | ||
#Byron A, Askari JA, Humphries JD, Jacquemet G, Koper EJ, Warwood S, Choi CK, Stroud MJ, Chen CS, Knight D, Humphries MJ, (2015) "A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting." <i>Nat Commun</i> <b>6</b>:6135; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25609142 25609142]; doi: [https://dx.doi.org/10.1038/ncomms7135 10.1038/ncomms7135]; GPMDB: [http://gpmdb.org/data/keyword/25609142 237]. | #Byron A, Askari JA, Humphries JD, Jacquemet G, Koper EJ, Warwood S, Choi CK, Stroud MJ, Chen CS, Knight D, Humphries MJ, (2015) "A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting." <i>Nat Commun</i> <b>6</b>:6135; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25609142 25609142]; doi: [https://dx.doi.org/10.1038/ncomms7135 10.1038/ncomms7135]; GPMDB: [http://gpmdb.org/data/keyword/25609142 237]. | ||
+ | #Braakman RB, Bezstarosti K, Sieuwerts AM, de Weerd V, van Galen AM, Stingl C, Luider TM, Timmermans MA, Smid M, Martens JW, Foekens JA, Demmers JA, Umar A, (2015) "Integrative analysis of genomics and proteomics data on clinical breast cancer tissue specimens extracted with acid guanidinium thiocyanate-phenol-chloroform." <i>J Proteome Res</i> <b>14</b>(3):1627–36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25611981 25611981]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00046 10.1021/acs.jproteome.5b00046]; GPMDB: [http://gpmdb.org/data/keyword/25611981 3]. | ||
#Deshmukh AS, Murgia M, Nagaraj N, Treebak JT, Cox J, Mann M, (2015) "Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors." <i>Mol Cell Proteomics</i> <b>14</b>(4):841–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25616865 25616865]; doi: [https://dx.doi.org/10.1074/mcp.M114.044222 10.1074/mcp.M114.044222]; GPMDB: [http://gpmdb.org/data/keyword/25616865 6]. | #Deshmukh AS, Murgia M, Nagaraj N, Treebak JT, Cox J, Mann M, (2015) "Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors." <i>Mol Cell Proteomics</i> <b>14</b>(4):841–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25616865 25616865]; doi: [https://dx.doi.org/10.1074/mcp.M114.044222 10.1074/mcp.M114.044222]; GPMDB: [http://gpmdb.org/data/keyword/25616865 6]. | ||
#Ramond E, Gesbert G, Guerrera IC, Chhuon C, Dupuis M, Rigard M, Henry T, Barel M, Charbit A, (2015) "Importance of host cell arginine uptake in Francisella phagosomal escape and ribosomal protein amounts." <i>Mol Cell Proteomics</i> <b>14</b>(4):870–81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25616868 25616868]; doi: [https://dx.doi.org/10.1074/mcp.M114.044552 10.1074/mcp.M114.044552]; GPMDB: [http://gpmdb.org/data/keyword/25616868 18]. | #Ramond E, Gesbert G, Guerrera IC, Chhuon C, Dupuis M, Rigard M, Henry T, Barel M, Charbit A, (2015) "Importance of host cell arginine uptake in Francisella phagosomal escape and ribosomal protein amounts." <i>Mol Cell Proteomics</i> <b>14</b>(4):870–81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25616868 25616868]; doi: [https://dx.doi.org/10.1074/mcp.M114.044552 10.1074/mcp.M114.044552]; GPMDB: [http://gpmdb.org/data/keyword/25616868 18]. | ||
Line 796: | Line 798: | ||
#Zanker D, Otto W, Chen W, von Bergen M, Tomm JM, (2015) "Compartment resolved reference proteome map from highly purified naïve, activated, effector, and memory CD8⁺ murine immune cells." <i>Proteomics</i> <b>15</b>(11):1808–12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25643623 25643623]; doi: [https://dx.doi.org/10.1002/pmic.201400405 10.1002/pmic.201400405]; GPMDB: [http://gpmdb.org/data/keyword/25643623 249]. | #Zanker D, Otto W, Chen W, von Bergen M, Tomm JM, (2015) "Compartment resolved reference proteome map from highly purified naïve, activated, effector, and memory CD8⁺ murine immune cells." <i>Proteomics</i> <b>15</b>(11):1808–12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25643623 25643623]; doi: [https://dx.doi.org/10.1002/pmic.201400405 10.1002/pmic.201400405]; GPMDB: [http://gpmdb.org/data/keyword/25643623 249]. | ||
#Murgia M, Nagaraj N, Deshmukh AS, Zeiler M, Cancellara P, Moretti I, Reggiani C, Schiaffino S, Mann M, (2015) "Single muscle fiber proteomics reveals unexpected mitochondrial specialization." <i>EMBO Rep</i> <b>16</b>(3):387–95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25643707 25643707]; doi: [https://dx.doi.org/10.15252/embr.201439757 10.15252/embr.201439757]; GPMDB: [http://gpmdb.org/data/keyword/25643707 89]. | #Murgia M, Nagaraj N, Deshmukh AS, Zeiler M, Cancellara P, Moretti I, Reggiani C, Schiaffino S, Mann M, (2015) "Single muscle fiber proteomics reveals unexpected mitochondrial specialization." <i>EMBO Rep</i> <b>16</b>(3):387–95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25643707 25643707]; doi: [https://dx.doi.org/10.15252/embr.201439757 10.15252/embr.201439757]; GPMDB: [http://gpmdb.org/data/keyword/25643707 89]. | ||
+ | #Eagle GL, Zhuang J, Jenkins RE, Till KJ, Jithesh PV, Lin K, Johnson GG, Oates M, Park K, Kitteringham NR, Pettitt AR, (2015) "Total proteome analysis identifies migration defects as a major pathogenetic factor in immunoglobulin heavy chain variable region (IGHV)-unmutated chronic lymphocytic leukemia." <i>Mol Cell Proteomics</i> <b>14</b>(4):933–45; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25645933 25645933]; doi: [https://dx.doi.org/10.1074/mcp.M114.044479 10.1074/mcp.M114.044479]; GPMDB: [http://gpmdb.org/data/keyword/25645933 3]. | ||
#Marza E, Taouji S, Barroso K, Raymond AA, Guignard L, Bonneu M, Pallares-Lupon N, Dupuy JW, Fernandez-Zapico ME, Rosenbaum J, Palladino F, Dupuy D, Chevet E, (2015) "Genome-wide screen identifies a novel p97/CDC-48-dependent pathway regulating ER-stress-induced gene transcription." <i>EMBO Rep</i> <b>16</b>(3):332–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25652260 25652260]; doi: [https://dx.doi.org/10.15252/embr.201439123 10.15252/embr.201439123]; GPMDB: [http://gpmdb.org/data/keyword/25652260 6]. | #Marza E, Taouji S, Barroso K, Raymond AA, Guignard L, Bonneu M, Pallares-Lupon N, Dupuy JW, Fernandez-Zapico ME, Rosenbaum J, Palladino F, Dupuy D, Chevet E, (2015) "Genome-wide screen identifies a novel p97/CDC-48-dependent pathway regulating ER-stress-induced gene transcription." <i>EMBO Rep</i> <b>16</b>(3):332–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25652260 25652260]; doi: [https://dx.doi.org/10.15252/embr.201439123 10.15252/embr.201439123]; GPMDB: [http://gpmdb.org/data/keyword/25652260 6]. | ||
