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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 May 5, 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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#Welinder C, Pawłowski K, Sugihara Y, Yakovleva M, Jönsson G, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Jansson B, Laurell T, Fehniger T, Döme B, Malm J, Wieslander E, Nishimura T, Marko-Varga G, (2015) "A protein deep sequencing evaluation of metastatic melanoma tissues." <i>PLoS One</i> <b>10</b>(4):e0123661; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25874936 25874936]; doi: [https://dx.doi.org/10.1371/journal.pone.0123661 10.1371/journal.pone.0123661]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25874936 11]. | #Welinder C, Pawłowski K, Sugihara Y, Yakovleva M, Jönsson G, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Jansson B, Laurell T, Fehniger T, Döme B, Malm J, Wieslander E, Nishimura T, Marko-Varga G, (2015) "A protein deep sequencing evaluation of metastatic melanoma tissues." <i>PLoS One</i> <b>10</b>(4):e0123661; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25874936 25874936]; doi: [https://dx.doi.org/10.1371/journal.pone.0123661 10.1371/journal.pone.0123661]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25874936 11]. | ||
#Hosp F, Scheltema RA, Eberl HC, Kulak NA, Keilhauer EC, Mayr K, Mann M, (2015) "A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day." <i>Mol Cell Proteomics</i> <b>14</b>(7):2030–41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25887394 25887394]; doi: [https://dx.doi.org/10.1074/mcp.O115.049460 10.1074/mcp.O115.049460]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25887394 234]. | #Hosp F, Scheltema RA, Eberl HC, Kulak NA, Keilhauer EC, Mayr K, Mann M, (2015) "A Double-Barrel Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) System to Quantify 96 Interactomes per Day." <i>Mol Cell Proteomics</i> <b>14</b>(7):2030–41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25887394 25887394]; doi: [https://dx.doi.org/10.1074/mcp.O115.049460 10.1074/mcp.O115.049460]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25887394 234]. | ||
+ | #Yu Y, Sikorski P, Bowman-Gholston C, Cacciabeve N, Nelson KE, Pieper R, (2015) "Diagnosing inflammation and infection in the urinary system via proteomics." <i>J Transl Med</i> <b>13</b>:111; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25889401 25889401]; doi: [https://dx.doi.org/10.1186/s12967-015-0475-3 10.1186/s12967-015-0475-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25889401 260]. | ||
#Xu R, Greening DW, Rai A, Ji H, Simpson RJ, (2015) "Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct." <i>Methods</i> <b>87</b>:11–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25890246 25890246]; doi: [https://dx.doi.org/10.1016/j.ymeth.2015.04.008 10.1016/j.ymeth.2015.04.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25890246 4]. | #Xu R, Greening DW, Rai A, Ji H, Simpson RJ, (2015) "Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct." <i>Methods</i> <b>87</b>:11–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25890246 25890246]; doi: [https://dx.doi.org/10.1016/j.ymeth.2015.04.008 10.1016/j.ymeth.2015.04.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25890246 4]. | ||
#van der Mijn JC, Labots M, Piersma SR, Pham TV, Knol JC, Broxterman HJ, Verheul HM, Jiménez CR, (2015) "Evaluation of different phospho-tyrosine antibodies for label-free phosphoproteomics." <i>J Proteomics</i> <b>127</b>(Pt B):259–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25890253 25890253]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.04.006 10.1016/j.jprot.2015.04.006]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25890253 10]. | #van der Mijn JC, Labots M, Piersma SR, Pham TV, Knol JC, Broxterman HJ, Verheul HM, Jiménez CR, (2015) "Evaluation of different phospho-tyrosine antibodies for label-free phosphoproteomics." <i>J Proteomics</i> <b>127</b>(Pt B):259–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25890253 25890253]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.04.006 10.1016/j.jprot.2015.04.006]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25890253 10]. | ||
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#Liu L, Phua YW, Lee RS, Ma X, Jenkins Y, Novy K, Humphrey ES, Chan H, Shearer R, Ong PC, Dai W, Saunders DN, Lucet IS, Daly RJ, (2016) "Homo- and Heterotypic Association Regulates Signaling by the SgK269/PEAK1 and SgK223 Pseudokinases." <i>J Biol Chem</i> <b>291</b>(41):21571–21583; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27531744 27531744]; doi: [https://dx.doi.org/10.1074/jbc.M116.748897 10.1074/jbc.M116.748897]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27531744 6]. | #Liu L, Phua YW, Lee RS, Ma X, Jenkins Y, Novy K, Humphrey ES, Chan H, Shearer R, Ong PC, Dai W, Saunders DN, Lucet IS, Daly RJ, (2016) "Homo- and Heterotypic Association Regulates Signaling by the SgK269/PEAK1 and SgK223 Pseudokinases." <i>J Biol Chem</i> <b>291</b>(41):21571–21583; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27531744 27531744]; doi: [https://dx.doi.org/10.1074/jbc.M116.748897 10.1074/jbc.M116.748897]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27531744 6]. | ||
#Mattei B, Spinelli F, Pontiggia D, De Lorenzo G, (2016) "Comprehensive Analysis of the Membrane Phosphoproteome Regulated by Oligogalacturonides in Arabidopsis thaliana." <i>Front Plant Sci</i> <b>7</b>:1107; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27532006 27532006]; doi: [https://dx.doi.org/10.3389/fpls.2016.01107 10.3389/fpls.2016.01107]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27532006 12]. | #Mattei B, Spinelli F, Pontiggia D, De Lorenzo G, (2016) "Comprehensive Analysis of the Membrane Phosphoproteome Regulated by Oligogalacturonides in Arabidopsis thaliana." <i>Front Plant Sci</i> <b>7</b>:1107; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27532006 27532006]; doi: [https://dx.doi.org/10.3389/fpls.2016.01107 10.3389/fpls.2016.01107]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27532006 12]. | ||
+ | #Zacharias LG, Hartmann AK, Song E, Zhao J, Zhu R, Mirzaei P, Mechref Y, (2016) "HILIC and ERLIC Enrichment of Glycopeptides Derived from Breast and Brain Cancer Cells." <i>J Proteome Res</i> <b>15</b>(10):3624–3634; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27533485 27533485]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00429 10.1021/acs.jproteome.6b00429]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27533485 36]. | ||
