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==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of | + | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of November 3, 2019. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#Bland C, Bellanger L, Armengaud J, (2014) "Magnetic immunoaffinity enrichment for selective capture and MS/MS analysis of N-terminal-TMPP-labeled peptides." <i>J Proteome Res</i> <b>13</b>(2):668–80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24313271 24313271]; doi: [https://dx.doi.org/10.1021/pr400774z 10.1021/pr400774z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24313271 9]. | #Bland C, Bellanger L, Armengaud J, (2014) "Magnetic immunoaffinity enrichment for selective capture and MS/MS analysis of N-terminal-TMPP-labeled peptides." <i>J Proteome Res</i> <b>13</b>(2):668–80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24313271 24313271]; doi: [https://dx.doi.org/10.1021/pr400774z 10.1021/pr400774z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24313271 9]. | ||
#Tsai CF, Hsu CC, Hung JN, Wang YT, Choong WK, Zeng MY, Lin PY, Hong RW, Sung TY, Chen YJ, (2014) "Sequential phosphoproteomic enrichment through complementary metal-directed immobilized metal ion affinity chromatography." <i>Anal Chem</i> <b>86</b>(1):685–93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24313913 24313913]; doi: [https://dx.doi.org/10.1021/ac4031175 10.1021/ac4031175]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24313913 27]. | #Tsai CF, Hsu CC, Hung JN, Wang YT, Choong WK, Zeng MY, Lin PY, Hong RW, Sung TY, Chen YJ, (2014) "Sequential phosphoproteomic enrichment through complementary metal-directed immobilized metal ion affinity chromatography." <i>Anal Chem</i> <b>86</b>(1):685–93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24313913 24313913]; doi: [https://dx.doi.org/10.1021/ac4031175 10.1021/ac4031175]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24313913 27]. | ||
+ | #Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG, (2014) "Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins." <i>Nat Methods</i> <b>11</b>(2):149–55; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24317253 24317253]; doi: [https://dx.doi.org/10.1038/nmeth.2763 10.1038/nmeth.2763]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24317253 221]. | ||
#Kao L, Wang YT, Chen YC, Tseng SF, Jhang JC, Chen YJ, Teng SC, (2014) "Global analysis of cdc14 dephosphorylation sites reveals essential regulatory role in mitosis and cytokinesis." <i>Mol Cell Proteomics</i> <b>13</b>(2):594–605; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24319056 24319056]; doi: [https://dx.doi.org/10.1074/mcp.M113.032680 10.1074/mcp.M113.032680]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24319056 9]. | #Kao L, Wang YT, Chen YC, Tseng SF, Jhang JC, Chen YJ, Teng SC, (2014) "Global analysis of cdc14 dephosphorylation sites reveals essential regulatory role in mitosis and cytokinesis." <i>Mol Cell Proteomics</i> <b>13</b>(2):594–605; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24319056 24319056]; doi: [https://dx.doi.org/10.1074/mcp.M113.032680 10.1074/mcp.M113.032680]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24319056 9]. | ||
#Beck F, Geiger J, Gambaryan S, Veit J, Vaudel M, Nollau P, Kohlbacher O, Martens L, Walter U, Sickmann A, Zahedi RP, (2014) "Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways." <i>Blood</i> <b>123</b>(5):e1–e10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24324209 24324209]; doi: [https://dx.doi.org/10.1182/blood-2013-07-512384 10.1182/blood-2013-07-512384]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24324209 19]. | #Beck F, Geiger J, Gambaryan S, Veit J, Vaudel M, Nollau P, Kohlbacher O, Martens L, Walter U, Sickmann A, Zahedi RP, (2014) "Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways." <i>Blood</i> <b>123</b>(5):e1–e10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24324209 24324209]; doi: [https://dx.doi.org/10.1182/blood-2013-07-512384 10.1182/blood-2013-07-512384]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/24324209 19]. | ||
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#Yang W, Ramachandran A, You S, Jeong H, Morley S, Mulone MD, Logvinenko T, Kim J, Hwang D, Freeman MR, Adam RM, (2014) "Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells." <i>Cell Commun Signal</i> <b>12</b>:44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25080971 25080971]; doi: [https://dx.doi.org/10.1186/s12964-014-0044-z 10.1186/s12964-014-0044-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25080971 30]. | #Yang W, Ramachandran A, You S, Jeong H, Morley S, Mulone MD, Logvinenko T, Kim J, Hwang D, Freeman MR, Adam RM, (2014) "Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells." <i>Cell Commun Signal</i> <b>12</b>:44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25080971 25080971]; doi: [https://dx.doi.org/10.1186/s12964-014-0044-z 10.1186/s12964-014-0044-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25080971 30]. | ||
#Labas V, Grasseau I, Cahier K, Gargaros A, Harichaux G, Teixeira-Gomes AP, Alves S, Bourin M, Gérard N, Blesbois E, (2015) "Qualitative and quantitative peptidomic and proteomic approaches to phenotyping chicken semen." <i>J Proteomics</i> <b>112</b>:313–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25086240 25086240]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.07.024 10.1016/j.jprot.2014.07.024]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25086240 44]. | #Labas V, Grasseau I, Cahier K, Gargaros A, Harichaux G, Teixeira-Gomes AP, Alves S, Bourin M, Gérard N, Blesbois E, (2015) "Qualitative and quantitative peptidomic and proteomic approaches to phenotyping chicken semen." <i>J Proteomics</i> <b>112</b>:313–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25086240 25086240]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.07.024 10.1016/j.jprot.2014.07.024]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25086240 44]. | ||
+ | #Berlin C, Kowalewski DJ, Schuster H, Mirza N, Walz S, Handel M, Schmid-Horch B, Salih HR, Kanz L, Rammensee HG, Stevanović S, Stickel JS, (2015) "Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy." <i>Leukemia</i> <b>29</b>(3):647–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25092142 25092142]; doi: [https://dx.doi.org/10.1038/leu.2014.233 10.1038/leu.2014.233]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25092142 73]. | ||
#Alqahtani A, Heesom K, Bramson JL, Curiel D, Ugai H, Matthews DA, (2014) "Analysis of purified wild type and mutant adenovirus particles by SILAC based quantitative proteomics." <i>J Gen Virol</i> <b>95</b>(Pt 11):2504–11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25096814 25096814]; doi: [https://dx.doi.org/10.1099/vir.0.068221-0 10.1099/vir.0.068221-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25096814 22]. | #Alqahtani A, Heesom K, Bramson JL, Curiel D, Ugai H, Matthews DA, (2014) "Analysis of purified wild type and mutant adenovirus particles by SILAC based quantitative proteomics." <i>J Gen Virol</i> <b>95</b>(Pt 11):2504–11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25096814 25096814]; doi: [https://dx.doi.org/10.1099/vir.0.068221-0 10.1099/vir.0.068221-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25096814 22]. | ||