#Corradini E, Burgers PP, Plank M, Heck AJ, Scholten A, (2015) "Huntingtin-associated protein 1 (HAP1) is a cGMP-dependent kinase anchoring protein (GKAP) specific for the cGMP-dependent protein kinase Iβ isoform." <i>J Biol Chem</i> <b>290</b>(12):7887–96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25653285 25653285]; doi: [https://dx.doi.org/10.1074/jbc.M114.622613 10.1074/jbc.M114.622613]; GPMDB: [http://gpmdb.org/data/keyword/25653285 6]. | #Corradini E, Burgers PP, Plank M, Heck AJ, Scholten A, (2015) "Huntingtin-associated protein 1 (HAP1) is a cGMP-dependent kinase anchoring protein (GKAP) specific for the cGMP-dependent protein kinase Iβ isoform." <i>J Biol Chem</i> <b>290</b>(12):7887–96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25653285 25653285]; doi: [https://dx.doi.org/10.1074/jbc.M114.622613 10.1074/jbc.M114.622613]; GPMDB: [http://gpmdb.org/data/keyword/25653285 6]. | ||
Line 823: | Line 826: | ||
#Martin-Perez M, Villén J, (2015) "Feasibility of protein turnover studies in prototroph Saccharomyces cerevisiae strains." <i>Anal Chem</i> <b>87</b>(7):4008–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25767917 25767917]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b00264 10.1021/acs.analchem.5b00264]; GPMDB: [http://gpmdb.org/data/keyword/25767917 22]. | #Martin-Perez M, Villén J, (2015) "Feasibility of protein turnover studies in prototroph Saccharomyces cerevisiae strains." <i>Anal Chem</i> <b>87</b>(7):4008–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25767917 25767917]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b00264 10.1021/acs.analchem.5b00264]; GPMDB: [http://gpmdb.org/data/keyword/25767917 22]. | ||
#Zub KA, Sousa MM, Sarno A, Sharma A, Demirovic A, Rao S, Young C, Aas PA, Ericsson I, Sundan A, Jensen ON, Slupphaug G, (2015) "Modulation of cell metabolic pathways and oxidative stress signaling contribute to acquired melphalan resistance in multiple myeloma cells." <i>PLoS One</i> <b>10</b>(3):e0119857; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25769101 25769101]; doi: [https://dx.doi.org/10.1371/journal.pone.0119857 10.1371/journal.pone.0119857]; GPMDB: [http://gpmdb.org/data/keyword/25769101 12]. | #Zub KA, Sousa MM, Sarno A, Sharma A, Demirovic A, Rao S, Young C, Aas PA, Ericsson I, Sundan A, Jensen ON, Slupphaug G, (2015) "Modulation of cell metabolic pathways and oxidative stress signaling contribute to acquired melphalan resistance in multiple myeloma cells." <i>PLoS One</i> <b>10</b>(3):e0119857; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25769101 25769101]; doi: [https://dx.doi.org/10.1371/journal.pone.0119857 10.1371/journal.pone.0119857]; GPMDB: [http://gpmdb.org/data/keyword/25769101 12]. | ||
+ | #Zigdon H, Savidor A, Levin Y, Meshcheriakova A, Schiffmann R, Futerman AH, (2015) "Identification of a biomarker in cerebrospinal fluid for neuronopathic forms of Gaucher disease." <i>PLoS One</i> <b>10</b>(3):e0120194; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25775479 25775479]; doi: [https://dx.doi.org/10.1371/journal.pone.0120194 10.1371/journal.pone.0120194]; GPMDB: [http://gpmdb.org/data/keyword/25775479 27]. | ||
#Shalit T, Elinger D, Savidor A, Gabashvili A, Levin Y, (2015) "MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer." <i>J Proteome Res</i> <b>14</b>(4):1979–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25780947 25780947]; doi: [https://dx.doi.org/10.1021/pr501045t 10.1021/pr501045t]; GPMDB: [http://gpmdb.org/data/keyword/25780947 12]. | #Shalit T, Elinger D, Savidor A, Gabashvili A, Levin Y, (2015) "MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer." <i>J Proteome Res</i> <b>14</b>(4):1979–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25780947 25780947]; doi: [https://dx.doi.org/10.1021/pr501045t 10.1021/pr501045t]; GPMDB: [http://gpmdb.org/data/keyword/25780947 12]. | ||
#Markmann S, Thelen M, Cornils K, Schweizer M, Brocke-Ahmadinejad N, Willnow T, Heeren J, Gieselmann V, Braulke T, Kollmann K, (2015) "Lrp1/LDL Receptor Play Critical Roles in Mannose 6-Phosphate-Independent Lysosomal Enzyme Targeting." <i>Traffic</i> <b>16</b>(7):743–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25786328 25786328]; doi: [https://dx.doi.org/10.1111/tra.12284 10.1111/tra.12284]; GPMDB: [http://gpmdb.org/data/keyword/25786328 3]. | #Markmann S, Thelen M, Cornils K, Schweizer M, Brocke-Ahmadinejad N, Willnow T, Heeren J, Gieselmann V, Braulke T, Kollmann K, (2015) "Lrp1/LDL Receptor Play Critical Roles in Mannose 6-Phosphate-Independent Lysosomal Enzyme Targeting." <i>Traffic</i> <b>16</b>(7):743–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25786328 25786328]; doi: [https://dx.doi.org/10.1111/tra.12284 10.1111/tra.12284]; GPMDB: [http://gpmdb.org/data/keyword/25786328 3]. | ||
Line 856: | Line 860: | ||
#Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E, (2015) "A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery." <i>J Proteome Res</i> <b>14</b>(7):2807–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25944384 25944384]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00315 10.1021/acs.jproteome.5b00315]; GPMDB: [http://gpmdb.org/data/keyword/25944384 238]. | #Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E, (2015) "A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery." <i>J Proteome Res</i> <b>14</b>(7):2807–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25944384 25944384]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00315 10.1021/acs.jproteome.5b00315]; GPMDB: [http://gpmdb.org/data/keyword/25944384 238]. | ||