#Solari FA, Mattheij NJ, Burkhart JM, Swieringa F, Collins PW, Cosemans JM, Sickmann A, Heemskerk JW, Zahedi RP, (2016) "Combined Quantification of the Global Proteome, Phosphoproteome, and Proteolytic Cleavage to Characterize Altered Platelet Functions in the Human Scott Syndrome." <i>Mol Cell Proteomics</i> <b>15</b>(10):3154–3169; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535140 27535140]; doi: [https://dx.doi.org/10.1074/mcp.M116.060368 10.1074/mcp.M116.060368]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27535140 23]. | #Solari FA, Mattheij NJ, Burkhart JM, Swieringa F, Collins PW, Cosemans JM, Sickmann A, Heemskerk JW, Zahedi RP, (2016) "Combined Quantification of the Global Proteome, Phosphoproteome, and Proteolytic Cleavage to Characterize Altered Platelet Functions in the Human Scott Syndrome." <i>Mol Cell Proteomics</i> <b>15</b>(10):3154–3169; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535140 27535140]; doi: [https://dx.doi.org/10.1074/mcp.M116.060368 10.1074/mcp.M116.060368]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27535140 23]. | ||
#Wei W, Luo W, Wu F, Peng X, Zhang Y, Zhang M, Zhao Y, Su N, Qi Y, Chen L, Zhang Y, Wen B, He F, Xu P, (2016) "Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer." <i>J Proteome Res</i> <b>15</b>(11):3988–3997; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535590 27535590]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00390 10.1021/acs.jproteome.6b00390]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27535590 150]. | #Wei W, Luo W, Wu F, Peng X, Zhang Y, Zhang M, Zhao Y, Su N, Qi Y, Chen L, Zhang Y, Wen B, He F, Xu P, (2016) "Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer." <i>J Proteome Res</i> <b>15</b>(11):3988–3997; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535590 27535590]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00390 10.1021/acs.jproteome.6b00390]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27535590 150]. | ||
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#van den Eshof BL, Hoogendijk AJ, Simpson PJ, van Alphen FPJ, Zanivan S, Mertens K, Meijer AB, van den Biggelaar M, (2017) "Paradigm of Biased PAR1 (Protease-Activated Receptor-1) Activation and Inhibition in Endothelial Cells Dissected by Phosphoproteomics." <i>Arterioscler Thromb Vasc Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28818855 28818855]; doi: [https://dx.doi.org/10.1161/ATVBAHA.117.309926 10.1161/ATVBAHA.117.309926]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28818855 57]. | #van den Eshof BL, Hoogendijk AJ, Simpson PJ, van Alphen FPJ, Zanivan S, Mertens K, Meijer AB, van den Biggelaar M, (2017) "Paradigm of Biased PAR1 (Protease-Activated Receptor-1) Activation and Inhibition in Endothelial Cells Dissected by Phosphoproteomics." <i>Arterioscler Thromb Vasc Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28818855 28818855]; doi: [https://dx.doi.org/10.1161/ATVBAHA.117.309926 10.1161/ATVBAHA.117.309926]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28818855 57]. | ||
#Ayre DC, Chute IC, Joy AP, Barnett DA, Hogan AM, Grüll MP, Peña-Castillo L, Lang AS, Lewis SM, Christian SL, (2017) "CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo." <i>Sci Rep</i> <b>7</b>(1):8642; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28819186 28819186]; doi: [https://dx.doi.org/10.1038/s41598-017-08094-8 10.1038/s41598-017-08094-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28819186 146]. | #Ayre DC, Chute IC, Joy AP, Barnett DA, Hogan AM, Grüll MP, Peña-Castillo L, Lang AS, Lewis SM, Christian SL, (2017) "CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo." <i>Sci Rep</i> <b>7</b>(1):8642; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28819186 28819186]; doi: [https://dx.doi.org/10.1038/s41598-017-08094-8 10.1038/s41598-017-08094-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28819186 146]. | ||
+ | #Singh H, Yu Y, Suh MJ, Torralba MG, Stenzel RD, Tovchigrechko A, Thovarai V, Harkins DM, Rajagopala SV, Osborne W, Cogen FR, Kaplowitz PB, Nelson KE, Madupu R, Pieper R, (2017) "Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function." <i>Theranostics</i> <b>7</b>(10):2704–2717; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28819457 28819457]; doi: [https://dx.doi.org/10.7150/thno.19679 10.7150/thno.19679]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28819457 663]. | ||
#Hung CL, Pan SH, Han CL, Chang CW, Hsu YL, Su CH, Shih SC, Lai YJ, Chiang Chiau JS, Yeh HI, Liu CY, Lee HC, Lam CSP, (2017) "Membrane Proteomics of Impaired Energetics and Cytoskeletal Disorganization in Elderly Diet-Induced Diabetic Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28823169 28823169]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00148 10.1021/acs.jproteome.7b00148]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28823169 14]. | #Hung CL, Pan SH, Han CL, Chang CW, Hsu YL, Su CH, Shih SC, Lai YJ, Chiang Chiau JS, Yeh HI, Liu CY, Lee HC, Lam CSP, (2017) "Membrane Proteomics of Impaired Energetics and Cytoskeletal Disorganization in Elderly Diet-Induced Diabetic Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28823169 28823169]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00148 10.1021/acs.jproteome.7b00148]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28823169 14]. | ||
#Fu L, Liu KK, Sun MA, Tian CP, Sun R, Morales Betanzos C, Tallman KA, Porter NA, Yang Y, Guo DJ, Liebler DC, Yang J, (2017) "Systematic and quantitative assessment of hydrogen peroxide reactivity with cysteines across human proteomes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28827280 28827280]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000108 10.1074/mcp.RA117.000108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28827280 12]. | #Fu L, Liu KK, Sun MA, Tian CP, Sun R, Morales Betanzos C, Tallman KA, Porter NA, Yang Y, Guo DJ, Liebler DC, Yang J, (2017) "Systematic and quantitative assessment of hydrogen peroxide reactivity with cysteines across human proteomes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28827280 28827280]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000108 10.1074/mcp.RA117.000108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28827280 12]. | ||
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#Liang P, Zhu W, Lan T, Tao Q, (2018) "Detection of salivary protein biomarkers of saliva secretion disorder in a primary Sjögren syndrome murine model." <i>J Pharm Biomed Anal</i> <b>154</b>:252–262; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29558726 29558726]; doi: [https://dx.doi.org/10.1016/j.jpba.2018.03.023 10.1016/j.jpba.2018.03.023]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29558726 2]. | #Liang P, Zhu W, Lan T, Tao Q, (2018) "Detection of salivary protein biomarkers of saliva secretion disorder in a primary Sjögren syndrome murine model." <i>J Pharm Biomed Anal</i> <b>154</b>:252–262; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29558726 29558726]; doi: [https://dx.doi.org/10.1016/j.jpba.2018.03.023 10.1016/j.jpba.2018.03.023]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29558726 2]. | ||