#Jin L, Huo Y, Zheng Z, Jiang X, Deng H, Chen Y, Lian Q, Ge R, Deng H, (2014) "Down-regulation of Ras-related protein Rab 5C-dependent endocytosis and glycolysis in cisplatin-resistant ovarian cancer cell lines." <i>Mol Cell Proteomics</i> <b>13</b>(11):3138–51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25096996 25096996]; doi: [https://dx.doi.org/10.1074/mcp.M113.033217 10.1074/mcp.M113.033217]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25096996 11]. | #Jin L, Huo Y, Zheng Z, Jiang X, Deng H, Chen Y, Lian Q, Ge R, Deng H, (2014) "Down-regulation of Ras-related protein Rab 5C-dependent endocytosis and glycolysis in cisplatin-resistant ovarian cancer cell lines." <i>Mol Cell Proteomics</i> <b>13</b>(11):3138–51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25096996 25096996]; doi: [https://dx.doi.org/10.1074/mcp.M113.033217 10.1074/mcp.M113.033217]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25096996 11]. | ||
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#He PH, Dong WX, Chu XL, Feng MG, Ying SH, (2016) "The cellular proteome is affected by a gelsolin (BbGEL1) during morphological transitions in aerobic surface versus liquid growth in the entomopathogenic fungus Beauveria bassiana." <i>Environ Microbiol</i> <b>18</b>(11):4153–4169; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554994 27554994]; doi: [https://dx.doi.org/10.1111/1462-2920.13500 10.1111/1462-2920.13500]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27554994 34]. | #He PH, Dong WX, Chu XL, Feng MG, Ying SH, (2016) "The cellular proteome is affected by a gelsolin (BbGEL1) during morphological transitions in aerobic surface versus liquid growth in the entomopathogenic fungus Beauveria bassiana." <i>Environ Microbiol</i> <b>18</b>(11):4153–4169; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554994 27554994]; doi: [https://dx.doi.org/10.1111/1462-2920.13500 10.1111/1462-2920.13500]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27554994 34]. | ||
#Viktorovskaya OV, Greco TM, Cristea IM, Thompson SR, (2016) "Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements." <i>PLoS Negl Trop Dis</i> <b>10</b>(8):e0004921; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27556644 27556644]; doi: [https://dx.doi.org/10.1371/journal.pntd.0004921 10.1371/journal.pntd.0004921]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27556644 7]. | #Viktorovskaya OV, Greco TM, Cristea IM, Thompson SR, (2016) "Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements." <i>PLoS Negl Trop Dis</i> <b>10</b>(8):e0004921; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27556644 27556644]; doi: [https://dx.doi.org/10.1371/journal.pntd.0004921 10.1371/journal.pntd.0004921]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27556644 7]. | ||
- | #Cassidy L, Prasse D, Linke D, Schmitz RA, Tholey A, (2016) "Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei." <i>J Proteome Res</i> <b>15</b>(10):3773–3783; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27557128 27557128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00569 10.1021/acs.jproteome.6b00569]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27557128 | + | #Cassidy L, Prasse D, Linke D, Schmitz RA, Tholey A, (2016) "Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei." <i>J Proteome Res</i> <b>15</b>(10):3773–3783; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27557128 27557128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00569 10.1021/acs.jproteome.6b00569]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27557128 12]. |
#Häupl B, Ihling CH, Sinz A, (2016) "Protein Interaction Network of Human Protein Kinase D2 Revealed by Chemical Cross-Linking/Mass Spectrometry." <i>J Proteome Res</i> <b>15</b>(10):3686–3699; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27559607 27559607]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00513 10.1021/acs.jproteome.6b00513]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27559607 81]. | #Häupl B, Ihling CH, Sinz A, (2016) "Protein Interaction Network of Human Protein Kinase D2 Revealed by Chemical Cross-Linking/Mass Spectrometry." <i>J Proteome Res</i> <b>15</b>(10):3686–3699; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27559607 27559607]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00513 10.1021/acs.jproteome.6b00513]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27559607 81]. | ||
#Jiang Y, Lee J, Lee JH, Lee JW, Kim JH, Choi WH, Yoo YD, Cha-Molstad H, Kim BY, Kwon YT, Noh SA, Kim KP, Lee MJ, (2016) "The arginylation branch of the N-end rule pathway positively regulates cellular autophagic flux and clearance of proteotoxic proteins." <i>Autophagy</i> <b>12</b>(11):2197–2212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27560450 27560450]; doi: [https://dx.doi.org/10.1080/15548627.2016.1222991 10.1080/15548627.2016.1222991]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27560450 2]. | #Jiang Y, Lee J, Lee JH, Lee JW, Kim JH, Choi WH, Yoo YD, Cha-Molstad H, Kim BY, Kwon YT, Noh SA, Kim KP, Lee MJ, (2016) "The arginylation branch of the N-end rule pathway positively regulates cellular autophagic flux and clearance of proteotoxic proteins." <i>Autophagy</i> <b>12</b>(11):2197–2212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27560450 27560450]; doi: [https://dx.doi.org/10.1080/15548627.2016.1222991 10.1080/15548627.2016.1222991]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27560450 2]. | ||
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#Clulow JA, Storck EM, Lanyon-Hogg T, Kalesh KA, Jones LH, Tate EW, (2017) "Competition-based, quantitative chemical proteomics in breast cancer cells identifies new target profiles for sulforaphane." <i>Chem Commun (Camb)</i> <b>53</b>(37):5182–5185; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28439590 28439590]; doi: [https://dx.doi.org/10.1039/c6cc08797c 10.1039/c6cc08797c]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28439590 32]. | #Clulow JA, Storck EM, Lanyon-Hogg T, Kalesh KA, Jones LH, Tate EW, (2017) "Competition-based, quantitative chemical proteomics in breast cancer cells identifies new target profiles for sulforaphane." <i>Chem Commun (Camb)</i> <b>53</b>(37):5182–5185; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28439590 28439590]; doi: [https://dx.doi.org/10.1039/c6cc08797c 10.1039/c6cc08797c]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28439590 32]. | ||
