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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 10, 2020. |
#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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#Walton A, Stes E, Cybulski N, Van Bel M, Iñigo S, Durand AN, Timmerman E, Heyman J, Pauwels L, De Veylder L, Goossens A, De Smet I, Coppens F, Goormachtig S, Gevaert K, (2016) "It's Time for Some "Site"-Seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis thaliana." <i>Plant Cell</i> <b>28</b>(1):6–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26744219 26744219]; doi: [https://dx.doi.org/10.1105/tpc.15.00878 10.1105/tpc.15.00878]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26744219 110]. | #Walton A, Stes E, Cybulski N, Van Bel M, Iñigo S, Durand AN, Timmerman E, Heyman J, Pauwels L, De Veylder L, Goossens A, De Smet I, Coppens F, Goormachtig S, Gevaert K, (2016) "It's Time for Some "Site"-Seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis thaliana." <i>Plant Cell</i> <b>28</b>(1):6–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26744219 26744219]; doi: [https://dx.doi.org/10.1105/tpc.15.00878 10.1105/tpc.15.00878]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26744219 110]. | ||
#Wandinger SK, Lahortiga I, Jacobs K, Klammer M, Jordan N, Elschenbroich S, Parade M, Jacoby E, Linders JT, Brehmer D, Cools J, Daub H, (2016) "Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling." <i>PLoS One</i> <b>11</b>(1):e0146100; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26745281 26745281]; doi: [https://dx.doi.org/10.1371/journal.pone.0146100 10.1371/journal.pone.0146100]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26745281 72]. | #Wandinger SK, Lahortiga I, Jacobs K, Klammer M, Jordan N, Elschenbroich S, Parade M, Jacoby E, Linders JT, Brehmer D, Cools J, Daub H, (2016) "Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling." <i>PLoS One</i> <b>11</b>(1):e0146100; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26745281 26745281]; doi: [https://dx.doi.org/10.1371/journal.pone.0146100 10.1371/journal.pone.0146100]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26745281 72]. | ||
+ | #Finne K, Marti HP, Leh S, Skogstrand T, Vethe H, Tenstad O, Berven FS, Scherer A, Vikse BE, (2016) "Proteomic Analysis of Minimally Damaged Renal Tubular Tissue from Two-Kidney-One-Clip Hypertensive Rats Demonstrates Extensive Changes Compared to Tissue from Controls." <i>Nephron</i> <b>132</b>(1):70–80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26745798 26745798]; doi: [https://dx.doi.org/10.1159/000442825 10.1159/000442825]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26745798 10]. | ||
#Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Martinez Arias A, Lilley KS, (2016) "A draft map of the mouse pluripotent stem cell spatial proteome." <i>Nat Commun</i> <b>7</b>:8992; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26754106 26754106]; doi: [https://dx.doi.org/10.1038/ncomms9992 10.1038/ncomms9992]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26754106 2]. | #Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Martinez Arias A, Lilley KS, (2016) "A draft map of the mouse pluripotent stem cell spatial proteome." <i>Nat Commun</i> <b>7</b>:8992; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26754106 26754106]; doi: [https://dx.doi.org/10.1038/ncomms9992 10.1038/ncomms9992]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26754106 2]. | ||
#Jin J, Tian R, Pasculescu A, Dai AY, Williton K, Taylor L, Savitski MM, Bantscheff M, Woodgett JR, Pawson T, Colwill K, (2016) "Mutational Analysis of Glycogen Synthase Kinase 3β Protein Kinase Together with Kinome-Wide Binding and Stability Studies Suggests Context-Dependent Recognition of Kinases by the Chaperone Heat Shock Protein 90." <i>Mol Cell Biol</i> <b>36</b>(6):1007–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26755559 26755559]; doi: [https://dx.doi.org/10.1128/MCB.01045-15 10.1128/MCB.01045-15]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26755559 17]. | #Jin J, Tian R, Pasculescu A, Dai AY, Williton K, Taylor L, Savitski MM, Bantscheff M, Woodgett JR, Pawson T, Colwill K, (2016) "Mutational Analysis of Glycogen Synthase Kinase 3β Protein Kinase Together with Kinome-Wide Binding and Stability Studies Suggests Context-Dependent Recognition of Kinases by the Chaperone Heat Shock Protein 90." <i>Mol Cell Biol</i> <b>36</b>(6):1007–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26755559 26755559]; doi: [https://dx.doi.org/10.1128/MCB.01045-15 10.1128/MCB.01045-15]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26755559 17]. | ||