#Saei AA, Sabatier P, Güler Tokat Ü, Chernobrovkin A, Pirmoradian M, Zubarev RA, (2018) "Comparative proteomics of dying and surviving cancer cells improves the identification of drug targets and sheds light on cell life/death decisions." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29572246 29572246]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000610 10.1074/mcp.RA118.000610]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29572246 90]. | #Saei AA, Sabatier P, Güler Tokat Ü, Chernobrovkin A, Pirmoradian M, Zubarev RA, (2018) "Comparative proteomics of dying and surviving cancer cells improves the identification of drug targets and sheds light on cell life/death decisions." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29572246 29572246]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000610 10.1074/mcp.RA118.000610]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29572246 90]. | ||
+ | #Zhang C, Leng W, Sun C, Lu T, Chen Z, Men X, Wang Y, Wang G, Zhen B, Qin J, (2018) "Urine Proteome Profiling Predicts Lung Cancer from Control Cases and Other Tumors." <i>EBioMedicine</i> <b>30</b>:120–128; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29576497 29576497]; doi: [https://dx.doi.org/10.1016/j.ebiom.2018.03.009 10.1016/j.ebiom.2018.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29576497 557]. | ||
#Haller C, Chaskar P, Piccand J, Cominetti O, Macron C, Dayon L, Kraus MR, (2018) "Insights into islet differentiation and maturation through proteomic characterization of a human iPSC-derived pancreatic endocrine model." <i>Proteomics Clin Appl</i> <b></b>:e1600173; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29578310 29578310]; doi: [https://dx.doi.org/10.1002/prca.201600173 10.1002/prca.201600173]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29578310 218]. | #Haller C, Chaskar P, Piccand J, Cominetti O, Macron C, Dayon L, Kraus MR, (2018) "Insights into islet differentiation and maturation through proteomic characterization of a human iPSC-derived pancreatic endocrine model." <i>Proteomics Clin Appl</i> <b></b>:e1600173; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29578310 29578310]; doi: [https://dx.doi.org/10.1002/prca.201600173 10.1002/prca.201600173]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29578310 218]. | ||
#Tucher C, Bode K, Schiller P, Claßen L, Birr C, Souto-Carneiro MM, Blank N, Lorenz HM, Schiller M, (2018) "Extracellular Vesicle Subtypes Released From Activated or Apoptotic T-Lymphocytes Carry a Specific and Stimulus-Dependent Protein Cargo." <i>Front Immunol</i> <b>9</b>:534; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29599781 29599781]; doi: [https://dx.doi.org/10.3389/fimmu.2018.00534 10.3389/fimmu.2018.00534]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29599781 24]. | #Tucher C, Bode K, Schiller P, Claßen L, Birr C, Souto-Carneiro MM, Blank N, Lorenz HM, Schiller M, (2018) "Extracellular Vesicle Subtypes Released From Activated or Apoptotic T-Lymphocytes Carry a Specific and Stimulus-Dependent Protein Cargo." <i>Front Immunol</i> <b>9</b>:534; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29599781 29599781]; doi: [https://dx.doi.org/10.3389/fimmu.2018.00534 10.3389/fimmu.2018.00534]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29599781 24]. | ||
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#Shraibman B, Barnea E, Melamed Kadosh D, Haimovich Y, Slobodin G, Rosner I, López-Larrea C, Hilf N, Kuttruff S, Song C, Britten C, Castle J, Kreiter S, Frenzel K, Tatagiba M, Tabatabai G, Dietrich PY, Dutoit V, Wick W, Platten M, Winkler F, Von Deimling A, Kroep J, Sahuquillo J, Martinez-Ricarte F, Rodon J, Lassen U, Ottensmeier C, van der Burg SH, Thor Straten P, Poulsen HS, Ponsati B, Okada H, Rammensee HG, Sahin U, Singh H, Admon A, (2018) "Identification of tumor antigens among the HLA peptidomes of Glioblastoma tumors and plasma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30072578 30072578]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000792 10.1074/mcp.RA118.000792]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30072578 75]. | #Shraibman B, Barnea E, Melamed Kadosh D, Haimovich Y, Slobodin G, Rosner I, López-Larrea C, Hilf N, Kuttruff S, Song C, Britten C, Castle J, Kreiter S, Frenzel K, Tatagiba M, Tabatabai G, Dietrich PY, Dutoit V, Wick W, Platten M, Winkler F, Von Deimling A, Kroep J, Sahuquillo J, Martinez-Ricarte F, Rodon J, Lassen U, Ottensmeier C, van der Burg SH, Thor Straten P, Poulsen HS, Ponsati B, Okada H, Rammensee HG, Sahin U, Singh H, Admon A, (2018) "Identification of tumor antigens among the HLA peptidomes of Glioblastoma tumors and plasma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30072578 30072578]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000792 10.1074/mcp.RA118.000792]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30072578 75]. | ||
#Park S, Park JH, Jung HJ, Jang JH, Ahn S, Kim Y, Suh PG, Chae S, Yoon JH, Ryu SH, Hwang D, (2018) "A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cells." <i>Exp Mol Med</i> <b>50</b>(8):93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076294 30076294]; doi: [https://dx.doi.org/10.1038/s12276-018-0120-3 10.1038/s12276-018-0120-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076294 24]. | #Park S, Park JH, Jung HJ, Jang JH, Ahn S, Kim Y, Suh PG, Chae S, Yoon JH, Ryu SH, Hwang D, (2018) "A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cells." <i>Exp Mol Med</i> <b>50</b>(8):93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076294 30076294]; doi: [https://dx.doi.org/10.1038/s12276-018-0120-3 10.1038/s12276-018-0120-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076294 24]. | ||
+ | #de la Parra C, Ernlund A, Alard A, Ruggles K, Ueberheide B, Schneider RJ, (2018) "A widespread alternate form of cap-dependent mRNA translation initiation." <i>Nat Commun</i> <b>9</b>(1):3068; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076308 30076308]; doi: [https://dx.doi.org/10.1038/s41467-018-05539-0 10.1038/s41467-018-05539-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076308 21]. | ||