#Svinkina T, Gu H, Silva JC, Mertins P, Qiao J, Fereshetian S, Jaffe JD, Kuhn E, Udeshi ND, Carr SA, (2015) "Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow." <i>Mol Cell Proteomics</i> <b>14</b>(9):2429–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25953088 25953088]; doi: [https://dx.doi.org/10.1074/mcp.O114.047555 10.1074/mcp.O114.047555]; GPMDB: [http://gpmdb.org/data/keyword/25953088 30]. | #Svinkina T, Gu H, Silva JC, Mertins P, Qiao J, Fereshetian S, Jaffe JD, Kuhn E, Udeshi ND, Carr SA, (2015) "Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow." <i>Mol Cell Proteomics</i> <b>14</b>(9):2429–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25953088 25953088]; doi: [https://dx.doi.org/10.1074/mcp.O114.047555 10.1074/mcp.O114.047555]; GPMDB: [http://gpmdb.org/data/keyword/25953088 30]. | ||
+ | #Madeira JP, Alpha-Bazin B, Armengaud J, Duport C, (2015) "Time dynamics of the Bacillus cereus exoproteome are shaped by cellular oxidation." <i>Front Microbiol</i> <b>6</b>:342; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25954265 25954265]; doi: [https://dx.doi.org/10.3389/fmicb.2015.00342 10.3389/fmicb.2015.00342]; GPMDB: [http://gpmdb.org/data/keyword/25954265 30]. | ||
#Walther DM, Kasturi P, Zheng M, Pinkert S, Vecchi G, Ciryam P, Morimoto RI, Dobson CM, Vendruscolo M, Mann M, Hartl FU, (2015) "Widespread Proteome Remodeling and Aggregation in Aging C. elegans." <i>Cell</i> <b>161</b>(4):919–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25957690 25957690]; doi: [https://dx.doi.org/10.1016/j.cell.2015.03.032 10.1016/j.cell.2015.03.032]; GPMDB: [http://gpmdb.org/data/keyword/25957690 278]. | #Walther DM, Kasturi P, Zheng M, Pinkert S, Vecchi G, Ciryam P, Morimoto RI, Dobson CM, Vendruscolo M, Mann M, Hartl FU, (2015) "Widespread Proteome Remodeling and Aggregation in Aging C. elegans." <i>Cell</i> <b>161</b>(4):919–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25957690 25957690]; doi: [https://dx.doi.org/10.1016/j.cell.2015.03.032 10.1016/j.cell.2015.03.032]; GPMDB: [http://gpmdb.org/data/keyword/25957690 278]. | ||
#Hosp F, Vossfeldt H, Heinig M, Vasiljevic D, Arumughan A, Wyler E, Genetic and Environmental Risk for Alzheimer’s Disease GERAD1 Consortium, Landthaler M, Hubner N, Wanker EE, Lannfelt L, Ingelsson M, Lalowski M, Voigt A, Selbach M, (2015) "Quantitative interaction proteomics of neurodegenerative disease proteins." <i>Cell Rep</i> <b>11</b>(7):1134–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25959826 25959826]; doi: [https://dx.doi.org/10.1016/j.celrep.2015.04.030 10.1016/j.celrep.2015.04.030]; GPMDB: [http://gpmdb.org/data/keyword/25959826 122]. | #Hosp F, Vossfeldt H, Heinig M, Vasiljevic D, Arumughan A, Wyler E, Genetic and Environmental Risk for Alzheimer’s Disease GERAD1 Consortium, Landthaler M, Hubner N, Wanker EE, Lannfelt L, Ingelsson M, Lalowski M, Voigt A, Selbach M, (2015) "Quantitative interaction proteomics of neurodegenerative disease proteins." <i>Cell Rep</i> <b>11</b>(7):1134–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25959826 25959826]; doi: [https://dx.doi.org/10.1016/j.celrep.2015.04.030 10.1016/j.celrep.2015.04.030]; GPMDB: [http://gpmdb.org/data/keyword/25959826 122]. | ||
Line 968: | Line 973: | ||
#Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT, (2015) "Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics." <i>J Proteome Res</i> <b>14</b>(11):4792–804; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26435507 26435507]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00575 10.1021/acs.jproteome.5b00575]; GPMDB: [http://gpmdb.org/data/keyword/26435507 3]. | #Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT, (2015) "Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics." <i>J Proteome Res</i> <b>14</b>(11):4792–804; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26435507 26435507]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00575 10.1021/acs.jproteome.5b00575]; GPMDB: [http://gpmdb.org/data/keyword/26435507 3]. | ||
#Alanko J, Mai A, Jacquemet G, Schauer K, Kaukonen R, Saari M, Goud B, Ivaska J, (2015) "Integrin endosomal signalling suppresses anoikis." <i>Nat Cell Biol</i> <b>17</b>(11):1412–21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26436690 26436690]; doi: [https://dx.doi.org/10.1038/ncb3250 10.1038/ncb3250]; GPMDB: [http://gpmdb.org/data/keyword/26436690 60]. | #Alanko J, Mai A, Jacquemet G, Schauer K, Kaukonen R, Saari M, Goud B, Ivaska J, (2015) "Integrin endosomal signalling suppresses anoikis." <i>Nat Cell Biol</i> <b>17</b>(11):1412–21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26436690 26436690]; doi: [https://dx.doi.org/10.1038/ncb3250 10.1038/ncb3250]; GPMDB: [http://gpmdb.org/data/keyword/26436690 60]. | ||
+ | #Hoffman NJ, Parker BL, Chaudhuri R, Fisher-Wellman KH, Kleinert M, Humphrey SJ, Yang P, Holliday M, Trefely S, Fazakerley DJ, Stöckli J, Burchfield JG, Jensen TE, Jothi R, Kiens B, Wojtaszewski JF, Richter EA, James DE, (2015) "Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates." <i>Cell Metab</i> <b>22</b>(5):922–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26437602 26437602]; doi: [https://dx.doi.org/10.1016/j.cmet.2015.09.001 10.1016/j.cmet.2015.09.001]; GPMDB: [http://gpmdb.org/data/keyword/26437602 28]. | ||
#Matheson NJ, Sumner J, Wals K, Rapiteanu R, Weekes MP, Vigan R, Weinelt J, Schindler M, Antrobus R, Costa AS, Frezza C, Clish CB, Neil SJ, Lehner PJ, (2015) "Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef." <i>Cell Host Microbe</i> <b>18</b>(4):409–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26439863 26439863]; doi: [https://dx.doi.org/10.1016/j.chom.2015.09.003 10.1016/j.chom.2015.09.003]; GPMDB: [http://gpmdb.org/data/keyword/26439863 10]. | #Matheson NJ, Sumner J, Wals K, Rapiteanu R, Weekes MP, Vigan R, Weinelt J, Schindler M, Antrobus R, Costa AS, Frezza C, Clish CB, Neil SJ, Lehner PJ, (2015) "Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef." <i>Cell Host Microbe</i> <b>18</b>(4):409–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26439863 26439863]; doi: [https://dx.doi.org/10.1016/j.chom.2015.09.003 10.1016/j.chom.2015.09.003]; GPMDB: [http://gpmdb.org/data/keyword/26439863 10]. | ||