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#Chymkowitch P, Nguéa P A, Aanes H, Robertson J, Klungland A, Enserink JM, (2017) "TORC1-dependent sumoylation of Rpc82 promotes RNA polymerase III assembly and activity." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(5):1039–1044; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096404 28096404]; doi: [https://dx.doi.org/10.1073/pnas.1615093114 10.1073/pnas.1615093114]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28096404 21]. | #Chymkowitch P, Nguéa P A, Aanes H, Robertson J, Klungland A, Enserink JM, (2017) "TORC1-dependent sumoylation of Rpc82 promotes RNA polymerase III assembly and activity." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(5):1039–1044; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096404 28096404]; doi: [https://dx.doi.org/10.1073/pnas.1615093114 10.1073/pnas.1615093114]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28096404 21]. | ||
#Reckel S, Hamelin R, Georgeon S, Armand F, Jolliet Q, Chiappe D, Moniatte M, Hantschel O, (2017) "Differential signaling networks of Bcr-Abl p210 and p190 kinases in leukemia cells defined by functional proteomics." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28111465 28111465]; doi: [https://dx.doi.org/10.1038/leu.2017.36 10.1038/leu.2017.36]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28111465 10]. | #Reckel S, Hamelin R, Georgeon S, Armand F, Jolliet Q, Chiappe D, Moniatte M, Hantschel O, (2017) "Differential signaling networks of Bcr-Abl p210 and p190 kinases in leukemia cells defined by functional proteomics." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28111465 28111465]; doi: [https://dx.doi.org/10.1038/leu.2017.36 10.1038/leu.2017.36]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28111465 10]. | ||
+ | #Tsiatsiani L, Giansanti P, Scheltema RA, van den Toorn H, Overall CM, Altelaar AF, Heck AJ, (2017) "Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)<sub>n</sub> and (X)<sub>n</sub>K/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics." <i>J Proteome Res</i> <b>16</b>(2):852–861; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28111955 28111955]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00825 10.1021/acs.jproteome.6b00825]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28111955 28]. | ||
#Hendriks IA, Lyon D, Young C, Jensen LJ, Vertegaal AC, Nielsen ML, (2017) "Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation." <i>Nat Struct Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28112733 28112733]; doi: [https://dx.doi.org/10.1038/nsmb.3366 10.1038/nsmb.3366]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28112733 311]. | #Hendriks IA, Lyon D, Young C, Jensen LJ, Vertegaal AC, Nielsen ML, (2017) "Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation." <i>Nat Struct Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28112733 28112733]; doi: [https://dx.doi.org/10.1038/nsmb.3366 10.1038/nsmb.3366]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28112733 311]. | ||
#Badalato N, Guillot A, Sabarly V, Dubois M, Pourette N, Pontoire B, Robert P, Bridier A, Monnet V, Sousa DZ, Durand S, Mazéas L, Buléon A, Bouchez T, Mortha G, Bize A, (2017) "Whole Proteome Analyses on Ruminiclostridium cellulolyticum Show a Modulation of the Cellulolysis Machinery in Response to Cellulosic Materials with Subtle Differences in Chemical and Structural Properties." <i>PLoS One</i> <b>12</b>(1):e0170524; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28114419 28114419]; doi: [https://dx.doi.org/10.1371/journal.pone.0170524 10.1371/journal.pone.0170524]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28114419 24]. | #Badalato N, Guillot A, Sabarly V, Dubois M, Pourette N, Pontoire B, Robert P, Bridier A, Monnet V, Sousa DZ, Durand S, Mazéas L, Buléon A, Bouchez T, Mortha G, Bize A, (2017) "Whole Proteome Analyses on Ruminiclostridium cellulolyticum Show a Modulation of the Cellulolysis Machinery in Response to Cellulosic Materials with Subtle Differences in Chemical and Structural Properties." <i>PLoS One</i> <b>12</b>(1):e0170524; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28114419 28114419]; doi: [https://dx.doi.org/10.1371/journal.pone.0170524 10.1371/journal.pone.0170524]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28114419 24]. | ||