#Yeung ATY, Hale C, Lee AH, Gill EE, Bushell W, Parry-Smith D, Goulding D, Pickard D, Roumeliotis T, Choudhary J, Thomson N, Skarnes WC, Dougan G, Hancock REW, (2017) "Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis." <i>Nat Commun</i> <b>8</b>:15013; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28440293 28440293]; doi: [https://dx.doi.org/10.1038/ncomms15013 10.1038/ncomms15013]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28440293 1]. | #Yeung ATY, Hale C, Lee AH, Gill EE, Bushell W, Parry-Smith D, Goulding D, Pickard D, Roumeliotis T, Choudhary J, Thomson N, Skarnes WC, Dougan G, Hancock REW, (2017) "Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis." <i>Nat Commun</i> <b>8</b>:15013; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28440293 28440293]; doi: [https://dx.doi.org/10.1038/ncomms15013 10.1038/ncomms15013]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28440293 1]. | ||
+ | #Labots M, van der Mijn JC, Beekhof R, Piersma SR, de Goeij-de Haas RR, Pham TV, Knol JC, Dekker H, van Grieken NCT, Verheul HMW, Jiménez CR, (2017) "Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection." <i>J Proteomics</i> <b>162</b>:99–107; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28442448 28442448]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.04.014 10.1016/j.jprot.2017.04.014]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28442448 40]. | ||
#Arntzen MØ, Várnai A, Mackie RI, Eijsink VGH, Pope PB, (2017) "Outer membrane vesicles from Fibrobacter succinogenes S85 contain an array of carbohydrate-active enzymes with versatile polysaccharide-degrading capacity." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28447389 28447389]; doi: [https://dx.doi.org/10.1111/1462-2920.13770 10.1111/1462-2920.13770]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28447389 20]. | #Arntzen MØ, Várnai A, Mackie RI, Eijsink VGH, Pope PB, (2017) "Outer membrane vesicles from Fibrobacter succinogenes S85 contain an array of carbohydrate-active enzymes with versatile polysaccharide-degrading capacity." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28447389 28447389]; doi: [https://dx.doi.org/10.1111/1462-2920.13770 10.1111/1462-2920.13770]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28447389 20]. | ||
#Nguyen EV, Huhtinen K, Goo YA, Kaipio K, Andersson N, Rantanen V, Hynninen J, Lahesmaa R, Carpen O, Goodlett DR, (2017) "Hyper-phosphorylation of Sequestosome-1 distinguishes resistance to cisplatin in patient derived high grade serous ovarian cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28455291 28455291]; doi: [https://dx.doi.org/10.1074/mcp.M116.058321 10.1074/mcp.M116.058321]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28455291 60]. | #Nguyen EV, Huhtinen K, Goo YA, Kaipio K, Andersson N, Rantanen V, Hynninen J, Lahesmaa R, Carpen O, Goodlett DR, (2017) "Hyper-phosphorylation of Sequestosome-1 distinguishes resistance to cisplatin in patient derived high grade serous ovarian cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28455291 28455291]; doi: [https://dx.doi.org/10.1074/mcp.M116.058321 10.1074/mcp.M116.058321]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28455291 60]. | ||
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#Wildburger NC, Esparza TJ, LeDuc RD, Fellers RT, Thomas PM, Cairns NJ, Kelleher NL, Bateman RJ, Brody DL, (2017) "Diversity of Amyloid-beta Proteoforms in the Alzheimer's Disease Brain." <i>Sci Rep</i> <b>7</b>(1):9520; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28842697 28842697]; doi: [https://dx.doi.org/10.1038/s41598-017-10422-x 10.1038/s41598-017-10422-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28842697 22]. | #Wildburger NC, Esparza TJ, LeDuc RD, Fellers RT, Thomas PM, Cairns NJ, Kelleher NL, Bateman RJ, Brody DL, (2017) "Diversity of Amyloid-beta Proteoforms in the Alzheimer's Disease Brain." <i>Sci Rep</i> <b>7</b>(1):9520; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28842697 28842697]; doi: [https://dx.doi.org/10.1038/s41598-017-10422-x 10.1038/s41598-017-10422-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28842697 22]. | ||
#Andersen PR, Tirian L, Vunjak M, Brennecke J, (2017) "A heterochromatin-dependent transcription machinery drives piRNA expression." <i>Nature</i> <b>549</b>(7670):54–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28847004 28847004]; doi: [https://dx.doi.org/10.1038/nature23482 10.1038/nature23482]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28847004 46]. | #Andersen PR, Tirian L, Vunjak M, Brennecke J, (2017) "A heterochromatin-dependent transcription machinery drives piRNA expression." <i>Nature</i> <b>549</b>(7670):54–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28847004 28847004]; doi: [https://dx.doi.org/10.1038/nature23482 10.1038/nature23482]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28847004 46]. | ||
+ | #Guo J, Wang P, Cheng Q, Sun L, Wang H, Wang Y, Kao L, Li Y, Qiu T, Yang W, Shen H, (2017) "Proteomic analysis reveals strong mitochondrial involvement in cytoplasmic male sterility of pepper (Capsicum annuum L.)." <i>J Proteomics</i> <b>168</b>:15–27; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28847649 28847649]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.08.013 10.1016/j.jprot.2017.08.013]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28847649 6]. | ||
#Mohl BP, Emmott E, Roy P, (2017) "Phosphoproteomic analysis reveals the importance of kinase regulation during orbivirus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28851738 28851738]; doi: [https://dx.doi.org/10.1074/mcp.M117.067355 10.1074/mcp.M117.067355]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28851738 6]. | #Mohl BP, Emmott E, Roy P, (2017) "Phosphoproteomic analysis reveals the importance of kinase regulation during orbivirus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28851738 28851738]; doi: [https://dx.doi.org/10.1074/mcp.M117.067355 10.1074/mcp.M117.067355]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28851738 6]. | ||
#Merkley ED, Sego LH, Lin A, Leiser OP, Kaiser BLD, Adkins JN, Keim PS, Wagner DM, Kreuzer HW, (2017) "Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague." <i>PLoS One</i> <b>12</b>(8):e0183478; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28854255 28854255]; doi: [https://dx.doi.org/10.1371/journal.pone.0183478 10.1371/journal.pone.0183478]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28854255 343]. | #Merkley ED, Sego LH, Lin A, Leiser OP, Kaiser BLD, Adkins JN, Keim PS, Wagner DM, Kreuzer HW, (2017) "Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague." <i>PLoS One</i> <b>12</b>(8):e0183478; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28854255 28854255]; doi: [https://dx.doi.org/10.1371/journal.pone.0183478 10.1371/journal.pone.0183478]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28854255 343]. | ||