#Kozono S, Lin YM, Seo HS, Pinch B, Lian X, Qiu C, Herbert MK, Chen CH, Tan L, Gao ZJ, Massefski W, Doctor ZM, Jackson BP, Chen Y, Dhe-Paganon S, Lu KP, Zhou XZ, (2018) "Arsenic targets Pin1 and cooperates with retinoic acid to inhibit cancer-driving pathways and tumor-initiating cells." <i>Nat Commun</i> <b>9</b>(1):3069; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30093655 30093655]; doi: [https://dx.doi.org/10.1038/s41467-018-05402-2 10.1038/s41467-018-05402-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30093655 12]. | #Kozono S, Lin YM, Seo HS, Pinch B, Lian X, Qiu C, Herbert MK, Chen CH, Tan L, Gao ZJ, Massefski W, Doctor ZM, Jackson BP, Chen Y, Dhe-Paganon S, Lu KP, Zhou XZ, (2018) "Arsenic targets Pin1 and cooperates with retinoic acid to inhibit cancer-driving pathways and tumor-initiating cells." <i>Nat Commun</i> <b>9</b>(1):3069; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30093655 30093655]; doi: [https://dx.doi.org/10.1038/s41467-018-05402-2 10.1038/s41467-018-05402-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30093655 12]. | ||
#Kumar G, Hummel K, Razzazi-Fazeli E, El-Matbouli M, (2018) "Proteome Profiles of Head Kidney and Spleen of Rainbow Trout (Oncorhynchus Mykiss)." <i>Proteomics</i> <b></b>:e1800101; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30094954 30094954]; doi: [https://dx.doi.org/10.1002/pmic.201800101 10.1002/pmic.201800101]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30094954 54]. | #Kumar G, Hummel K, Razzazi-Fazeli E, El-Matbouli M, (2018) "Proteome Profiles of Head Kidney and Spleen of Rainbow Trout (Oncorhynchus Mykiss)." <i>Proteomics</i> <b></b>:e1800101; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30094954 30094954]; doi: [https://dx.doi.org/10.1002/pmic.201800101 10.1002/pmic.201800101]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30094954 54]. | ||
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#Hwang H, Jeong JE, Lee HK, Yun KN, An HJ, Lee B, Paik YK, Jeong TS, Yee GT, Kim JY, Yoo JS, (2018) "Identification of Missing Proteins in Human Olfactory Epithelial Tissue by Liquid Chromatography-Tandem Mass Spectrometry." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30113170 30113170]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00408 10.1021/acs.jproteome.8b00408]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30113170 23]. | #Hwang H, Jeong JE, Lee HK, Yun KN, An HJ, Lee B, Paik YK, Jeong TS, Yee GT, Kim JY, Yoo JS, (2018) "Identification of Missing Proteins in Human Olfactory Epithelial Tissue by Liquid Chromatography-Tandem Mass Spectrometry." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30113170 30113170]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00408 10.1021/acs.jproteome.8b00408]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30113170 23]. | ||
#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]. | ||
#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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#El-Rami FE, Zielke RA, Wi T, Sikora AE, Unemo M, (2018) "Quantitative proteomics of the 2016 WHO <i>Neisseria gonorrhoeae</i> reference strains surveys vaccine candidates and antimicrobial resistance determinants." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352803 30352803]; doi: [https://dx.doi.org/10.1074/mcp.RA118.001125 10.1074/mcp.RA118.001125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352803 8]. | #El-Rami FE, Zielke RA, Wi T, Sikora AE, Unemo M, (2018) "Quantitative proteomics of the 2016 WHO <i>Neisseria gonorrhoeae</i> reference strains surveys vaccine candidates and antimicrobial resistance determinants." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30352803 30352803]; doi: [https://dx.doi.org/10.1074/mcp.RA118.001125 10.1074/mcp.RA118.001125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30352803 8]. | ||
#Serra A, Gallart-Palau X, Park JE, Lim GGY, Lim KL, Ho HH, Tam JP, Sze SK, (2018) "Vascular Bed Molecular Profiling by Differential Systemic Decellularization In Vivo." <i>Arterioscler Thromb Vasc Biol</i> <b>38</b>(10):2396–2409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30354219 30354219]; doi: [https://dx.doi.org/10.1161/ATVBAHA.118.311552 10.1161/ATVBAHA.118.311552]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30354219 16]. | #Serra A, Gallart-Palau X, Park JE, Lim GGY, Lim KL, Ho HH, Tam JP, Sze SK, (2018) "Vascular Bed Molecular Profiling by Differential Systemic Decellularization In Vivo." <i>Arterioscler Thromb Vasc Biol</i> <b>38</b>(10):2396–2409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30354219 30354219]; doi: [https://dx.doi.org/10.1161/ATVBAHA.118.311552 10.1161/ATVBAHA.118.311552]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30354219 16]. | ||
+ | #Zhao Y, Wilmarth PA, Cheng C, Limi S, Fowler VM, Zheng D, David LL, Cvekl A, (2019) "Proteome-transcriptome analysis and proteome remodeling in mouse lens epithelium and fibers." <i>Exp Eye Res</i> <b>179</b>:32–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30359574 30359574]; doi: [https://dx.doi.org/10.1016/j.exer.2018.10.011 10.1016/j.exer.2018.10.011]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30359574 3]. | ||
#Magagnotti C, Zerbini G, Fermo I, Carletti RM, Bonfanti R, Vallone F, Andolfo A, (2018) "Identification of nephropathy predictors in urine from children with a recent diagnosis of type 1 diabetes." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30366120 30366120]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.10.010 10.1016/j.jprot.2018.10.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30366120 51]. | #Magagnotti C, Zerbini G, Fermo I, Carletti RM, Bonfanti R, Vallone F, Andolfo A, (2018) "Identification of nephropathy predictors in urine from children with a recent diagnosis of type 1 diabetes." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30366120 30366120]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.10.010 10.1016/j.jprot.2018.10.010]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30366120 51]. | ||
#Tamminen M, Betz A, Pereira AL, Thali M, Matthews B, Suter MJ, Narwani A, (2018) "Proteome evolution under non-substitutable resource limitation." <i>Nat Commun</i> <b>9</b>(1):4650; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30405128 30405128]; doi: [https://dx.doi.org/10.1038/s41467-018-07106-z 10.1038/s41467-018-07106-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30405128 32]. | #Tamminen M, Betz A, Pereira AL, Thali M, Matthews B, Suter MJ, Narwani A, (2018) "Proteome evolution under non-substitutable resource limitation." <i>Nat Commun</i> <b>9</b>(1):4650; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30405128 30405128]; doi: [https://dx.doi.org/10.1038/s41467-018-07106-z 10.1038/s41467-018-07106-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30405128 32]. | ||