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#Drabikowski K, Ferralli J, Kistowski M, Oledzki J, Dadlez M, Chiquet-Ehrismann R, (2018) "Comprehensive list of SUMO targets in Caenorhabditis elegans and its implication for evolutionary conservation of SUMO signaling." <i>Sci Rep</i> <b>8</b>(1):1139; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29348603 29348603]; doi: [https://dx.doi.org/10.1038/s41598-018-19424-9 10.1038/s41598-018-19424-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29348603 37]. | #Drabikowski K, Ferralli J, Kistowski M, Oledzki J, Dadlez M, Chiquet-Ehrismann R, (2018) "Comprehensive list of SUMO targets in Caenorhabditis elegans and its implication for evolutionary conservation of SUMO signaling." <i>Sci Rep</i> <b>8</b>(1):1139; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29348603 29348603]; doi: [https://dx.doi.org/10.1038/s41598-018-19424-9 10.1038/s41598-018-19424-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29348603 37]. | ||
#Gao Y, Ge W, (2018) "The histone methyltransferase DOT1L inhibits osteoclastogenesis and protects against osteoporosis." <i>Cell Death Dis</i> <b>9</b>(2):33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29348610 29348610]; doi: [https://dx.doi.org/10.1038/s41419-017-0040-5 10.1038/s41419-017-0040-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29348610 2]. | #Gao Y, Ge W, (2018) "The histone methyltransferase DOT1L inhibits osteoclastogenesis and protects against osteoporosis." <i>Cell Death Dis</i> <b>9</b>(2):33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29348610 29348610]; doi: [https://dx.doi.org/10.1038/s41419-017-0040-5 10.1038/s41419-017-0040-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29348610 2]. | ||
+ | #Phuyal S, Kasem M, Knittelfelder O, Sharma A, Fonseca DM, Vebraite V, Shaposhnikov S, Slupphaug G, Skaug V, Zienolddiny S, (2018) "Characterization of the proteome and lipidome profiles of human lung cells after low dose and chronic exposure to multiwalled carbon nanotubes." <i>Nanotoxicology</i> <b>12</b>(2):138–152; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350075 29350075]; doi: [https://dx.doi.org/10.1080/17435390.2018.1425500 10.1080/17435390.2018.1425500]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29350075 24]. | ||
#Mustafa DAM, Pedrosa RMSM, Smid M, van der Weiden M, de Weerd V, Nigg AL, Berrevoets C, Zeneyedpour L, Priego N, Valiente M, Luider TM, Debets R, Martens JWM, Foekens JA, Sieuwerts AM, Kros JM, (2018) "T lymphocytes facilitate brain metastasis of breast cancer by inducing Guanylate-Binding Protein 1 expression." <i>Acta Neuropathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350274 29350274]; doi: [https://dx.doi.org/10.1007/s00401-018-1806-2 10.1007/s00401-018-1806-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29350274 6]. | #Mustafa DAM, Pedrosa RMSM, Smid M, van der Weiden M, de Weerd V, Nigg AL, Berrevoets C, Zeneyedpour L, Priego N, Valiente M, Luider TM, Debets R, Martens JWM, Foekens JA, Sieuwerts AM, Kros JM, (2018) "T lymphocytes facilitate brain metastasis of breast cancer by inducing Guanylate-Binding Protein 1 expression." <i>Acta Neuropathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350274 29350274]; doi: [https://dx.doi.org/10.1007/s00401-018-1806-2 10.1007/s00401-018-1806-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29350274 6]. | ||
#Schönke M, Björnholm M, Chibalin AV, Zierath JR, Deshmukh AS, (2018) "Proteomics Analysis of Skeletal Muscle from Leptin-Deficient Ob/Ob Mice Reveals Adaptive Remodeling of Metabolic Characteristics and Fiber Type Composition." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350465 29350465]; doi: [https://dx.doi.org/10.1002/pmic.201700375 10.1002/pmic.201700375]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29350465 22]. | #Schönke M, Björnholm M, Chibalin AV, Zierath JR, Deshmukh AS, (2018) "Proteomics Analysis of Skeletal Muscle from Leptin-Deficient Ob/Ob Mice Reveals Adaptive Remodeling of Metabolic Characteristics and Fiber Type Composition." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350465 29350465]; doi: [https://dx.doi.org/10.1002/pmic.201700375 10.1002/pmic.201700375]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29350465 22]. | ||
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#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]. | #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]. | ||
#Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | #Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | ||
+ | #Guneykaya D, Ivanov A, Hernandez DP, Haage V, Wojtas B, Meyer N, Maricos M, Jordan P, Buonfiglioli A, Gielniewski B, Ochocka N, Cömert C, Friedrich C, Artiles LS, Kaminska B, Mertins P, Beule D, Kettenmann H, Wolf SA, (2018) "Transcriptional and Translational Differences of Microglia from Male and Female Brains." <i>Cell Rep</i> <b>24</b>(10):2773–2783.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30184509 30184509]; doi: [https://dx.doi.org/10.1016/j.celrep.2018.08.001 10.1016/j.celrep.2018.08.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30184509 8]. | ||
#Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | #Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | ||
#Abreha MH, Dammer EB, Ping L, Zhang T, Duong DM, Gearing M, Lah JJ, Levey AI, Seyfried NT, (2018) "Quantitative Analysis of the Brain Ubiquitylome in Alzheimer's Disease." <i>Proteomics</i> <b>18</b>(20):e1800108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30230243 30230243]; doi: [https://dx.doi.org/10.1002/pmic.201800108 10.1002/pmic.201800108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30230243 29]. | #Abreha MH, Dammer EB, Ping L, Zhang T, Duong DM, Gearing M, Lah JJ, Levey AI, Seyfried NT, (2018) "Quantitative Analysis of the Brain Ubiquitylome in Alzheimer's Disease." <i>Proteomics</i> <b>18</b>(20):e1800108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30230243 30230243]; doi: [https://dx.doi.org/10.1002/pmic.201800108 10.1002/pmic.201800108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30230243 29]. | ||
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#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]. | #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]. | #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]. | ||
+ | #West KL, Byrum SD, Mackintosh SG, Edmondson RD, Taverna SD, Tackett AJ, (2019) "Proteomic characterization of the arsenic response locus in S. cerevisiae." <i>Epigenetics</i> <b>14</b>(2):130–145; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30739529 30739529]; doi: [https://dx.doi.org/10.1080/15592294.2019.1580110 10.1080/15592294.2019.1580110]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30739529 9]. | ||
#Dikicioglu D, Nightingale DJH, Wood V, Lilley KS, Oliver SG, (2019) "Transcriptional regulation of the genes involved in protein metabolism and processing in Saccharomyces cerevisiae." <i>FEMS Yeast Res</i> <b>19</b>(2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30753445 30753445]; doi: [https://dx.doi.org/10.1093/femsyr/foz014 10.1093/femsyr/foz014]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30753445 48]. | #Dikicioglu D, Nightingale DJH, Wood V, Lilley KS, Oliver SG, (2019) "Transcriptional regulation of the genes involved in protein metabolism and processing in Saccharomyces cerevisiae." <i>FEMS Yeast Res</i> <b>19</b>(2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30753445 30753445]; doi: [https://dx.doi.org/10.1093/femsyr/foz014 10.1093/femsyr/foz014]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30753445 48]. | ||
#Ramello MC, Benzaïd I, Kuenzi BM, Lienlaf-Moreno M, Kandell WM, Santiago DN, Pabón-Saldaña M, Darville L, Fang B, Rix U, Yoder S, Berglund A, Koomen JM, Haura EB, Abate-Daga D, (2019) "An immunoproteomic approach to characterize the CAR interactome and signalosome." <i>Sci Signal</i> <b>12</b>(568):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30755478 30755478]; doi: [https://dx.doi.org/10.1126/scisignal.aap9777 10.1126/scisignal.aap9777]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30755478 54]. | #Ramello MC, Benzaïd I, Kuenzi BM, Lienlaf-Moreno M, Kandell WM, Santiago DN, Pabón-Saldaña M, Darville L, Fang B, Rix U, Yoder S, Berglund A, Koomen JM, Haura EB, Abate-Daga D, (2019) "An immunoproteomic approach to characterize the CAR interactome and signalosome." <i>Sci Signal</i> <b>12</b>(568):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30755478 30755478]; doi: [https://dx.doi.org/10.1126/scisignal.aap9777 10.1126/scisignal.aap9777]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30755478 54]. | ||
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#Fang EF, Hou Y, Lautrup S, Jensen MB, Yang B, SenGupta T, Caponio D, Khezri R, Demarest TG, Aman Y, Figueroa D, Morevati M, Lee HJ, Kato H, Kassahun H, Lee JH, Filippelli D, Okur MN, Mangerich A, Croteau DL, Maezawa Y, Lyssiotis CA, Tao J, Yokote K, Rusten TE, Mattson MP, Jasper H, Nilsen H, Bohr VA, (2019) "NAD<sup>+</sup> augmentation restores mitophagy and limits accelerated aging in Werner syndrome." <i>Nat Commun</i> <b>10</b>(1):5284; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31754102 31754102]; doi: [https://dx.doi.org/10.1038/s41467-019-13172-8 10.1038/s41467-019-13172-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31754102 32]. | #Fang EF, Hou Y, Lautrup S, Jensen MB, Yang B, SenGupta T, Caponio D, Khezri R, Demarest TG, Aman Y, Figueroa D, Morevati M, Lee HJ, Kato H, Kassahun H, Lee JH, Filippelli D, Okur MN, Mangerich A, Croteau DL, Maezawa Y, Lyssiotis CA, Tao J, Yokote K, Rusten TE, Mattson MP, Jasper H, Nilsen H, Bohr VA, (2019) "NAD<sup>+</sup> augmentation restores mitophagy and limits accelerated aging in Werner syndrome." <i>Nat Commun</i> <b>10</b>(1):5284; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31754102 31754102]; doi: [https://dx.doi.org/10.1038/s41467-019-13172-8 10.1038/s41467-019-13172-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31754102 32]. | ||