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#Abdelmegid S, Murugaiyan J, Abo-Ismail M, Caswell JL, Kelton D, Kirby GM, (2017) "Identification of Host Defense-Related Proteins Using Label-Free Quantitative Proteomic Analysis of Milk Whey from Cows with Staphylococcus aureus Subclinical Mastitis." <i>Int J Mol Sci</i> <b>19</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29283389 29283389]; doi: [https://dx.doi.org/10.3390/ijms19010078 10.3390/ijms19010078]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29283389 11]. | #Abdelmegid S, Murugaiyan J, Abo-Ismail M, Caswell JL, Kelton D, Kirby GM, (2017) "Identification of Host Defense-Related Proteins Using Label-Free Quantitative Proteomic Analysis of Milk Whey from Cows with Staphylococcus aureus Subclinical Mastitis." <i>Int J Mol Sci</i> <b>19</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29283389 29283389]; doi: [https://dx.doi.org/10.3390/ijms19010078 10.3390/ijms19010078]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29283389 11]. | ||
#Kelley RC, McDonagh B, Ferreira LF, (2018) "Advanced aging causes diaphragm functional abnormalities, global proteome remodeling, and loss of mitochondrial cysteine redox flexibility in mice." <i>Exp Gerontol</i> <b>103</b>:69–79; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29289553 29289553]; doi: [https://dx.doi.org/10.1016/j.exger.2017.12.017 10.1016/j.exger.2017.12.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29289553 24]. | #Kelley RC, McDonagh B, Ferreira LF, (2018) "Advanced aging causes diaphragm functional abnormalities, global proteome remodeling, and loss of mitochondrial cysteine redox flexibility in mice." <i>Exp Gerontol</i> <b>103</b>:69–79; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29289553 29289553]; doi: [https://dx.doi.org/10.1016/j.exger.2017.12.017 10.1016/j.exger.2017.12.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29289553 24]. | ||
+ | #Behr M, Sergeant K, Leclercq CC, Planchon S, Guignard C, Lenouvel A, Renaut J, Hausman JF, Lutts S, Guerriero G, (2018) "Insights into the molecular regulation of monolignol-derived product biosynthesis in the growing hemp hypocotyl." <i>BMC Plant Biol</i> <b>18</b>(1):1; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29291729 29291729]; doi: [https://dx.doi.org/10.1186/s12870-017-1213-1 10.1186/s12870-017-1213-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29291729 20]. | ||
#Ritz D, Sani E, Debiec H, Ronco P, Neri D, Fugmann T, (2018) "Membranal and blood-soluble HLA class II peptidome analyses using data-dependent and independent acquisition." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29314611 29314611]; doi: [https://dx.doi.org/10.1002/pmic.201700246 10.1002/pmic.201700246]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29314611 27]. | #Ritz D, Sani E, Debiec H, Ronco P, Neri D, Fugmann T, (2018) "Membranal and blood-soluble HLA class II peptidome analyses using data-dependent and independent acquisition." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29314611 29314611]; doi: [https://dx.doi.org/10.1002/pmic.201700246 10.1002/pmic.201700246]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29314611 27]. | ||
#Kooijman S, Brummelman J, van Els CACM, Marino F, Heck AJR, Mommen GPM, Metz B, Kersten GFA, Pennings JLA, Meiring HD, (2018) "Novel identified aluminum hydroxide-induced pathways prove monocyte activation and pro-inflammatory preparedness." <i>J Proteomics</i> <b>175</b>:144–155; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29317357 29317357]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.12.021 10.1016/j.jprot.2017.12.021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29317357 55]. | #Kooijman S, Brummelman J, van Els CACM, Marino F, Heck AJR, Mommen GPM, Metz B, Kersten GFA, Pennings JLA, Meiring HD, (2018) "Novel identified aluminum hydroxide-induced pathways prove monocyte activation and pro-inflammatory preparedness." <i>J Proteomics</i> <b>175</b>:144–155; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29317357 29317357]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.12.021 10.1016/j.jprot.2017.12.021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29317357 55]. | ||
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#Karayel Ö, Şanal E, Giese SH, Üretmen Kagıalı ZC, Polat AN, Hu CK, Renard BY, Tuncbag N, Özlü N, (2018) "Comparative phosphoproteomic analysis reveals signaling networks regulating monopolar and bipolar cytokinesis." <i>Sci Rep</i> <b>8</b>(1):2269; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29396449 29396449]; doi: [https://dx.doi.org/10.1038/s41598-018-20231-5 10.1038/s41598-018-20231-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29396449 16]. | #Karayel Ö, Şanal E, Giese SH, Üretmen Kagıalı ZC, Polat AN, Hu CK, Renard BY, Tuncbag N, Özlü N, (2018) "Comparative phosphoproteomic analysis reveals signaling networks regulating monopolar and bipolar cytokinesis." <i>Sci Rep</i> <b>8</b>(1):2269; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29396449 29396449]; doi: [https://dx.doi.org/10.1038/s41598-018-20231-5 10.1038/s41598-018-20231-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29396449 16]. | ||
#Ikoma M, Gantt S, Casper C, Ogata Y, Zhang Q, Basom R, Dyen MR, Rose TM, Barcy S, (2018) "KSHV oral shedding and plasma viremia result in significant changes in the extracellular tumorigenic miRNA expression profile in individuals infected with the malaria parasite." <i>PLoS One</i> <b>13</b>(2):e0192659; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29425228 29425228]; doi: [https://dx.doi.org/10.1371/journal.pone.0192659 10.1371/journal.pone.0192659]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29425228 3]. | #Ikoma M, Gantt S, Casper C, Ogata Y, Zhang Q, Basom R, Dyen MR, Rose TM, Barcy S, (2018) "KSHV oral shedding and plasma viremia result in significant changes in the extracellular tumorigenic miRNA expression profile in individuals infected with the malaria parasite." <i>PLoS One</i> <b>13</b>(2):e0192659; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29425228 29425228]; doi: [https://dx.doi.org/10.1371/journal.pone.0192659 10.1371/journal.pone.0192659]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29425228 3]. | ||
+ | #Vornhagen J, Quach P, Santana-Ufret V, Alishetti V, Brokaw A, Armistead B, Qing Tang H, MacDonald JW, Bammler TK, Adams Waldorf KM, Uldbjerg N, Rajagopal L, (2018) "Human Cervical Mucus Plugs Exhibit Insufficiencies in Antimicrobial Activity Towards Group B Streptococcus." <i>J Infect Dis</i> <b>217</b>(10):1626–1636; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29425317 29425317]; doi: [https://dx.doi.org/10.1093/infdis/jiy076 10.1093/infdis/jiy076]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29425317 1]. | ||