#Zhang H, Ramakrishnan SK, Triner D, Centofanti B, Maitra D, Győrffy B, Sebolt-Leopold JS, Dame MK, Varani J, Brenner DE, Fearon ER, Omary MB, Shah YM, (2015) "Tumor-selective proteotoxicity of verteporfin inhibits colon cancer progression independently of YAP1." <i>Sci Signal</i> <b>8</b>(397):ra98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26443705 26443705]; doi: [https://dx.doi.org/10.1126/scisignal.aac5418 10.1126/scisignal.aac5418]; GPMDB: [http://gpmdb.org/data/keyword/26443705 2]. | #Zhang H, Ramakrishnan SK, Triner D, Centofanti B, Maitra D, Győrffy B, Sebolt-Leopold JS, Dame MK, Varani J, Brenner DE, Fearon ER, Omary MB, Shah YM, (2015) "Tumor-selective proteotoxicity of verteporfin inhibits colon cancer progression independently of YAP1." <i>Sci Signal</i> <b>8</b>(397):ra98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26443705 26443705]; doi: [https://dx.doi.org/10.1126/scisignal.aac5418 10.1126/scisignal.aac5418]; GPMDB: [http://gpmdb.org/data/keyword/26443705 2]. | ||
#Kwon OK, Kim SJ, Lee YM, Lee YH, Bae YS, Kim JY, Peng X, Cheng Z, Zhao Y, Lee S, (2016) "Global analysis of phosphoproteome dynamics in embryonic development of zebrafish (Danio rerio)." <i>Proteomics</i> <b>16</b>(1):136–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26449285 26449285]; doi: [https://dx.doi.org/10.1002/pmic.201500017 10.1002/pmic.201500017]; GPMDB: [http://gpmdb.org/data/keyword/26449285 32]. | #Kwon OK, Kim SJ, Lee YM, Lee YH, Bae YS, Kim JY, Peng X, Cheng Z, Zhao Y, Lee S, (2016) "Global analysis of phosphoproteome dynamics in embryonic development of zebrafish (Danio rerio)." <i>Proteomics</i> <b>16</b>(1):136–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26449285 26449285]; doi: [https://dx.doi.org/10.1002/pmic.201500017 10.1002/pmic.201500017]; GPMDB: [http://gpmdb.org/data/keyword/26449285 32]. | ||
- | #Geddes JM, Croll D, Caza M, Stoynov N, Foster LJ, Kronstad JW, (2015) "Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A." <i>BMC Microbiol</i> <b>15</b> | + | #Geddes JM, Croll D, Caza M, Stoynov N, Foster LJ, Kronstad JW, (2015) "Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A." <i>BMC Microbiol</i> <b>15</b>:206; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26453029 26453029]; doi: [https://dx.doi.org/10.1186/s12866-015-0532-3 10.1186/s12866-015-0532-3]; GPMDB: [http://gpmdb.org/data/keyword/26453029 48]. |
#Gomez-Auli A, Hillebrand LE, Biniossek ML, Peters C, Reinheckel T, Schilling O, (2016) "Impact of cathepsin B on the interstitial fluid proteome of murine breast cancers." <i>Biochimie</i> <b>122</b>:88–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26455267 26455267]; doi: [https://dx.doi.org/10.1016/j.biochi.2015.10.009 10.1016/j.biochi.2015.10.009]; GPMDB: [http://gpmdb.org/data/keyword/26455267 1]. | #Gomez-Auli A, Hillebrand LE, Biniossek ML, Peters C, Reinheckel T, Schilling O, (2016) "Impact of cathepsin B on the interstitial fluid proteome of murine breast cancers." <i>Biochimie</i> <b>122</b>:88–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26455267 26455267]; doi: [https://dx.doi.org/10.1016/j.biochi.2015.10.009 10.1016/j.biochi.2015.10.009]; GPMDB: [http://gpmdb.org/data/keyword/26455267 1]. | ||
#Poli M, Ori A, Child T, Jaroudi S, Spath K, Beck M, Wells D, (2015) "Characterization and quantification of proteins secreted by single human embryos prior to implantation." <i>EMBO Mol Med</i> <b>7</b>(11):1465–79; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26471863 26471863]; doi: [https://dx.doi.org/10.15252/emmm.201505344 10.15252/emmm.201505344]; GPMDB: [http://gpmdb.org/data/keyword/26471863 11]. | #Poli M, Ori A, Child T, Jaroudi S, Spath K, Beck M, Wells D, (2015) "Characterization and quantification of proteins secreted by single human embryos prior to implantation." <i>EMBO Mol Med</i> <b>7</b>(11):1465–79; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26471863 26471863]; doi: [https://dx.doi.org/10.15252/emmm.201505344 10.15252/emmm.201505344]; GPMDB: [http://gpmdb.org/data/keyword/26471863 11]. | ||
#Schlage P, Kockmann T, Sabino F, Kizhakkedathu JN, Auf dem Keller U, (2015) "Matrix Metalloproteinase 10 Degradomics in Keratinocytes and Epidermal Tissue Identifies Bioactive Substrates With Pleiotropic Functions." <i>Mol Cell Proteomics</i> <b>14</b>(12):3234–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26475864 26475864]; doi: [https://dx.doi.org/10.1074/mcp.M115.053520 10.1074/mcp.M115.053520]; GPMDB: [http://gpmdb.org/data/keyword/26475864 25]. | #Schlage P, Kockmann T, Sabino F, Kizhakkedathu JN, Auf dem Keller U, (2015) "Matrix Metalloproteinase 10 Degradomics in Keratinocytes and Epidermal Tissue Identifies Bioactive Substrates With Pleiotropic Functions." <i>Mol Cell Proteomics</i> <b>14</b>(12):3234–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26475864 26475864]; doi: [https://dx.doi.org/10.1074/mcp.M115.053520 10.1074/mcp.M115.053520]; GPMDB: [http://gpmdb.org/data/keyword/26475864 25]. | ||
+ | #Horton ER, Byron A, Askari JA, Ng DH, Millon-Frémillon A, Robertson J, Koper EJ, Paul NR, Warwood S, Knight D, Humphries JD, Humphries MJ, (2015) "Definition of a consensus integrin adhesome and its dynamics during adhesion complex assembly and disassembly." <i>Nat Cell Biol</i> <b>17</b>(12):1577–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26479319 26479319]; doi: [https://dx.doi.org/10.1038/ncb3257 10.1038/ncb3257]; GPMDB: [http://gpmdb.org/data/keyword/26479319 100]. | ||
#Hein MY, Hubner NC, Poser I, Cox J, Nagaraj N, Toyoda Y, Gak IA, Weisswange I, Mansfeld J, Buchholz F, Hyman AA, Mann M, (2015) "A human interactome in three quantitative dimensions organized by stoichiometries and abundances." <i>Cell</i> <b>163</b>(3):712–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26496610 26496610]; doi: [https://dx.doi.org/10.1016/j.cell.2015.09.053 10.1016/j.cell.2015.09.053]; GPMDB: [http://gpmdb.org/data/keyword/26496610 4296]. | #Hein MY, Hubner NC, Poser I, Cox J, Nagaraj N, Toyoda Y, Gak IA, Weisswange I, Mansfeld J, Buchholz F, Hyman AA, Mann M, (2015) "A human interactome in three quantitative dimensions organized by stoichiometries and abundances." <i>Cell</i> <b>163</b>(3):712–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26496610 26496610]; doi: [https://dx.doi.org/10.1016/j.cell.2015.09.053 10.1016/j.cell.2015.09.053]; GPMDB: [http://gpmdb.org/data/keyword/26496610 4296]. | ||