#Zhang Y, Lin Z, Tan Y, Bu F, Hao P, Zhang K, Yang H, Liu S, Ren Y, (2019) "Exploration of Missing Proteins by a Combination Approach to Enrich the Low-Abundance Hydrophobic Proteins from Four Cancer Cell Lines." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31773964 31773964]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00590 10.1021/acs.jproteome.9b00590]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31773964 16]. | #Zhang Y, Lin Z, Tan Y, Bu F, Hao P, Zhang K, Yang H, Liu S, Ren Y, (2019) "Exploration of Missing Proteins by a Combination Approach to Enrich the Low-Abundance Hydrophobic Proteins from Four Cancer Cell Lines." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31773964 31773964]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00590 10.1021/acs.jproteome.9b00590]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31773964 16]. | ||
+ | #Löffler MW, Nussbaum B, Jäger G, Jurmeister PS, Budczies J, Pereira PL, Clasen S, Kowalewski DJ, Mühlenbruch L, Königsrainer I, Beckert S, Ladurner R, Wagner S, Bullinger F, Gross TH, Schroeder C, Sipos B, Königsrainer A, Stevanović S, Denkert C, Rammensee HG, Gouttefangeas C, Haen SP, (2019) "A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer." <i>Front Immunol</i> <b>10</b>:2526; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31803175 31803175]; doi: [https://dx.doi.org/10.3389/fimmu.2019.02526 10.3389/fimmu.2019.02526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31803175 76]. | ||
#Szibor M, Gainutdinov T, Fernandez-Vizarra E, Dufour E, Gizatullina Z, Debska-Vielhaber G, Heidler J, Wittig I, Viscomi C, Gellerich F, Moore AL, (2020) "Bioenergetic consequences from xenotopic expression of a tunicate AOX in mouse mitochondria: Switch from RET and ROS to FET." <i>Biochim Biophys Acta Bioenerg</i> <b>1861</b>(2):148137; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31825809 31825809]; doi: [https://dx.doi.org/10.1016/j.bbabio.2019.148137 10.1016/j.bbabio.2019.148137]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31825809 96]. | #Szibor M, Gainutdinov T, Fernandez-Vizarra E, Dufour E, Gizatullina Z, Debska-Vielhaber G, Heidler J, Wittig I, Viscomi C, Gellerich F, Moore AL, (2020) "Bioenergetic consequences from xenotopic expression of a tunicate AOX in mouse mitochondria: Switch from RET and ROS to FET." <i>Biochim Biophys Acta Bioenerg</i> <b>1861</b>(2):148137; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31825809 31825809]; doi: [https://dx.doi.org/10.1016/j.bbabio.2019.148137 10.1016/j.bbabio.2019.148137]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31825809 96]. | ||
#Solleder M, Guillaume P, Racle J, Michaux J, Pak HS, Müller M, Coukos G, Bassani-Sternberg M, Gfeller D, (2019) "Mass spectrometry based immunopeptidomics leads to robust predictions of phosphorylated HLA class I ligands." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31848261 31848261]; doi: [https://dx.doi.org/10.1074/mcp.TIR119.001641 10.1074/mcp.TIR119.001641]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31848261 208]. | #Solleder M, Guillaume P, Racle J, Michaux J, Pak HS, Müller M, Coukos G, Bassani-Sternberg M, Gfeller D, (2019) "Mass spectrometry based immunopeptidomics leads to robust predictions of phosphorylated HLA class I ligands." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31848261 31848261]; doi: [https://dx.doi.org/10.1074/mcp.TIR119.001641 10.1074/mcp.TIR119.001641]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31848261 208]. | ||
#Nobre LV, Nightingale K, Ravenhill BJ, Antrobus R, Soday L, Nichols J, Davies JA, Seirafian S, Wang EC, Davison AJ, Wilkinson GW, Stanton RJ, Huttlin EL, Weekes MP, (2019) "Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31873071 31873071]; doi: [https://dx.doi.org/10.7554/eLife.49894 10.7554/eLife.49894]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31873071 354]. | #Nobre LV, Nightingale K, Ravenhill BJ, Antrobus R, Soday L, Nichols J, Davies JA, Seirafian S, Wang EC, Davison AJ, Wilkinson GW, Stanton RJ, Huttlin EL, Weekes MP, (2019) "Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31873071 31873071]; doi: [https://dx.doi.org/10.7554/eLife.49894 10.7554/eLife.49894]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31873071 354]. | ||