#Sandow JJ, Rainczuk A, Infusini G, Makanji M, Bilandzic M, Wilson AL, Fairweather N, Stanton PG, Garama D, Gough D, Jobling TW, Webb AI, Stephens AN, (2018) "Discovery and Validation of Novel Protein Biomarkers in Ovarian Cancer Patient Urine." <i>Proteomics Clin Appl</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29426060 29426060]; doi: [https://dx.doi.org/10.1002/prca.201700135 10.1002/prca.201700135]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29426060 10]. | #Sandow JJ, Rainczuk A, Infusini G, Makanji M, Bilandzic M, Wilson AL, Fairweather N, Stanton PG, Garama D, Gough D, Jobling TW, Webb AI, Stephens AN, (2018) "Discovery and Validation of Novel Protein Biomarkers in Ovarian Cancer Patient Urine." <i>Proteomics Clin Appl</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29426060 29426060]; doi: [https://dx.doi.org/10.1002/prca.201700135 10.1002/prca.201700135]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29426060 10]. | ||
#De Muyt A, Pyatnitskaya A, Andréani J, Ranjha L, Ramus C, Laureau R, Fernandez-Vega A, Holoch D, Girard E, Govin J, Margueron R, Couté Y, Cejka P, Guérois R, Borde V, (2018) "A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation." <i>Genes Dev</i> <b>32</b>(3-4):283–296; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29440262 29440262]; doi: [https://dx.doi.org/10.1101/gad.308510.117 10.1101/gad.308510.117]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29440262 19]. | #De Muyt A, Pyatnitskaya A, Andréani J, Ranjha L, Ramus C, Laureau R, Fernandez-Vega A, Holoch D, Girard E, Govin J, Margueron R, Couté Y, Cejka P, Guérois R, Borde V, (2018) "A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation." <i>Genes Dev</i> <b>32</b>(3-4):283–296; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29440262 29440262]; doi: [https://dx.doi.org/10.1101/gad.308510.117 10.1101/gad.308510.117]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29440262 19]. | ||
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#Simunovic F, Winninger O, Strassburg S, Koch HG, Finkenzeller G, Stark GB, Lampert FM, (2019) "Increased differentiation and production of extracellular matrix components of primary human osteoblasts after cocultivation with endothelial cells: A quantitative proteomics approach." <i>J Cell Biochem</i> <b>120</b>(1):396–404; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30126049 30126049]; doi: [https://dx.doi.org/10.1002/jcb.27394 10.1002/jcb.27394]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30126049 20]. | #Simunovic F, Winninger O, Strassburg S, Koch HG, Finkenzeller G, Stark GB, Lampert FM, (2019) "Increased differentiation and production of extracellular matrix components of primary human osteoblasts after cocultivation with endothelial cells: A quantitative proteomics approach." <i>J Cell Biochem</i> <b>120</b>(1):396–404; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30126049 30126049]; doi: [https://dx.doi.org/10.1002/jcb.27394 10.1002/jcb.27394]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30126049 20]. | ||
#Shen ZQ, Shi B, Wang TR, Jiao J, Shang X, Wu QJ, Zhou YM, Cao TF, Du Q, Wang XX, Li D, (2018) "Characterization of the Sperm Proteome and Reproductive Outcomes with <i>in Vitro</i> Fertilization after a Reduction in Male Ejaculatory Abstinence Period." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30126978 30126978]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000541 10.1074/mcp.RA117.000541]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30126978 18]. | #Shen ZQ, Shi B, Wang TR, Jiao J, Shang X, Wu QJ, Zhou YM, Cao TF, Du Q, Wang XX, Li D, (2018) "Characterization of the Sperm Proteome and Reproductive Outcomes with <i>in Vitro</i> Fertilization after a Reduction in Male Ejaculatory Abstinence Period." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30126978 30126978]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000541 10.1074/mcp.RA117.000541]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30126978 18]. | ||
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#DeLeon-Pennell KY, Mouton AJ, Ero OK, Ma Y, Padmanabhan Iyer R, Flynn ER, Espinoza I, Musani SK, Vasan RS, Hall ME, Fox ER, Lindsey ML, (2018) "LXR/RXR signaling and neutrophil phenotype following myocardial infarction classify sex differences in remodeling." <i>Basic Res Cardiol</i> <b>113</b>(5):40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30132266 30132266]; doi: [https://dx.doi.org/10.1007/s00395-018-0699-5 10.1007/s00395-018-0699-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30132266 120]. | #DeLeon-Pennell KY, Mouton AJ, Ero OK, Ma Y, Padmanabhan Iyer R, Flynn ER, Espinoza I, Musani SK, Vasan RS, Hall ME, Fox ER, Lindsey ML, (2018) "LXR/RXR signaling and neutrophil phenotype following myocardial infarction classify sex differences in remodeling." <i>Basic Res Cardiol</i> <b>113</b>(5):40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30132266 30132266]; doi: [https://dx.doi.org/10.1007/s00395-018-0699-5 10.1007/s00395-018-0699-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30132266 120]. | ||
#Weßbecher IM, Hinrichsen I, Funke S, Oellerich T, Plotz G, Zeuzem S, Grus FH, Biondi RM, Brieger A, (2018) "DNA mismatch repair activity of MutLα is regulated by CK2-dependent phosphorylation of MLH1 (S477)." <i>Mol Carcinog</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30136313 30136313]; doi: [https://dx.doi.org/10.1002/mc.22892 10.1002/mc.22892]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30136313 2]. | #Weßbecher IM, Hinrichsen I, Funke S, Oellerich T, Plotz G, Zeuzem S, Grus FH, Biondi RM, Brieger A, (2018) "DNA mismatch repair activity of MutLα is regulated by CK2-dependent phosphorylation of MLH1 (S477)." <i>Mol Carcinog</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30136313 30136313]; doi: [https://dx.doi.org/10.1002/mc.22892 10.1002/mc.22892]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30136313 2]. | ||
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#Varland S, Aksnes H, Kryuchkov F, Impens F, Van Haver D, Jonckheere V, Ziegler M, Gevaert K, Van Damme P, Arnesen T, (2018) "N-terminal acetylation levels are maintained during acetyl-CoA deficiency in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30150368 30150368]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000982 10.1074/mcp.RA118.000982]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30150368 17]. | #Varland S, Aksnes H, Kryuchkov F, Impens F, Van Haver D, Jonckheere V, Ziegler M, Gevaert K, Van Damme P, Arnesen T, (2018) "N-terminal acetylation levels are maintained during acetyl-CoA deficiency in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30150368 30150368]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000982 10.1074/mcp.RA118.000982]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30150368 17]. | ||
#Béguin EP, van den Eshof BL, Hoogendijk AJ, Nota B, Mertens K, Meijer AB, van den Biggelaar M, (2018) "Integrated proteomic analysis of tumor necrosis factor α and interleukin 1β-induced endothelial inflammation." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30153514 30153514]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.08.011 10.1016/j.jprot.2018.08.011]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30153514 51]. | #Béguin EP, van den Eshof BL, Hoogendijk AJ, Nota B, Mertens K, Meijer AB, van den Biggelaar M, (2018) "Integrated proteomic analysis of tumor necrosis factor α and interleukin 1β-induced endothelial inflammation." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30153514 30153514]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.08.011 10.1016/j.jprot.2018.08.011]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30153514 51]. | ||