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#Aloui C, Barlier C, Claverol S, Fagan J, Awounou D, Tavernier E, Guyotat D, Hamzeh-Cognasse H, Cognasse F, Garraud O, Laradi S, (2019) "Differential protein expression of blood platelet components associated with adverse transfusion reactions." <i>J Proteomics</i> <b>194</b>:25–36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30590131 30590131]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.12.019 10.1016/j.jprot.2018.12.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30590131 48]. | #Aloui C, Barlier C, Claverol S, Fagan J, Awounou D, Tavernier E, Guyotat D, Hamzeh-Cognasse H, Cognasse F, Garraud O, Laradi S, (2019) "Differential protein expression of blood platelet components associated with adverse transfusion reactions." <i>J Proteomics</i> <b>194</b>:25–36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30590131 30590131]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.12.019 10.1016/j.jprot.2018.12.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30590131 48]. | ||
#Zhou Z, Chen Y, Jin M, He J, Guli A, Yan C, Ding S, (2018) "Comprehensive analysis of lysine acetylome reveals a site-specific pattern in rapamycin-induced autophagy." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30592415 30592415]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00533 10.1021/acs.jproteome.8b00533]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30592415 6]. | #Zhou Z, Chen Y, Jin M, He J, Guli A, Yan C, Ding S, (2018) "Comprehensive analysis of lysine acetylome reveals a site-specific pattern in rapamycin-induced autophagy." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30592415 30592415]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00533 10.1021/acs.jproteome.8b00533]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30592415 6]. | ||
+ | #Merlos Rodrigo MA, Buchtelova H, de Los Rios V, Casal JI, Eckschlager T, Hrabeta J, Belhajova M, Heger Z, Adam V, (2019) "Proteomic Signature of Neuroblastoma Cells UKF-NB-4 Reveals Key Role of Lysosomal Sequestration and the Proteasome Complex in Acquiring Chemoresistance to Cisplatin." <i>J Proteome Res</i> <b>18</b>(3):1255–1263; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30592607 30592607]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00867 10.1021/acs.jproteome.8b00867]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30592607 9]. | ||
#Dunn J, Ferluga S, Sharma V, Futschik M, Hilton DA, Adams CL, Lasonder E, Hannemann OC, (2018) "Proteomic analysis discovers the differential expression of novel proteins and phosphoproteins in meningioma including NEK9, HK2 and SET and deregulation of RNA metabolism." <i>EBioMedicine</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30594554 30594554]; doi: [https://dx.doi.org/10.1016/j.ebiom.2018.12.048 10.1016/j.ebiom.2018.12.048]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30594554 78]. | #Dunn J, Ferluga S, Sharma V, Futschik M, Hilton DA, Adams CL, Lasonder E, Hannemann OC, (2018) "Proteomic analysis discovers the differential expression of novel proteins and phosphoproteins in meningioma including NEK9, HK2 and SET and deregulation of RNA metabolism." <i>EBioMedicine</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30594554 30594554]; doi: [https://dx.doi.org/10.1016/j.ebiom.2018.12.048 10.1016/j.ebiom.2018.12.048]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30594554 78]. | ||
#Żylicz JJ, Bousard A, Žumer K, Dossin F, Mohammad E, da Rocha ST, Schwalb B, Syx L, Dingli F, Loew D, Cramer P, Heard E, (2019) "The Implication of Early Chromatin Changes in X Chromosome Inactivation." <i>Cell</i> <b>176</b>(1-2):182–197.e23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30595450 30595450]; doi: [https://dx.doi.org/10.1016/j.cell.2018.11.041 10.1016/j.cell.2018.11.041]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30595450 10]. | #Żylicz JJ, Bousard A, Žumer K, Dossin F, Mohammad E, da Rocha ST, Schwalb B, Syx L, Dingli F, Loew D, Cramer P, Heard E, (2019) "The Implication of Early Chromatin Changes in X Chromosome Inactivation." <i>Cell</i> <b>176</b>(1-2):182–197.e23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30595450 30595450]; doi: [https://dx.doi.org/10.1016/j.cell.2018.11.041 10.1016/j.cell.2018.11.041]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30595450 10]. | ||
+ | #Liebelt F, Sebastian RM, Moore CL, Mulder MPC, Ovaa H, Shoulders MD, Vertegaal ACO, (2019) "SUMOylation and the HSF1-Regulated Chaperone Network Converge to Promote Proteostasis in Response to Heat Shock." <i>Cell Rep</i> <b>26</b>(1):236–249.e4; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30605679 30605679]; doi: [https://dx.doi.org/10.1016/j.celrep.2018.12.027 10.1016/j.celrep.2018.12.027]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30605679 57]. | ||
#Queiroz RML, Smith T, Villanueva E, Marti-Solano M, Monti M, Pizzinga M, Mirea DM, Ramakrishna M, Harvey RF, Dezi V, Thomas GH, Willis AE, Lilley KS, (2019) "Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS)." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30607034 30607034]; doi: [https://dx.doi.org/10.1038/s41587-018-0001-2 10.1038/s41587-018-0001-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30607034 106]. | #Queiroz RML, Smith T, Villanueva E, Marti-Solano M, Monti M, Pizzinga M, Mirea DM, Ramakrishna M, Harvey RF, Dezi V, Thomas GH, Willis AE, Lilley KS, (2019) "Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS)." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30607034 30607034]; doi: [https://dx.doi.org/10.1038/s41587-018-0001-2 10.1038/s41587-018-0001-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30607034 106]. | ||
#Orre LM, Vesterlund M, Pan Y, Arslan T, Zhu Y, Fernandez Woodbridge A, Frings O, Fredlund E, Lehtiö J, (2019) "SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization." <i>Mol Cell</i> <b>73</b>(1):166–182.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30609389 30609389]; doi: [https://dx.doi.org/10.1016/j.molcel.2018.11.035 10.1016/j.molcel.2018.11.035]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30609389 18]. | #Orre LM, Vesterlund M, Pan Y, Arslan T, Zhu Y, Fernandez Woodbridge A, Frings O, Fredlund E, Lehtiö J, (2019) "SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization." <i>Mol Cell</i> <b>73</b>(1):166–182.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30609389 30609389]; doi: [https://dx.doi.org/10.1016/j.molcel.2018.11.035 10.1016/j.molcel.2018.11.035]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30609389 18]. | ||