#Mühlhofer M, Berchtold E, Stratil CG, Csaba G, Kunold E, Bach NC, Sieber SA, Haslbeck M, Zimmer R, Buchner J, (2019) "The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins." <i>Cell Rep</i> <b>29</b>(13):4593–4607.e8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31875563 31875563]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.11.109 10.1016/j.celrep.2019.11.109]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31875563 15]. | #Mühlhofer M, Berchtold E, Stratil CG, Csaba G, Kunold E, Bach NC, Sieber SA, Haslbeck M, Zimmer R, Buchner J, (2019) "The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins." <i>Cell Rep</i> <b>29</b>(13):4593–4607.e8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31875563 31875563]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.11.109 10.1016/j.celrep.2019.11.109]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31875563 15]. | ||
+ | #Matas-Nadal C, Bech-Serra JJ, Guasch-Vallés M, Fernández-Armenteros JM, Barceló C, Casanova JM, de la Torre Gómez C, Aguayo Ortiz R, Garí E, (2020) "Evaluation of Tumor Interstitial Fluid-Extraction Methods for Proteome Analysis: Comparison of Biopsy Elution versus Centrifugation." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31877049 31877049]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00770 10.1021/acs.jproteome.9b00770]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31877049 10]. | ||
#Van JAD, Clotet-Freixas S, Zhou J, Batruch I, Sun C, Glogauer M, Rampoldi L, Elia Y, Mahmud F, Sochett E, Diamandis EP, Scholey J, Konvalinka A, (2019) "Peptidomic analysis of urine from youths with early type 1 diabetes reveals novel bioactivity of uromodulin peptides <i>in vitro</i>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879271 31879271]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001858 10.1074/mcp.RA119.001858]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879271 90]. | #Van JAD, Clotet-Freixas S, Zhou J, Batruch I, Sun C, Glogauer M, Rampoldi L, Elia Y, Mahmud F, Sochett E, Diamandis EP, Scholey J, Konvalinka A, (2019) "Peptidomic analysis of urine from youths with early type 1 diabetes reveals novel bioactivity of uromodulin peptides <i>in vitro</i>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879271 31879271]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001858 10.1074/mcp.RA119.001858]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879271 90]. | ||
#Nguyen AM, Zhou J, Sicairos B, Sonney S, Du Y, (2019) "Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-Selected Pancreatic Cancer Cells in a Mesenchymal State." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879272 31879272]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001779 10.1074/mcp.RA119.001779]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879272 20]. | #Nguyen AM, Zhou J, Sicairos B, Sonney S, Du Y, (2019) "Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-Selected Pancreatic Cancer Cells in a Mesenchymal State." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879272 31879272]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001779 10.1074/mcp.RA119.001779]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879272 20]. | ||
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#Hose J, Escalante LE, Clowers KJ, Dutcher HA, Robinson D, Bouriakov V, Coon JJ, Shishkova E, Gasch AP, (2020) "The genetic basis of aneuploidy tolerance in wild yeast." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31909711 31909711]; doi: [https://dx.doi.org/10.7554/eLife.52063 10.7554/eLife.52063]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31909711 24]. | #Hose J, Escalante LE, Clowers KJ, Dutcher HA, Robinson D, Bouriakov V, Coon JJ, Shishkova E, Gasch AP, (2020) "The genetic basis of aneuploidy tolerance in wild yeast." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31909711 31909711]; doi: [https://dx.doi.org/10.7554/eLife.52063 10.7554/eLife.52063]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31909711 24]. | ||
#Bian Y, Zheng R, Bayer FP, Wong C, Chang YC, Meng C, Zolg DP, Reinecke M, Zecha J, Wiechmann S, Heinzlmeir S, Scherr J, Hemmer B, Baynham M, Gingras AC, Boychenko O, Kuster B, (2020) "Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS." <i>Nat Commun</i> <b>11</b>(1):157; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31919466 31919466]; doi: [https://dx.doi.org/10.1038/s41467-019-13973-x 10.1038/s41467-019-13973-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31919466 2175]. | #Bian Y, Zheng R, Bayer FP, Wong C, Chang YC, Meng C, Zolg DP, Reinecke M, Zecha J, Wiechmann S, Heinzlmeir S, Scherr J, Hemmer B, Baynham M, Gingras AC, Boychenko O, Kuster B, (2020) "Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS." <i>Nat Commun</i> <b>11</b>(1):157; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31919466 31919466]; doi: [https://dx.doi.org/10.1038/s41467-019-13973-x 10.1038/s41467-019-13973-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31919466 2175]. | ||