+ | #Yanovich G, Agmon H, Harel M, Sonnenblick A, Peretz T, Geiger T, (2018) "Clinical Proteomics of Breast Cancer Reveals a Novel Layer of Breast Cancer Classification." <i>Cancer Res</i> <b>78</b>(20):6001–6010; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30154156 30154156]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-18-1079 10.1158/0008-5472.CAN-18-1079]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30154156 30]. | ||
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#Bonnet J, Garcia C, Leger T, Couquet MP, Vignoles P, Gedeao V, Ndung'u J, Boudot C, Bisser S, Courtioux B, (2018) "Proteome characterization in various biological fluids of Trypanosoma brucei gambiense-infected subjects." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30414516 30414516]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.11.005 10.1016/j.jprot.2018.11.005]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30414516 40]. | #Bonnet J, Garcia C, Leger T, Couquet MP, Vignoles P, Gedeao V, Ndung'u J, Boudot C, Bisser S, Courtioux B, (2018) "Proteome characterization in various biological fluids of Trypanosoma brucei gambiense-infected subjects." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30414516 30414516]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.11.005 10.1016/j.jprot.2018.11.005]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30414516 40]. | ||
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#Cominetti O, Núñez Galindo A, Corthésy J, Valsesia A, Irincheeva I, Kussmann M, Saris WHM, Astrup A, McPherson R, Harper ME, Dent R, Hager J, Dayon L, (2018) "Obesity shows preserved plasma proteome in large independent clinical cohorts." <i>Sci Rep</i> <b>8</b>(1):16981; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30451909 30451909]; doi: [https://dx.doi.org/10.1038/s41598-018-35321-7 10.1038/s41598-018-35321-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30451909 318]. | #Cominetti O, Núñez Galindo A, Corthésy J, Valsesia A, Irincheeva I, Kussmann M, Saris WHM, Astrup A, McPherson R, Harper ME, Dent R, Hager J, Dayon L, (2018) "Obesity shows preserved plasma proteome in large independent clinical cohorts." <i>Sci Rep</i> <b>8</b>(1):16981; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30451909 30451909]; doi: [https://dx.doi.org/10.1038/s41598-018-35321-7 10.1038/s41598-018-35321-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30451909 318]. | ||
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#Roustan V, Weckwerth W, (2018) "Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in <i>Chlamydomonas reinhardtii</i>." <i>Front Plant Sci</i> <b>9</b>:1590; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30546371 30546371]; doi: [https://dx.doi.org/10.3389/fpls.2018.01590 10.3389/fpls.2018.01590]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30546371 54]. | #Roustan V, Weckwerth W, (2018) "Quantitative Phosphoproteomic and System-Level Analysis of TOR Inhibition Unravel Distinct Organellar Acclimation in <i>Chlamydomonas reinhardtii</i>." <i>Front Plant Sci</i> <b>9</b>:1590; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30546371 30546371]; doi: [https://dx.doi.org/10.3389/fpls.2018.01590 10.3389/fpls.2018.01590]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30546371 54]. | ||
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#Pfaff F, Hägglund S, Zoli M, Blaise-Boisseau S, Laloy E, Koethe S, Zühlke D, Riedel K, Zientara S, Bakkali-Kassimi L, Valarcher JF, Höper D, Beer M, Eschbaumer M, (2019) "Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus." <i>Viruses</i> <b>11</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30642035 30642035]; doi: [https://dx.doi.org/10.3390/v11010053 10.3390/v11010053]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30642035 110]. | #Pfaff F, Hägglund S, Zoli M, Blaise-Boisseau S, Laloy E, Koethe S, Zühlke D, Riedel K, Zientara S, Bakkali-Kassimi L, Valarcher JF, Höper D, Beer M, Eschbaumer M, (2019) "Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus." <i>Viruses</i> <b>11</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30642035 30642035]; doi: [https://dx.doi.org/10.3390/v11010053 10.3390/v11010053]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30642035 110]. | ||
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#Pauwels AM, Härtlova A, Peltier J, Driege Y, Baudelet G, Brodin P, Trost M, Beyaert R, Hoffmann E, (2019) "Spatiotemporal changes of the phagosomal proteome in dendritic cells in response to LPS stimulation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30808727 30808727]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001316 10.1074/mcp.RA119.001316]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30808727 20]. | #Pauwels AM, Härtlova A, Peltier J, Driege Y, Baudelet G, Brodin P, Trost M, Beyaert R, Hoffmann E, (2019) "Spatiotemporal changes of the phagosomal proteome in dendritic cells in response to LPS stimulation." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30808727 30808727]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001316 10.1074/mcp.RA119.001316]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30808727 20]. | ||
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#Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK, (2019) "Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming." <i>Cell Syst</i> <b>8</b>(5):412–426.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078528 31078528]; doi: [https://dx.doi.org/10.1016/j.cels.2019.03.009 10.1016/j.cels.2019.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078528 24]. | #Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK, (2019) "Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming." <i>Cell Syst</i> <b>8</b>(5):412–426.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078528 31078528]; doi: [https://dx.doi.org/10.1016/j.cels.2019.03.009 10.1016/j.cels.2019.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078528 24]. | ||