#Hu CW, Hsu CL, Wang YC, Ishihama Y, Ku WC, Huang HC, Juan HF, (2015) "Temporal Phosphoproteome Dynamics Induced by an ATP Synthase Inhibitor Citreoviridin." <i>Mol Cell Proteomics</i> <b>14</b>(12):3284–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26503892 26503892]; doi: [https://dx.doi.org/10.1074/mcp.M115.051383 10.1074/mcp.M115.051383]; GPMDB: [http://gpmdb.org/data/keyword/26503892 48]. | #Hu CW, Hsu CL, Wang YC, Ishihama Y, Ku WC, Huang HC, Juan HF, (2015) "Temporal Phosphoproteome Dynamics Induced by an ATP Synthase Inhibitor Citreoviridin." <i>Mol Cell Proteomics</i> <b>14</b>(12):3284–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26503892 26503892]; doi: [https://dx.doi.org/10.1074/mcp.M115.051383 10.1074/mcp.M115.051383]; GPMDB: [http://gpmdb.org/data/keyword/26503892 48]. | ||
Line 991: | Line 998: | ||
#Kito K, Ito H, Nohara T, Ohnishi M, Ishibashi Y, Takeda D, (2016) "Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication." <i>Mol Cell Proteomics</i> <b>15</b>(1):218–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26560065 26560065]; doi: [https://dx.doi.org/10.1074/mcp.M115.051854 10.1074/mcp.M115.051854]; GPMDB: [http://gpmdb.org/data/keyword/26560065 150]. | #Kito K, Ito H, Nohara T, Ohnishi M, Ishibashi Y, Takeda D, (2016) "Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication." <i>Mol Cell Proteomics</i> <b>15</b>(1):218–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26560065 26560065]; doi: [https://dx.doi.org/10.1074/mcp.M115.051854 10.1074/mcp.M115.051854]; GPMDB: [http://gpmdb.org/data/keyword/26560065 150]. | ||
#Zhao Y, Valbuena G, Walker DH, Gazi M, Hidalgo M, DeSousa R, Oteo JA, Goez Y, Brasier AR, (2016) "Endothelial Cell Proteomic Response to Rickettsia conorii Infection Reveals Activation of the Janus Kinase (JAK)-Signal Transducer and Activator of Transcription (STAT)-Inferferon Stimulated Gene (ISG)15 Pathway and Reprogramming Plasma Membrane Integrin/Cadherin Signaling." <i>Mol Cell Proteomics</i> <b>15</b>(1):289–304; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26560068 26560068]; doi: [https://dx.doi.org/10.1074/mcp.M115.054361 10.1074/mcp.M115.054361]; GPMDB: [http://gpmdb.org/data/keyword/26560068 7]. | #Zhao Y, Valbuena G, Walker DH, Gazi M, Hidalgo M, DeSousa R, Oteo JA, Goez Y, Brasier AR, (2016) "Endothelial Cell Proteomic Response to Rickettsia conorii Infection Reveals Activation of the Janus Kinase (JAK)-Signal Transducer and Activator of Transcription (STAT)-Inferferon Stimulated Gene (ISG)15 Pathway and Reprogramming Plasma Membrane Integrin/Cadherin Signaling." <i>Mol Cell Proteomics</i> <b>15</b>(1):289–304; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26560068 26560068]; doi: [https://dx.doi.org/10.1074/mcp.M115.054361 10.1074/mcp.M115.054361]; GPMDB: [http://gpmdb.org/data/keyword/26560068 7]. | ||
- | #Tutakhel OA, Jeleń S, Valdez-Flores M, Dimke H, Piersma SR, Jimenez CR, Deinum J, Lenders JW, Hoenderop JG, Bindels RJ, (2016) "Alternative splice variant of the thiazide-sensitive NaCl cotransporter: a novel player in renal salt handling." <i>Am J Physiol Renal Physiol</i> <b>310</b>(3):F204–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26561651 26561651]; doi: [https://dx.doi.org/10.1152/ajprenal.00429.2015 10.1152/ajprenal.00429.2015]; GPMDB: [http://gpmdb.org/data/keyword/26561651 | + | #Tutakhel OA, Jeleń S, Valdez-Flores M, Dimke H, Piersma SR, Jimenez CR, Deinum J, Lenders JW, Hoenderop JG, Bindels RJ, (2016) "Alternative splice variant of the thiazide-sensitive NaCl cotransporter: a novel player in renal salt handling." <i>Am J Physiol Renal Physiol</i> <b>310</b>(3):F204–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26561651 26561651]; doi: [https://dx.doi.org/10.1152/ajprenal.00429.2015 10.1152/ajprenal.00429.2015]; GPMDB: [http://gpmdb.org/data/keyword/26561651 2]. |
#Sun S, Shah P, Eshghi ST, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Höti N, Zhang Z, Chan DW, Zhang H, (2016) "Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides." <i>Nat Biotechnol</i> <b>34</b>(1):84–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26571101 26571101]; doi: [https://dx.doi.org/10.1038/nbt.3403 10.1038/nbt.3403]; GPMDB: [http://gpmdb.org/data/keyword/26571101 55]. | #Sun S, Shah P, Eshghi ST, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Höti N, Zhang Z, Chan DW, Zhang H, (2016) "Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides." <i>Nat Biotechnol</i> <b>34</b>(1):84–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26571101 26571101]; doi: [https://dx.doi.org/10.1038/nbt.3403 10.1038/nbt.3403]; GPMDB: [http://gpmdb.org/data/keyword/26571101 55]. | ||
#Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H, Beli P, (2016) "ATR inhibition rewires cellular signaling networks induced by replication stress." <i>Proteomics</i> <b>16</b>(3):402–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26572502 26572502]; doi: [https://dx.doi.org/10.1002/pmic.201500172 10.1002/pmic.201500172]; GPMDB: [http://gpmdb.org/data/keyword/26572502 20]. | #Wagner SA, Oehler H, Voigt A, Dalic D, Freiwald A, Serve H, Beli P, (2016) "ATR inhibition rewires cellular signaling networks induced by replication stress." <i>Proteomics</i> <b>16</b>(3):402–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26572502 26572502]; doi: [https://dx.doi.org/10.1002/pmic.201500172 10.1002/pmic.201500172]; GPMDB: [http://gpmdb.org/data/keyword/26572502 20]. | ||
Line 1,100: | Line 1,107: | ||