- | #Bai B, Wang X, Li Y, Chen PC, Yu K, Dey KK, Yarbro JM, Han X, Lutz BM, Rao S, Jiao Y, Sifford JM, Han J, Wang M, Tan H, Shaw TI, Cho JH, Zhou S, Wang H, Niu M, Mancieri A, Messler KA, Sun X, Wu Z, Pagala V, High AA, Bi W, Zhang H, Chi H, Haroutunian V, Zhang B, Beach TG, Yu G, Peng J, (2020) "Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression." <i>Neuron</i> <b>105</b>(6):975–991.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31926610 31926610]; doi: [https://dx.doi.org/10.1016/j.neuron.2019.12.015 10.1016/j.neuron.2019.12.015]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31926610 | + | #Bai B, Wang X, Li Y, Chen PC, Yu K, Dey KK, Yarbro JM, Han X, Lutz BM, Rao S, Jiao Y, Sifford JM, Han J, Wang M, Tan H, Shaw TI, Cho JH, Zhou S, Wang H, Niu M, Mancieri A, Messler KA, Sun X, Wu Z, Pagala V, High AA, Bi W, Zhang H, Chi H, Haroutunian V, Zhang B, Beach TG, Yu G, Peng J, (2020) "Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression." <i>Neuron</i> <b>105</b>(6):975–991.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31926610 31926610]; doi: [https://dx.doi.org/10.1016/j.neuron.2019.12.015 10.1016/j.neuron.2019.12.015]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31926610 158]. |
#Hijazi M, Smith R, Rajeeve V, Bessant C, Cutillas PR, (2020) "Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31959955 31959955]; doi: [https://dx.doi.org/10.1038/s41587-019-0391-9 10.1038/s41587-019-0391-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31959955 874]. | #Hijazi M, Smith R, Rajeeve V, Bessant C, Cutillas PR, (2020) "Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31959955 31959955]; doi: [https://dx.doi.org/10.1038/s41587-019-0391-9 10.1038/s41587-019-0391-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31959955 874]. | ||
#Xu K, Yang L, Zhang L, Qi H, (2020) "Lack of AKAP3 disrupts integrity of the subcellular structure and proteome of mouse sperm and causes male sterility." <i>Development</i> <b>147</b>(2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31969357 31969357]; doi: [https://dx.doi.org/10.1242/dev.181057 10.1242/dev.181057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31969357 3]. | #Xu K, Yang L, Zhang L, Qi H, (2020) "Lack of AKAP3 disrupts integrity of the subcellular structure and proteome of mouse sperm and causes male sterility." <i>Development</i> <b>147</b>(2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31969357 31969357]; doi: [https://dx.doi.org/10.1242/dev.181057 10.1242/dev.181057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31969357 3]. | ||
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#Zhang J, Tang N, Zhao Y, Zhao R, Fu X, Zhao D, Zhao Y, Huang L, Li C, Qiu Y, Xue B, Fang L, (2020) "Global Phosphoproteomic Analysis Reveals Significant Metabolic Reprogramming in the Termination of Liver Regeneration in Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32105074 32105074]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00028 10.1021/acs.jproteome.0c00028]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32105074 24]. | #Zhang J, Tang N, Zhao Y, Zhao R, Fu X, Zhao D, Zhao Y, Huang L, Li C, Qiu Y, Xue B, Fang L, (2020) "Global Phosphoproteomic Analysis Reveals Significant Metabolic Reprogramming in the Termination of Liver Regeneration in Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32105074 32105074]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00028 10.1021/acs.jproteome.0c00028]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32105074 24]. | ||
#Kwon OK, Ha YS, Na AY, Chun SY, Kwon TG, Lee JN, Lee S, (2020) "Identification of Novel Prognosis and Prediction Markers in Advanced Prostate Cancer Tissues Based on Quantitative Proteomics." <i>Cancer Genomics Proteomics</i> <b>17</b>(2):195–208; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32108042 32108042]; doi: [https://dx.doi.org/10.21873/cgp.20180 10.21873/cgp.20180]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32108042 5]. | #Kwon OK, Ha YS, Na AY, Chun SY, Kwon TG, Lee JN, Lee S, (2020) "Identification of Novel Prognosis and Prediction Markers in Advanced Prostate Cancer Tissues Based on Quantitative Proteomics." <i>Cancer Genomics Proteomics</i> <b>17</b>(2):195–208; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32108042 32108042]; doi: [https://dx.doi.org/10.21873/cgp.20180 10.21873/cgp.20180]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32108042 5]. | ||