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#Kosack L, Wingelhofer B, Popa A, Orlova A, Agerer B, Vilagos B, Majek P, Parapatics K, Lercher A, Ringler A, Klughammer J, Smyth M, Khamina K, Baazim H, de Araujo ED, Rosa DA, Park J, Tin G, Ahmar S, Gunning PT, Bock C, Siddle HV, Woods GM, Kubicek S, Murchison EP, Bennett KL, Moriggl R, Bergthaler A, (2019) "The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease." <i>Cancer Cell</i> <b>35</b>(1):125–139.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30645971 30645971]; doi: [https://dx.doi.org/10.1016/j.ccell.2018.11.018 10.1016/j.ccell.2018.11.018]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30645971 20]. | #Kosack L, Wingelhofer B, Popa A, Orlova A, Agerer B, Vilagos B, Majek P, Parapatics K, Lercher A, Ringler A, Klughammer J, Smyth M, Khamina K, Baazim H, de Araujo ED, Rosa DA, Park J, Tin G, Ahmar S, Gunning PT, Bock C, Siddle HV, Woods GM, Kubicek S, Murchison EP, Bennett KL, Moriggl R, Bergthaler A, (2019) "The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease." <i>Cancer Cell</i> <b>35</b>(1):125–139.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30645971 30645971]; doi: [https://dx.doi.org/10.1016/j.ccell.2018.11.018 10.1016/j.ccell.2018.11.018]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30645971 20]. | ||
#van Oorschot R, Hansen M, Koornneef JM, Marneth AE, Bergevoet SM, van Bergen MGJM, van Alphen FPJ, van der Zwaan C, Martens JHA, Vermeulen M, Jansen PWTC, Baltissen MPA, Laros-van Gorkom BAP, Janssen H, Jansen JH, von Lindern M, Meijer AB, van den Akker E, van der Reijden BA, (2019) "Molecular mechanisms of bleeding disorder-associated GFI1BQ287* mutation and its affected pathways in megakaryocytes and platelets." <i>Haematologica</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30655368 30655368]; doi: [https://dx.doi.org/10.3324/haematol.2018.194555 10.3324/haematol.2018.194555]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30655368 63]. | #van Oorschot R, Hansen M, Koornneef JM, Marneth AE, Bergevoet SM, van Bergen MGJM, van Alphen FPJ, van der Zwaan C, Martens JHA, Vermeulen M, Jansen PWTC, Baltissen MPA, Laros-van Gorkom BAP, Janssen H, Jansen JH, von Lindern M, Meijer AB, van den Akker E, van der Reijden BA, (2019) "Molecular mechanisms of bleeding disorder-associated GFI1BQ287* mutation and its affected pathways in megakaryocytes and platelets." <i>Haematologica</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30655368 30655368]; doi: [https://dx.doi.org/10.3324/haematol.2018.194555 10.3324/haematol.2018.194555]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30655368 63]. | ||
+ | #Tsukada T, Isowa Y, Kito K, Yoshida S, Toneri S, Horiguchi K, Fujiwara K, Yashiro T, Kato T, Kato Y, (2019) "Identification of TGFβ-induced proteins in non-endocrine mouse pituitary cell line TtT/GF by SILAC-assisted quantitative mass spectrometry." <i>Cell Tissue Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30666536 30666536]; doi: [https://dx.doi.org/10.1007/s00441-018-02989-2 10.1007/s00441-018-02989-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30666536 11]. | ||
#Gärtner SMK, Hundertmark T, Nolte H, Theofel I, Eren-Ghiani Z, Tetzner C, Duchow TB, Rathke C, Krüger M, Renkawitz-Pohl R, (2019) "Stage-specific testes proteomics of Drosophila melanogaster identifies essential proteins for male fertility." <i>Eur J Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30679029 30679029]; doi: [https://dx.doi.org/10.1016/j.ejcb.2019.01.001 10.1016/j.ejcb.2019.01.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30679029 180]. | #Gärtner SMK, Hundertmark T, Nolte H, Theofel I, Eren-Ghiani Z, Tetzner C, Duchow TB, Rathke C, Krüger M, Renkawitz-Pohl R, (2019) "Stage-specific testes proteomics of Drosophila melanogaster identifies essential proteins for male fertility." <i>Eur J Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30679029 30679029]; doi: [https://dx.doi.org/10.1016/j.ejcb.2019.01.001 10.1016/j.ejcb.2019.01.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30679029 180]. | ||
- | #McKetney J, Runde RM, Hebert AS, Salamat S, Roy S, Coon JJ, (2019) "Proteomic Atlas of the Human Brain in Alzheimer's Disease." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30735395 30735395]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00004 10.1021/acs.jproteome.9b00004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30735395 12]. | + | #Fornecker LM, Muller L, Bertrand F, Paul N, Pichot A, Herbrecht R, Chenard MP, Mauvieux L, Vallat L, Bahram S, Cianférani S, Carapito R, Carapito C, (2019) "Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma." <i>Sci Rep</i> <b>9</b>(1):895; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30696890 30696890]; doi: [https://dx.doi.org/10.1038/s41598-018-37273-4 10.1038/s41598-018-37273-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30696890 20]. |
+ | #McKetney J, Runde RM, Hebert AS, Salamat S, Roy S, Coon JJ, (2019) "Proteomic Atlas of the Human Brain in Alzheimer's Disease." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30735395 30735395]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00004 10.1021/acs.jproteome.9b00004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30735395 22]. | ||
+ | #Furuyama K, Chera S, van Gurp L, Oropeza D, Ghila L, Damond N, Vethe H, Paulo JA, Joosten AM, Berney T, Bosco D, Dorrell C, Grompe M, Ræder H, Roep BO, Thorel F, Herrera PL, (2019) "Diabetes relief in mice by glucose-sensing insulin-secreting human α-cells." <i>Nature</i> <b>567</b>(7746):43–48; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30760930 30760930]; doi: [https://dx.doi.org/10.1038/s41586-019-0942-8 10.1038/s41586-019-0942-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30760930 1]. | ||
+ | #Mohanty V, Subbannayya Y, Najar MA, Pinto SM, Kasaragod S, Karuppiah H, Sreeramulu B, Singh KK, Dalal S, Manikkoth S, Arunachalam C, Prasad TSK, Murthy KR, (2019) "Proteomics and Visual Health Research: Proteome of the Human Sclera Using High-Resolution Mass Spectrometry." <i>OMICS</i> <b>23</b>(2):98–110; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30767726 30767726]; doi: [https://dx.doi.org/10.1089/omi.2018.0185 10.1089/omi.2018.0185]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30767726 2]. | ||
+ | #Patil S, Subbannayya T, Mohan SV, Babu N, Advani J, Sathe G, Rajagopalan P, Patel K, Bhandi S, Solanki H, Sidransky D, Gowda H, Chatterjee A, Ferrari M, (2019) "Proteomic Changes in Oral Keratinocytes Chronically Exposed to Shisha (Water Pipe)." <i>OMICS</i> <b>23</b>(2):86–97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30767727 30767727]; doi: [https://dx.doi.org/10.1089/omi.2018.0173 10.1089/omi.2018.0173]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30767727 18]. | ||
+ | #Eraslan B, Wang D, Gusic M, Prokisch H, Hallström BM, Uhlén M, Asplund A, Pontén F, Wieland T, Hopf T, Hahne H, Kuster B, Gagneur J, (2019) "Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues." <i>Mol Syst Biol</i> <b>15</b>(2):e8513; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30777893 30777893]; doi: [https://dx.doi.org/10.15252/msb.20188513 10.15252/msb.20188513]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30777893 28]. | ||