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#Wang Y, Tatham MH, Schmidt-Heck W, Swann C, Singh-Dolt K, Meseguer-Ripolles J, Lucendo-Villarin B, Kunath T, Rudd TR, Smith AJH, Hengstler JG, Godoy P, Hay RT, Hay DC, (2019) "Multiomics Analyses of HNF4α Protein Domain Function during Human Pluripotent Stem Cell Differentiation." <i>iScience</i> <b>16</b>:206–217; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31185456 31185456]; doi: [https://dx.doi.org/10.1016/j.isci.2019.05.028 10.1016/j.isci.2019.05.028]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31185456 96]. | #Wang Y, Tatham MH, Schmidt-Heck W, Swann C, Singh-Dolt K, Meseguer-Ripolles J, Lucendo-Villarin B, Kunath T, Rudd TR, Smith AJH, Hengstler JG, Godoy P, Hay RT, Hay DC, (2019) "Multiomics Analyses of HNF4α Protein Domain Function during Human Pluripotent Stem Cell Differentiation." <i>iScience</i> <b>16</b>:206–217; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31185456 31185456]; doi: [https://dx.doi.org/10.1016/j.isci.2019.05.028 10.1016/j.isci.2019.05.028]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31185456 96]. | ||
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+ | #Hillier C, Pardo M, Yu L, Bushell E, Sanderson T, Metcalf T, Herd C, Anar B, Rayner JC, Billker O, Choudhary JS, (2019) "Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality." <i>Cell Rep</i> <b>28</b>(6):1635–1647.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31390575 31390575]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.07.019 10.1016/j.celrep.2019.07.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31390575 723]. | ||
+ | #Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, Koomen JM, Eschrich SA, Haura EB, (2019) "Proteogenomic landscape of squamous cell lung cancer." <i>Nat Commun</i> <b>10</b>(1):3578; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31395880 31395880]; doi: [https://dx.doi.org/10.1038/s41467-019-11452-x 10.1038/s41467-019-11452-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31395880 58]. | ||
+ | #Olson MG, Widner RE, Jorgenson LM, Lawrence A, Lagundzin D, Woods NT, Ouellette SP, Rucks EA, (2019) "Proximity Labeling To Map Host-Pathogen Interactions at the Membrane of a Bacterium-Containing Vacuole in Chlamydia trachomatis-Infected Human Cells." <i>Infect Immun</i> <b>87</b>(11):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31405957 31405957]; doi: [https://dx.doi.org/10.1128/IAI.00537-19 10.1128/IAI.00537-19]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31405957 117]. | ||
+ | #Brophy RH, Cai L, Duan X, Zhang Q, Townsend RR, Nunley RM, Guilak F, Rai MF, (2019) "Proteomic analysis of synovial fluid identifies periostin as a biomarker for anterior cruciate ligament injury." <i>Osteoarthritis Cartilage</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31430535 31430535]; doi: [https://dx.doi.org/10.1016/j.joca.2019.08.002 10.1016/j.joca.2019.08.002]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31430535 11]. | ||
+ | #Ong JWJ, Tan KS, Ler SG, Gunaratne J, Choi H, Seet JE, Chow VT, (2019) "Insights into Early Recovery from Influenza Pneumonia by Spatial and Temporal Quantification of Putative Lung Regenerating Cells and by Lung Proteomics." <i>Cells</i> <b>8</b>(9):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31455003 31455003]; doi: [https://dx.doi.org/10.3390/cells8090975 10.3390/cells8090975]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31455003 1]. | ||
+ | #Denes BJ, Bolton C, Illsley CS, Kok WL, Walker JV, Poetsch A, Tredwin C, Kiliaridis S, Hu B, (2019) "Notch Coordinates Periodontal Ligament Maturation through Regulating Lamin A." <i>J Dent Res</i> <b></b>:22034519871448; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31461625 31461625]; doi: [https://dx.doi.org/10.1177/0022034519871448 10.1177/0022034519871448]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31461625 1]. | ||
+ | #Schulte F, Hasturk H, Hardt M, (2019) "Mapping Relative Differences in Human Salivary Gland Secretions by Dried Saliva Spot Sampling and nanoLC-MS/MS." <i>Proteomics</i> <b></b>:e1900023; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31476108 31476108]; doi: [https://dx.doi.org/10.1002/pmic.201900023 10.1002/pmic.201900023]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31476108 36]. | ||
+ | #Defenouillère Q, Verraes A, Laussel C, Friedrich A, Schacherer J, Léon S, (2019) "The induction of HAD-like phosphatases by multiple signaling pathways confers resistance to the metabolic inhibitor 2-deoxyglucose." <i>Sci Signal</i> <b>12</b>(597):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31481524 31481524]; doi: [https://dx.doi.org/10.1126/scisignal.aaw8000 10.1126/scisignal.aaw8000]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31481524 6]. | ||
+ | #Gao Y, Lee H, Kwon OK, Tan M, Kim KT, Lee S, (2019) "Global Proteomic Analysis of Lysine Succinylation in Zebrafish (<i>Danio rerio</i>)." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31483678 31483678]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00462 10.1021/acs.jproteome.9b00462]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31483678 4]. | ||
+ | #Al Ahmad A, Paffrath V, Clima R, Busch JF, Rabien A, Kilic E, Villegas S, Timmermann B, Attimonelli M, Jung K, Meierhofer D, (2019) "Papillary Renal Cell Carcinomas Rewire Glutathione Metabolism and Are Deficient in Both Anabolic Glucose Synthesis and Oxidative Phosphorylation." <i>Cancers (Basel)</i> <b>11</b>(9):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31484429 31484429]; doi: [https://dx.doi.org/10.3390/cancers11091298 10.3390/cancers11091298]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31484429 33]. | ||
+ | #Liebelt F, Jansen NS, Kumar S, Gracheva E, Claessens LA, Verlaan-de Vries M, Willemstein E, Vertegaal ACO, (2019) "The poly-SUMO2/3 protease SENP6 enables assembly of the constitutive centromere-associated network by group deSUMOylation." <i>Nat Commun</i> <b>10</b>(1):3987; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31485003 31485003]; doi: [https://dx.doi.org/10.1038/s41467-019-11773-x 10.1038/s41467-019-11773-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31485003 46]. | ||
+ | #Sleat DE, Wiseman JA, El-Banna M, Zheng H, Zhao C, Soherwardy A, Moore DF, Lobel P, (2019) "Analysis of brain and cerebrospinal fluid from mouse models of the three major forms of neuronal ceroid lipofuscinosis reveals changes in the lysosomal proteome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31501224 31501224]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001587 10.1074/mcp.RA119.001587]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31501224 132]. | ||
+ | #Wilson R, Gundamaraju R, Vemuri R, Angelucci C, Geraghty D, Gueven N, Eri RD, (2019) "Identification of Key Pro-Survival Proteins in Isolated Colonic Goblet Cells of Winnie, a Murine Model of Spontaneous Colitis." <i>Inflamm Bowel Dis</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31504521 31504521]; doi: [https://dx.doi.org/10.1093/ibd/izz179 10.1093/ibd/izz179]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31504521 6]. | ||
+ | #Piano D, Cocco E, Guadalupi G, Kalaji HM, Kirkpatrick J, Farci D, (2019) "Characterization under quasi-native conditions of the capsanthin/capsorubin synthase from Capsicum annuum L." <i>Plant Physiol Biochem</i> <b>143</b>:165–175; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31505449 31505449]; doi: [https://dx.doi.org/10.1016/j.plaphy.2019.09.007 10.1016/j.plaphy.2019.09.007]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31505449 4]. | ||