#Mostafa I, Zhu N, Yoo MJ, Balmant KM, Misra BB, Dufresne C, Abou-Hashem M, Chen S, El-Domiaty M, (2016) "New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants." <i>J Proteomics</i> <b>138</b>:1–19; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26915584 26915584]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.012 10.1016/j.jprot.2016.02.012]; GPMDB: [http://gpmdb.org/data/keyword/26915584 24]. | #Mostafa I, Zhu N, Yoo MJ, Balmant KM, Misra BB, Dufresne C, Abou-Hashem M, Chen S, El-Domiaty M, (2016) "New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants." <i>J Proteomics</i> <b>138</b>:1–19; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26915584 26915584]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.012 10.1016/j.jprot.2016.02.012]; GPMDB: [http://gpmdb.org/data/keyword/26915584 24]. | ||
#Xu B, Gao Y, Zhan S, Xiong F, Qiu W, Qian X, Wang T, Wang N, Zhang D, Yang Q, Wang R, Bao X, Dou W, Tian R, Meng S, Gai WP, Huang Y, Yan XX, Ge W, Ma C, (2016) "Quantitative protein profiling of hippocampus during human aging." <i>Neurobiol Aging</i> <b>39</b>:46–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26923401 26923401]; doi: [https://dx.doi.org/10.1016/j.neurobiolaging.2015.11.029 10.1016/j.neurobiolaging.2015.11.029]; GPMDB: [http://gpmdb.org/data/keyword/26923401 20]. | #Xu B, Gao Y, Zhan S, Xiong F, Qiu W, Qian X, Wang T, Wang N, Zhang D, Yang Q, Wang R, Bao X, Dou W, Tian R, Meng S, Gai WP, Huang Y, Yan XX, Ge W, Ma C, (2016) "Quantitative protein profiling of hippocampus during human aging." <i>Neurobiol Aging</i> <b>39</b>:46–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26923401 26923401]; doi: [https://dx.doi.org/10.1016/j.neurobiolaging.2015.11.029 10.1016/j.neurobiolaging.2015.11.029]; GPMDB: [http://gpmdb.org/data/keyword/26923401 20]. | ||
+ | #Reddy RJ, Gajadhar AS, Swenson EJ, Rothenberg DA, Curran TG, White FM, (2016) "Early signaling dynamics of the epidermal growth factor receptor." <i>Proc Natl Acad Sci U S A</i> <b>113</b>(11):3114–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26929352 26929352]; doi: [https://dx.doi.org/10.1073/pnas.1521288113 10.1073/pnas.1521288113]; GPMDB: [http://gpmdb.org/data/keyword/26929352 30]. | ||
#de Torre-Minguela C, Barberà-Cremades M, Gómez AI, Martín-Sánchez F, Pelegrín P, (2016) "Macrophage activation and polarization modify P2X7 receptor secretome influencing the inflammatory process." <i>Sci Rep</i> <b>6</b>:22586; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26935289 26935289]; doi: [https://dx.doi.org/10.1038/srep22586 10.1038/srep22586]; GPMDB: [http://gpmdb.org/data/keyword/26935289 118]. | #de Torre-Minguela C, Barberà-Cremades M, Gómez AI, Martín-Sánchez F, Pelegrín P, (2016) "Macrophage activation and polarization modify P2X7 receptor secretome influencing the inflammatory process." <i>Sci Rep</i> <b>6</b>:22586; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26935289 26935289]; doi: [https://dx.doi.org/10.1038/srep22586 10.1038/srep22586]; GPMDB: [http://gpmdb.org/data/keyword/26935289 118]. | ||
#Ly A, Merl-Pham J, Priller M, Gruhn F, Senninger N, Ueffing M, Hauck SM, (2016) "Proteomic Profiling Suggests Central Role Of STAT Signaling during Retinal Degeneration in the rd10 Mouse Model." <i>J Proteome Res</i> <b>15</b>(4):1350–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26939627 26939627]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00111 10.1021/acs.jproteome.6b00111]; GPMDB: [http://gpmdb.org/data/keyword/26939627 24]. | #Ly A, Merl-Pham J, Priller M, Gruhn F, Senninger N, Ueffing M, Hauck SM, (2016) "Proteomic Profiling Suggests Central Role Of STAT Signaling during Retinal Degeneration in the rd10 Mouse Model." <i>J Proteome Res</i> <b>15</b>(4):1350–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26939627 26939627]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00111 10.1021/acs.jproteome.6b00111]; GPMDB: [http://gpmdb.org/data/keyword/26939627 24]. | ||
#Salih M, Demmers JA, Bezstarosti K, Leonhard WN, Losekoot M, van Kooten C, Gansevoort RT, Peters DJ, Zietse R, Hoorn EJ, DIPAK Consortium, (2016) "Proteomics of Urinary Vesicles Links Plakins and Complement to Polycystic Kidney Disease." <i>J Am Soc Nephrol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26940098 26940098]; doi: [https://dx.doi.org/10.1681/ASN.2015090994 10.1681/ASN.2015090994]; GPMDB: [http://gpmdb.org/data/keyword/26940098 7]. | #Salih M, Demmers JA, Bezstarosti K, Leonhard WN, Losekoot M, van Kooten C, Gansevoort RT, Peters DJ, Zietse R, Hoorn EJ, DIPAK Consortium, (2016) "Proteomics of Urinary Vesicles Links Plakins and Complement to Polycystic Kidney Disease." <i>J Am Soc Nephrol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26940098 26940098]; doi: [https://dx.doi.org/10.1681/ASN.2015090994 10.1681/ASN.2015090994]; GPMDB: [http://gpmdb.org/data/keyword/26940098 7]. | ||
#Kamkina P, Snoek LB, Grossmann J, Volkers RJ, Sterken MG, Daube M, Roschitzki B, Fortes C, Schlapbach R, Roth A, von Mering C, Hengartner MO, Schrimpf SP, Kammenga JE, (2016) "Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans." <i>Mol Cell Proteomics</i> <b>15</b>(5):1670–80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26944343 26944343]; doi: [https://dx.doi.org/10.1074/mcp.M115.052548 10.1074/mcp.M115.052548]; GPMDB: [http://gpmdb.org/data/keyword/26944343 12]. | #Kamkina P, Snoek LB, Grossmann J, Volkers RJ, Sterken MG, Daube M, Roschitzki B, Fortes C, Schlapbach R, Roth A, von Mering C, Hengartner MO, Schrimpf SP, Kammenga JE, (2016) "Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans." <i>Mol Cell Proteomics</i> <b>15</b>(5):1670–80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26944343 26944343]; doi: [https://dx.doi.org/10.1074/mcp.M115.052548 10.1074/mcp.M115.052548]; GPMDB: [http://gpmdb.org/data/keyword/26944343 12]. | ||
+ | #Zhang T, Shen S, Qu J, Ghaemmaghami S, (2016) "Global Analysis of Cellular Protein Flux Quantifies the Selectivity of Basal Autophagy." <i>Cell Rep</i> <b>14</b>(10):2426–39; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26947064 26947064]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.02.040 10.1016/j.celrep.2016.02.040]; GPMDB: [http://gpmdb.org/data/keyword/26947064 13]. | ||