+ | #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]. | ||
+ | #Angelidis I, Simon LM, Fernandez IE, Strunz M, Mayr CH, Greiffo FR, Tsitsiridis G, Ansari M, Graf E, Strom TM, Nagendran M, Desai T, Eickelberg O, Mann M, Theis FJ, Schiller HB, (2019) "An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics." <i>Nat Commun</i> <b>10</b>(1):963; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30814501 30814501]; doi: [https://dx.doi.org/10.1038/s41467-019-08831-9 10.1038/s41467-019-08831-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30814501 32]. | ||
+ | #Parker BL, Calkin AC, Seldin MM, Keating MF, Tarling EJ, Yang P, Moody SC, Liu Y, Zerenturk EJ, Needham EJ, Miller ML, Clifford BL, Morand P, Watt MJ, Meex RCR, Peng KY, Lee R, Jayawardana K, Pan C, Mellett NA, Weir JM, Lazarus R, Lusis AJ, Meikle PJ, James DE, de Aguiar Vallim TQ, Drew BG, (2019) "An integrative systems genetic analysis of mammalian lipid metabolism." <i>Nature</i> <b>567</b>(7747):187–193; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30814737 30814737]; doi: [https://dx.doi.org/10.1038/s41586-019-0984-y 10.1038/s41586-019-0984-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30814737 78]. | ||
+ | #Jiang Y, Sun A, Zhao Y, Ying W, Sun H, Yang X, Xing B, Sun W, Ren L, Hu B, Li C, Zhang L, Qin G, Zhang M, Chen N, Zhang M, Huang Y, Zhou J, Zhao Y, Liu M, Zhu X, Qiu Y, Sun Y, Huang C, Yan M, Wang M, Liu W, Tian F, Xu H, Zhou J, Wu Z, Shi T, Zhu W, Qin J, Xie L, Fan J, Qian X, He F, Chinese Human Proteome Project (CNHPP) Consortium., (2019) "Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma." <i>Nature</i> <b>567</b>(7747):257–261; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30814741 30814741]; doi: [https://dx.doi.org/10.1038/s41586-019-0987-8 10.1038/s41586-019-0987-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30814741 688]. | ||
+ | #Brummer T, Müller SA, Pan-Montojo F, Yoshida F, Fellgiebel A, Tomita T, Endres K, Lichtenthaler SF, (2019) "NrCAM is a marker for substrate-selective activation of ADAM10 in Alzheimer's disease." <i>EMBO Mol Med</i> <b>11</b>(4):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30833305 30833305]; doi: [https://dx.doi.org/10.15252/emmm.201809695 10.15252/emmm.201809695]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30833305 36]. | ||
+ | #Hansen BK, Gupta R, Baldus L, Lyon D, Narita T, Lammers M, Choudhary C, Weinert BT, (2019) "Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation." <i>Nat Commun</i> <b>10</b>(1):1055; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30837475 30837475]; doi: [https://dx.doi.org/10.1038/s41467-019-09024-0 10.1038/s41467-019-09024-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30837475 123]. | ||
+ | #Marei WFA, Van Raemdonck G, Baggerman G, Bols PEJ, Leroy JLMR, (2019) "Proteomic changes in oocytes after in vitro maturation in lipotoxic conditions are different from those in cumulus cells." <i>Sci Rep</i> <b>9</b>(1):3673; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30842615 30842615]; doi: [https://dx.doi.org/10.1038/s41598-019-40122-7 10.1038/s41598-019-40122-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30842615 2]. | ||
+ | #Lin YH, Eguez RV, Torralba MG, Singh H, Golusinski P, Golusinski W, Masternak M, Nelson KE, Freire M, Yu Y, (2019) "Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30848925 30848925]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00037 10.1021/acs.jproteome.9b00037]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30848925 51]. | ||
+ | #Herbst FA, Gonçalves SCL, Behr T, McIlroy SJ, Nielsen PH, (2019) "Proteogenomic Refinement of the Neomegalonema perideroedes<sup>T</sup> Genome Annotation." <i>Proteomics</i> <b></b>:e1800330; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30865376 30865376]; doi: [https://dx.doi.org/10.1002/pmic.201800330 10.1002/pmic.201800330]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30865376 9]. | ||
+ | #Gallud A, Klöditz K, Ytterberg J, Östberg N, Katayama S, Skoog T, Gogvadze V, Chen YZ, Xue D, Moya S, Ruiz J, Astruc D, Zubarev R, Kere J, Fadeel B, (2019) "Cationic gold nanoparticles elicit mitochondrial dysfunction: a multi-omics study." <i>Sci Rep</i> <b>9</b>(1):4366; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30867451 30867451]; doi: [https://dx.doi.org/10.1038/s41598-019-40579-6 10.1038/s41598-019-40579-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30867451 45]. | ||
+ | #Obradović MMS, Hamelin B, Manevski N, Couto JP, Sethi A, Coissieux MM, Münst S, Okamoto R, Kohler H, Schmidt A, Bentires-Alj M, (2019) "Glucocorticoids promote breast cancer metastasis." <i>Nature</i> <b>567</b>(7749):540–544; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30867597 30867597]; doi: [https://dx.doi.org/10.1038/s41586-019-1019-4 10.1038/s41586-019-1019-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30867597 23]. | ||
+ | #Berg P, McConnell EW, Hicks LM, Popescu SC, Popescu GV, (2019) "Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics." <i>BMC Bioinformatics</i> <b>20</b>(Suppl 2):102; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30871482 30871482]; doi: [https://dx.doi.org/10.1186/s12859-019-2619-6 10.1186/s12859-019-2619-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30871482 1]. | ||
+ | #Vandervore LV, Schot R, Kasteleijn E, Oegema R, Stouffs K, Gheldof A, Grochowska MM, van der Sterre MLT, van Unen LMA, Wilke M, Elfferich P, van der Spek PJ, Heijsman D, Grandone A, Demmers JAA, Dekkers DHW, Slotman JA, Kremers GJ, Schaaf GJ, Masius RG, van Essen AJ, Rump P, van Haeringen A, Peeters E, Altunoglu U, Kalayci T, Poot RA, Dobyns WB, Bahi-Buisson N, Verheijen FW, Jansen AC, Mancini GMS, (2019) "Heterogeneous clinical phenotypes and cerebral malformations reflected by rotatin cellular dynamics." <i>Brain</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30879067 30879067]; doi: [https://dx.doi.org/10.1093/brain/awz045 10.1093/brain/awz045]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30879067 14]. | ||
+ | #Sacco F, Seelig A, Humphrey SJ, Krahmer N, Volta F, Reggio A, Marchetti P, Gerdes J, Mann M, (2019) "Phosphoproteomics Reveals the GSK3-PDX1 Axis as a Key Pathogenic Signaling Node in Diabetic Islets." <i>Cell Metab</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30879985 30879985]; doi: [https://dx.doi.org/10.1016/j.cmet.2019.02.012 10.1016/j.cmet.2019.02.012]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30879985 24]. | ||