+ | #Dou M, Clair G, Tsai CF, Xu K, Chrisler WB, Sontag RL, Zhao R, Moore RJ, Liu T, Pasa-Tolic L, Smith RD, Shi T, Adkins JN, Qian WJ, Kelly RT, Ansong C, Zhu Y, (2019) "High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31509397 31509397]; doi: [https://dx.doi.org/10.1021/acs.analchem.9b03349 10.1021/acs.analchem.9b03349]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31509397 20]. | ||
+ | #Lugli F, Di Rocco G, Vazzana A, Genovese F, Pinetti D, Cilli E, Carile MC, Silvestrini S, Gabanini G, Arrighi S, Buti L, Bortolini E, Cipriani A, Figus C, Marciani G, Oxilia G, Romandini M, Sorrentino R, Sola M, Benazzi S, (2019) "Enamel peptides reveal the sex of the Late Antique 'Lovers of Modena'." <i>Sci Rep</i> <b>9</b>(1):13130; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31511583 31511583]; doi: [https://dx.doi.org/10.1038/s41598-019-49562-7 10.1038/s41598-019-49562-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31511583 16]. | ||
+ | #Gnanasundram SV, Kos-Braun IC, Koš M, (2019) "At least two molecules of the RNA helicase Has1 are simultaneously present in pre-ribosomes during ribosome biogenesis." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31511893 31511893]; doi: [https://dx.doi.org/10.1093/nar/gkz767 10.1093/nar/gkz767]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31511893 17]. | ||
+ | #Kampstra ASB, van Heemst J, Janssen GM, de Ru AH, van Lummel M, van Veelen PA, Toes REM, (2019) "Ligandomes obtained from different HLA-class II-molecules are homologous for N- and C-terminal residues outside the peptide-binding cleft." <i>Immunogenetics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31520135 31520135]; doi: [https://dx.doi.org/10.1007/s00251-019-01129-6 10.1007/s00251-019-01129-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31520135 77]. | ||
+ | #Sjödin S, Brinkmalm G, Öhrfelt A, Parnetti L, Paciotti S, Hansson O, Hardy J, Blennow K, Zetterberg H, Brinkmalm A, (2019) "Endo-lysosomal proteins and ubiquitin CSF concentrations in Alzheimer's and Parkinson's disease." <i>Alzheimers Res Ther</i> <b>11</b>(1):82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31521194 31521194]; doi: [https://dx.doi.org/10.1186/s13195-019-0533-9 10.1186/s13195-019-0533-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31521194 27]. | ||
+ | #Israel S, Ernst M, Psathaki OE, Drexler HCA, Casser E, Suzuki Y, Makalowski W, Boiani M, Fuellen G, Taher L, (2019) "An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo." <i>Sci Rep</i> <b>9</b>(1):13356; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31527703 31527703]; doi: [https://dx.doi.org/10.1038/s41598-019-49817-3 10.1038/s41598-019-49817-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31527703 14]. | ||
+ | #Uckeley ZM, Moeller R, Kühn LI, Nilsson E, Robens C, Lasswitz L, Lindqvist R, Lenman A, Passos V, Voss Y, Sommerauer C, Kampmann M, Goffinet C, Meissner F, Överby AK, Lozach PY, Gerold G, (2019) "Quantitative proteomics of Uukuniemi virus - host cell interactions reveals GBF1 as proviral host factor for phleboviruses." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31570497 31570497]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001631 10.1074/mcp.RA119.001631]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31570497 20]. | ||
+ | #Kawahara R, Recuero S, Nogueira FCS, Domont GB, Leite KRM, Srougi M, Thaysen-Andersen M, Palmisano G, (2019) "Tissue Proteome Signatures Associated with Five Grades of Prostate Cancer and Benign Prostatic Hyperplasia." <i>Proteomics</i> <b></b>:e1900174; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31576646 31576646]; doi: [https://dx.doi.org/10.1002/pmic.201900174 10.1002/pmic.201900174]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31576646 5]. | ||
+ | #Velásquez E, Martins de Souza D, Velásquez I, Carneiro GRA, Schmitt A, Falkai P, Domont GB, Nogueira FCS, (2019) "QUANTITATIVE SUBCELLULAR PROTEOMICS OF THE ORBITOFRONTAL CORTEX OF SCHIZOPHRENIA PATIENTS." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31581776 31581776]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00398 10.1021/acs.jproteome.9b00398]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31581776 46]. | ||
+ | #Lundby A, Franciosa G, Emdal KB, Refsgaard JC, Gnosa SP, Bekker-Jensen DB, Secher A, Maurya SR, Paul I, Mendez BL, Kelstrup CD, Francavilla C, Kveiborg M, Montoya G, Jensen LJ, Olsen JV, (2019) "Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites." <i>Cell</i> <b>179</b>(2):543–560.e26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31585087 31585087]; doi: [https://dx.doi.org/10.1016/j.cell.2019.09.008 10.1016/j.cell.2019.09.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31585087 255]. | ||
+ | #Bichmann L, Nelde A, Ghosh M, Heumos L, Mohr C, Peltzer A, Kuchenbecker L, Sachsenberg T, Walz JS, Stevanović S, Rammensee HG, Kohlbacher O, (2019) "MHCquant: Automated and reproducible data analysis for immunopeptidomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31589052 31589052]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00313 10.1021/acs.jproteome.9b00313]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31589052 38]. | ||
+ | #Lin Z, Zhang Y, Pan H, Hao P, Li S, He Y, Yang H, Liu S, Ren Y, (2019) "An alternative strategy to explore missing proteins with low molecular weight." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31592669 31592669]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00353 10.1021/acs.jproteome.9b00353]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31592669 3]. | ||
+ | #Noya SB, Colameo D, Brüning F, Spinnler A, Mircsof D, Opitz L, Mann M, Tyagarajan SK, Robles MS, Brown SA, (2019) "The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep." <i>Science</i> <b>366</b>(6462):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31601739 31601739]; doi: [https://dx.doi.org/10.1126/science.aav2642 10.1126/science.aav2642]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31601739 96]. | ||
+ | #Racle J, Michaux J, Rockinger GA, Arnaud M, Bobisse S, Chong C, Guillaume P, Coukos G, Harari A, Jandus C, Bassani-Sternberg M, Gfeller D, (2019) "Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31611696 31611696]; doi: [https://dx.doi.org/10.1038/s41587-019-0289-6 10.1038/s41587-019-0289-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31611696 131]. | ||
+ | #Stadlmann J, Hudecz O, Krššáková G, Ctortecka C, Van Raemdonck G, Op De Beeck J, Desmet G, Penninger JM, Jacobs P, Mechtler K, (2019) "Improved Sensitivity in Low-Input Proteomics using Micro-Pillar Array-based Chromatography." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31612716 31612716]; doi: [https://dx.doi.org/10.1021/acs.analchem.9b02899 10.1021/acs.analchem.9b02899]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31612716 68]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of November 3, 2019.