#Xin L, Xu B, Ma L, Hou Q, Ye M, Meng S, Ding X, Ge W, (2016) "Proteomics study reveals that the dysregulation of focal adhesion and ribosome contribute to early pregnancy loss." <i>Proteomics Clin Appl</i> <b>10</b>(5):554–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26947931 26947931]; doi: [https://dx.doi.org/10.1002/prca.201500136 10.1002/prca.201500136]; GPMDB: [http://gpmdb.org/data/keyword/26947931 1]. | #Xin L, Xu B, Ma L, Hou Q, Ye M, Meng S, Ding X, Ge W, (2016) "Proteomics study reveals that the dysregulation of focal adhesion and ribosome contribute to early pregnancy loss." <i>Proteomics Clin Appl</i> <b>10</b>(5):554–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26947931 26947931]; doi: [https://dx.doi.org/10.1002/prca.201500136 10.1002/prca.201500136]; GPMDB: [http://gpmdb.org/data/keyword/26947931 1]. | ||
#Adewole OO, Erhabor GE, Adewole TO, Ojo AO, Oshokoya H, Wolfe LM, Prenni JE, (2016) "Proteomic profiling of eccrine sweat reveals its potential as a diagnostic biofluid for active tuberculosis." <i>Proteomics Clin Appl</i> <b>10</b>(5):547–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26948146 26948146]; doi: [https://dx.doi.org/10.1002/prca.201500071 10.1002/prca.201500071]; GPMDB: [http://gpmdb.org/data/keyword/26948146 10]. | #Adewole OO, Erhabor GE, Adewole TO, Ojo AO, Oshokoya H, Wolfe LM, Prenni JE, (2016) "Proteomic profiling of eccrine sweat reveals its potential as a diagnostic biofluid for active tuberculosis." <i>Proteomics Clin Appl</i> <b>10</b>(5):547–53; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26948146 26948146]; doi: [https://dx.doi.org/10.1002/prca.201500071 10.1002/prca.201500071]; GPMDB: [http://gpmdb.org/data/keyword/26948146 10]. | ||
Line 1,159: | Line 1,168: | ||
#Gupta I, Villanyi Z, Kassem S, Hughes C, Panasenko OO, Steinmetz LM, Collart MA, (2016) "Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex." <i>Cell Rep</i> <b>15</b>(8):1782–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27184853 27184853]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.04.055 10.1016/j.celrep.2016.04.055]; GPMDB: [http://gpmdb.org/data/keyword/27184853 4]. | #Gupta I, Villanyi Z, Kassem S, Hughes C, Panasenko OO, Steinmetz LM, Collart MA, (2016) "Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex." <i>Cell Rep</i> <b>15</b>(8):1782–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27184853 27184853]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.04.055 10.1016/j.celrep.2016.04.055]; GPMDB: [http://gpmdb.org/data/keyword/27184853 4]. | ||
#Kliuchnikova AA, Samokhina NI, Ilina IY, Karpov DS, Pyatnitskiy MA, Kuznetsova KG, Toropygin IY, Kochergin SA, Alekseev IB, Zgoda VG, Archakov AI, Moshkovskii SA, (2016) "Human aqueous humor proteome in cataract, glaucoma and pseudoexfoliation syndrome." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193151 27193151]; doi: [https://dx.doi.org/10.1002/pmic.201500423 10.1002/pmic.201500423]; GPMDB: [http://gpmdb.org/data/keyword/27193151 86]. | #Kliuchnikova AA, Samokhina NI, Ilina IY, Karpov DS, Pyatnitskiy MA, Kuznetsova KG, Toropygin IY, Kochergin SA, Alekseev IB, Zgoda VG, Archakov AI, Moshkovskii SA, (2016) "Human aqueous humor proteome in cataract, glaucoma and pseudoexfoliation syndrome." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193151 27193151]; doi: [https://dx.doi.org/10.1002/pmic.201500423 10.1002/pmic.201500423]; GPMDB: [http://gpmdb.org/data/keyword/27193151 86]. | ||
- | #Heaven MR, Flint D, Randall SM, Sosunov AA, Wilson L, Barnes S, Goldman JE, Muddiman DC, Brenner M, (2016) "Composition of Rosenthal Fibers, the Protein Aggregate Hallmark of Alexander Disease." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193225 27193225]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00316 10.1021/acs.jproteome.6b00316]; GPMDB: [http://gpmdb.org/data/keyword/27193225 8]. | + | #Heaven MR, Flint D, Randall SM, Sosunov AA, Wilson L, Barnes S, Goldman JE, Muddiman DC, Brenner M, (2016) "Composition of Rosenthal Fibers, the Protein Aggregate Hallmark of Alexander Disease." <i>J Proteome Res</i> <b>15</b>(7):2265–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27193225 27193225]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00316 10.1021/acs.jproteome.6b00316]; GPMDB: [http://gpmdb.org/data/keyword/27193225 8]. |
#Yang W, Jackson B, Zhang H, (2016) "Identification of glycoproteins associated with HIV latently infected cells using quantitative glycoproteomics." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27195445 27195445]; doi: [https://dx.doi.org/10.1002/pmic.201500215 10.1002/pmic.201500215]; GPMDB: [http://gpmdb.org/data/keyword/27195445 12]. | #Yang W, Jackson B, Zhang H, (2016) "Identification of glycoproteins associated with HIV latently infected cells using quantitative glycoproteomics." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27195445 27195445]; doi: [https://dx.doi.org/10.1002/pmic.201500215 10.1002/pmic.201500215]; GPMDB: [http://gpmdb.org/data/keyword/27195445 12]. | ||
#Liang W, Ward LJ, Karlsson H, Ljunggren SA, Li W, Lindahl M, Yuan XM, (2016) "Distinctive proteomic profiles among different regions of human carotid plaques in men and women." <i>Sci Rep</i> <b>6</b>:26231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27198765 27198765]; doi: [https://dx.doi.org/10.1038/srep26231 10.1038/srep26231]; GPMDB: [http://gpmdb.org/data/keyword/27198765 60]. | #Liang W, Ward LJ, Karlsson H, Ljunggren SA, Li W, Lindahl M, Yuan XM, (2016) "Distinctive proteomic profiles among different regions of human carotid plaques in men and women." <i>Sci Rep</i> <b>6</b>:26231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27198765 27198765]; doi: [https://dx.doi.org/10.1038/srep26231 10.1038/srep26231]; GPMDB: [http://gpmdb.org/data/keyword/27198765 60]. | ||
Line 1,165: | Line 1,174: | ||