+ | #Sinha A, Huang V, Livingstone J, Wang J, Fox NS, Kurganovs N, Ignatchenko V, Fritsch K, Donmez N, Heisler LE, Shiah YJ, Yao CQ, Alfaro JA, Volik S, Lapuk A, Fraser M, Kron K, Murison A, Lupien M, Sahinalp C, Collins CC, Tetu B, Masoomian M, Berman DM, van der Kwast T, Bristow RG, Kislinger T, Boutros PC, (2019) "The Proteogenomic Landscape of Curable Prostate Cancer." <i>Cancer Cell</i> <b>35</b>(3):414–427.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30889379 30889379]; doi: [https://dx.doi.org/10.1016/j.ccell.2019.02.005 10.1016/j.ccell.2019.02.005]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30889379 108]. | ||
+ | #Xu B, Zheng C, Chen X, Zhang Z, Liu J, Spencer P, Yang X, (2019) "Dysregulation of Myosin Complex and Striated Muscle Contraction Pathway in the Brain of ALS-SOD1 mouse model." <i>ACS Chem Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30889949 30889949]; doi: [https://dx.doi.org/10.1021/acschemneuro.8b00704 10.1021/acschemneuro.8b00704]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30889949 1]. | ||
+ | #Borgermann N, Ackermann L, Schwertman P, Hendriks IA, Thijssen K, Liu JC, Lans H, Nielsen ML, Mailand N, (2019) "SUMOylation promotes protective responses to DNA-protein crosslinks." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30914427 30914427]; doi: [https://dx.doi.org/10.15252/embj.2019101496 10.15252/embj.2019101496]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30914427 52]. | ||
+ | #Betancourt LH, Pawłowski K, Eriksson J, Szasz AM, Mitra S, Pla I, Welinder C, Ekedahl H, Broberg P, Appelqvist R, Yakovleva M, Sugihara Y, Miharada K, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Wieslander E, Horvatovich P, Malm J, Jönsson G, Marko-Varga G, (2019) "Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data." <i>Sci Rep</i> <b>9</b>(1):5154; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30914758 30914758]; doi: [https://dx.doi.org/10.1038/s41598-019-41625-z 10.1038/s41598-019-41625-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30914758 111]. | ||
+ | #Sinclair LV, Howden AJ, Brenes A, Spinelli L, Hukelmann JL, Macintyre AN, Liu X, Thomson S, Taylor PM, Rathmell JC, Locasale JW, Lamond AI, Cantrell DA, (2019) "Antigen receptor control of methionine metabolism in T cells." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30916644 30916644]; doi: [https://dx.doi.org/10.7554/eLife.44210 10.7554/eLife.44210]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30916644 7]. | ||
+ | #Chachami G, Stankovic-Valentin N, Karagiota A, Basagianni A, Plessmann U, Urlaub H, Melchior F, Simos G, (2019) "Hypoxia-induced changes in SUMO conjugation affect transcriptional regulation under low oxygen." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30926672 30926672]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001401 10.1074/mcp.RA119.001401]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30926672 69]. | ||
+ | #Musiani D, Bok J, Massignani E, Wu L, Tabaglio T, Ippolito MR, Cuomo A, Ozbek U, Zorgati H, Ghoshdastider U, Robinson RC, Guccione E, Bonaldi T, (2019) "Proteomics profiling of arginine methylation defines PRMT5 substrate specificity." <i>Sci Signal</i> <b>12</b>(575):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30940768 30940768]; doi: [https://dx.doi.org/10.1126/scisignal.aat8388 10.1126/scisignal.aat8388]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30940768 76]. | ||
+ | #Yang M, Vesterlund M, Siavelis I, Moura-Castro LH, Castor A, Fioretos T, Jafari R, Lilljebjörn H, Odom DT, Olsson L, Ravi N, Woodward EL, Harewood L, Lehtiö J, Paulsson K, (2019) "Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia." <i>Nat Commun</i> <b>10</b>(1):1519; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30944321 30944321]; doi: [https://dx.doi.org/10.1038/s41467-019-09469-3 10.1038/s41467-019-09469-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30944321 3]. | ||
+ | #Johansson HJ, Socciarelli F, Vacanti NM, Haugen MH, Zhu Y, Siavelis I, Fernandez-Woodbridge A, Aure MR, Sennblad B, Vesterlund M, Branca RM, Orre LM, Huss M, Fredlund E, Beraki E, Garred Ø, Boekel J, Sauer T, Zhao W, Nord S, Höglander EK, Jans DC, Brismar H, Haukaas TH, Bathen TF, Schlichting E, Naume B, Consortia Oslo Breast Cancer Research Consortium (OSBREAC)., Luders T, Borgen E, Kristensen VN, Russnes HG, Lingjærde OC, Mills GB, Sahlberg KK, Børresen-Dale AL, Lehtiö J, (2019) "Breast cancer quantitative proteome and proteogenomic landscape." <i>Nat Commun</i> <b>10</b>(1):1600; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30962452 30962452]; doi: [https://dx.doi.org/10.1038/s41467-019-09018-y 10.1038/s41467-019-09018-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30962452 12]. | ||
+ | #Erhart F, Weiss T, Klingenbrunner S, Fischhuber K, Reitermaier R, Halfmann A, Blauensteiner B, Lötsch D, Spiegl-Kreinecker S, Berger W, Sialana FJ, Lubec G, Felzmann T, Dohnal A, Visus C, (2019) "Spheroid glioblastoma culture conditions as antigen source for dendritic cell-based immunotherapy: spheroid proteins are survival-relevant targets but can impair immunogenic interferon γ production." <i>Cytotherapy</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30975602 30975602]; doi: [https://dx.doi.org/10.1016/j.jcyt.2019.03.002 10.1016/j.jcyt.2019.03.002]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30975602 8]. | ||
+ | #Na CH, Sharma N, Madugundu AK, Chen R, Atalar Aksit M, Rosson GD, Cutting GR, Pandey A, (2019) "Integrated transcriptomic and proteomic analysis of human eccrine sweat glands identifies missing and novel proteins." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30979791 30979791]; doi: [https://dx.doi.org/10.1074/mcp.RA118.001101 10.1074/mcp.RA118.001101]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30979791 3]. | ||
+ | #Guergues J, Zhang P, Liu B, Stevens SM Jr, (2019) "Improved Methodology for Sensitive and Rapid Quantitative Proteomic Analysis of Adult-Derived Mouse Microglia: Application to a Novel In Vitro Mouse Microglial Cell Model." <i>Proteomics</i> <b></b>:e1800469; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30980500 30980500]; doi: [https://dx.doi.org/10.1002/pmic.201800469 10.1002/pmic.201800469]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30980500 6]. | ||
+ | #Zhou B, Yan Y, Wang Y, You S, Freeman MR, Yang W, (2019) "Quantitative proteomic analysis of prostate tissue specimens identifies deregulated protein complexes in primary prostate cancer." <i>Clin Proteomics</i> <b>16</b>:15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31011308 31011308]; doi: [https://dx.doi.org/10.1186/s12014-019-9236-2 10.1186/s12014-019-9236-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31011308 1]. |
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 May 5, 2019.