#Yu J, Storer BE, Kushekhar K, Abu Zaid M, Zhang Q, Gafken PR, Ogata Y, Martin PJ, Flowers ME, Hansen JA, Arora M, Cutler C, Jagasia M, Pidala J, Hamilton BK, Chen GL, Pusic I, Lee SJ, Paczesny S, (2016) "Biomarker Panel for Chronic Graft-Versus-Host Disease." <i>J Clin Oncol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27217465 27217465]; doi: [https://dx.doi.org/10.1200/JCO.2015.65.9615 10.1200/JCO.2015.65.9615]; GPMDB: [http://gpmdb.org/data/keyword/27217465 3]. | #Yu J, Storer BE, Kushekhar K, Abu Zaid M, Zhang Q, Gafken PR, Ogata Y, Martin PJ, Flowers ME, Hansen JA, Arora M, Cutler C, Jagasia M, Pidala J, Hamilton BK, Chen GL, Pusic I, Lee SJ, Paczesny S, (2016) "Biomarker Panel for Chronic Graft-Versus-Host Disease." <i>J Clin Oncol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27217465 27217465]; doi: [https://dx.doi.org/10.1200/JCO.2015.65.9615 10.1200/JCO.2015.65.9615]; GPMDB: [http://gpmdb.org/data/keyword/27217465 3]. | ||
#Wang B, Pfeiffer MJ, Drexler HC, Fuellen G, Boiani M, (2016) "Proteomic analysis of mouse oocytes identifies PRMT7 as reprogramming factor that replaces SOX2 in the induction of pluripotent stem cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27225728 27225728]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01083 10.1021/acs.jproteome.5b01083]; GPMDB: [http://gpmdb.org/data/keyword/27225728 14]. | #Wang B, Pfeiffer MJ, Drexler HC, Fuellen G, Boiani M, (2016) "Proteomic analysis of mouse oocytes identifies PRMT7 as reprogramming factor that replaces SOX2 in the induction of pluripotent stem cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27225728 27225728]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01083 10.1021/acs.jproteome.5b01083]; GPMDB: [http://gpmdb.org/data/keyword/27225728 14]. | ||
- | #Lodrini M, Poschmann G, Schmidt V, Wünschel J, Dreidax D, Witt O, Höfer T, Meyer HE, Stühler K, Eggert A, Deubzer HE, (2016) "Minichromosome Maintenance Complex Is a Critical Node in the miR-183 Signaling Network of MYCN-Amplified Neuroblastoma Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27239679 27239679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00134 10.1021/acs.jproteome.6b00134]; GPMDB: [http://gpmdb.org/data/keyword/27239679 12]. | + | #Lodrini M, Poschmann G, Schmidt V, Wünschel J, Dreidax D, Witt O, Höfer T, Meyer HE, Stühler K, Eggert A, Deubzer HE, (2016) "Minichromosome Maintenance Complex Is a Critical Node in the miR-183 Signaling Network of MYCN-Amplified Neuroblastoma Cells." <i>J Proteome Res</i> <b>15</b>(7):2178–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27239679 27239679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00134 10.1021/acs.jproteome.6b00134]; GPMDB: [http://gpmdb.org/data/keyword/27239679 12]. |
#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: [http://gpmdb.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: [http://gpmdb.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>; 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: [http://gpmdb.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: [http://gpmdb.org/data/keyword/27246970 25]. |
#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: [http://gpmdb.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: [http://gpmdb.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>; 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: [http://gpmdb.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>; 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: [http://gpmdb.org/data/keyword/27259358 112]. | ||
#Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W, (2016) "Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2]. | #Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W, (2016) "Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2]. | ||
#Prendergast L, Müller S, Liu Y, Huang H, Dingli F, Loew D, Vassias I, Patel DJ, Sullivan KF, Almouzni G, (2016) "The CENP-T/-W complex is a binding partner of the histone chaperone FACT." <i>Genes Dev</i> <b>30</b>(11):1313–26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27284163 27284163]; doi: [https://dx.doi.org/10.1101/gad.275073.115 10.1101/gad.275073.115]; GPMDB: [http://gpmdb.org/data/keyword/27284163 47]. | #Prendergast L, Müller S, Liu Y, Huang H, Dingli F, Loew D, Vassias I, Patel DJ, Sullivan KF, Almouzni G, (2016) "The CENP-T/-W complex is a binding partner of the histone chaperone FACT." <i>Genes Dev</i> <b>30</b>(11):1313–26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27284163 27284163]; doi: [https://dx.doi.org/10.1101/gad.275073.115 10.1101/gad.275073.115]; GPMDB: [http://gpmdb.org/data/keyword/27284163 47]. | ||
+ | #Wiśniewski JR, Mann M, (2016) "A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting." <i>J Proteome Res</i> <b>15</b>(7):2321–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27297043 27297043]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00403 10.1021/acs.jproteome.6b00403]; GPMDB: [http://gpmdb.org/data/keyword/27297043 64]. | ||
+ | #Rakus D, Gizak A, Wiśniewski JR, (2016) "Proteomics Unveils Fibroblast-Cardiomyocyte Lactate Shuttle and Hexokinase Paradox in Mouse Muscles." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27302655 27302655]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01149 10.1021/acs.jproteome.5b01149]; GPMDB: [http://gpmdb.org/data/keyword/27302655 60]. | ||
+ | #Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SP, (2016) "Defining the consequences of genetic variation on a proteome-wide scale." <i>Nature</i> <b>534</b>(7608):500–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27309819 27309819]; doi: [https://dx.doi.org/10.1038/nature18270 10.1038/nature18270]; GPMDB: [http://gpmdb.org/data/keyword/27309819 18]. | ||
+ | #Szklanna PB, Foy M, Wynne K, Byrne D, Maguire PB, (2016) "Analysis of the proteins associated with platelet detergent resistant membranes." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27329341 27329341]; doi: [https://dx.doi.org/10.1002/pmic.201500309 10.1002/pmic.201500309]; GPMDB: [http://gpmdb.org/data/keyword/27329341 18]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of July 3, 2016.