+ | #Villaseñor R, Pfaendler R, Ambrosi C, Butz S, Giuliani S, Bryan E, Sheahan TW, Gable AL, Schmolka N, Manzo M, Wirz J, Feller C, von Mering C, Aebersold R, Voigt P, Baubec T, (2020) "ChromID identifies the protein interactome at chromatin marks." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32123383 32123383]; doi: [https://dx.doi.org/10.1038/s41587-020-0434-2 10.1038/s41587-020-0434-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32123383 32]. | ||
#Subbannayya Y, Pinto SM, Mohanty V, Dagamajalu S, Prasad TSK, Murthy KR, (2020) "What Makes Cornea Immunologically Unique and Privileged? Mechanistic Clues from a High-Resolution Proteomic Landscape of the Human Cornea." <i>OMICS</i> <b>24</b>(3):129–139; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32125911 32125911]; doi: [https://dx.doi.org/10.1089/omi.2019.0190 10.1089/omi.2019.0190]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32125911 2]. | #Subbannayya Y, Pinto SM, Mohanty V, Dagamajalu S, Prasad TSK, Murthy KR, (2020) "What Makes Cornea Immunologically Unique and Privileged? Mechanistic Clues from a High-Resolution Proteomic Landscape of the Human Cornea." <i>OMICS</i> <b>24</b>(3):129–139; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32125911 32125911]; doi: [https://dx.doi.org/10.1089/omi.2019.0190 10.1089/omi.2019.0190]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32125911 2]. | ||
#Ding H, Fazelinia H, Spruce LA, Weiss DA, Zderic SA, Seeholzer SH, (2020) "Urine proteomics: Evaluation of different sample preparation workflows for quantitative, reproducible and improved depth of analysis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32129078 32129078]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00772 10.1021/acs.jproteome.9b00772]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32129078 16]. | #Ding H, Fazelinia H, Spruce LA, Weiss DA, Zderic SA, Seeholzer SH, (2020) "Urine proteomics: Evaluation of different sample preparation workflows for quantitative, reproducible and improved depth of analysis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32129078 32129078]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00772 10.1021/acs.jproteome.9b00772]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32129078 16]. | ||
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#Shayan R, Rinaldi D, Larburu N, Plassart L, Balor S, Bouyssié D, Lebaron S, Marcoux J, Gleizes PE, Plisson-Chastang C, (2020) "Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy." <i>Molecules</i> <b>25</b>(5):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32138239 32138239]; doi: [https://dx.doi.org/10.3390/molecules25051125 10.3390/molecules25051125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32138239 2]. | #Shayan R, Rinaldi D, Larburu N, Plassart L, Balor S, Bouyssié D, Lebaron S, Marcoux J, Gleizes PE, Plisson-Chastang C, (2020) "Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy." <i>Molecules</i> <b>25</b>(5):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32138239 32138239]; doi: [https://dx.doi.org/10.3390/molecules25051125 10.3390/molecules25051125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32138239 2]. | ||
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#Rinfret Robert C, McManus FP, Lamoliatte F, Thibault P, (2020) "Interplay of Ubiquitin-Like Modifiers Following Arsenic Trioxide Treatment." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32223133 32223133]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00807 10.1021/acs.jproteome.9b00807]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32223133 18]. | #Rinfret Robert C, McManus FP, Lamoliatte F, Thibault P, (2020) "Interplay of Ubiquitin-Like Modifiers Following Arsenic Trioxide Treatment." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32223133 32223133]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00807 10.1021/acs.jproteome.9b00807]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32223133 18]. | ||
#Hör J, Garriss G, Di Giorgio S, Hack LM, Vanselow JT, Förstner KU, Schlosser A, Henriques-Normark B, Vogel J, (2020) "Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control." <i>EMBO J</i> <b></b>:e103852; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32227509 32227509]; doi: [https://dx.doi.org/10.15252/embj.2019103852 10.15252/embj.2019103852]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32227509 184]. | #Hör J, Garriss G, Di Giorgio S, Hack LM, Vanselow JT, Förstner KU, Schlosser A, Henriques-Normark B, Vogel J, (2020) "Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control." <i>EMBO J</i> <b></b>:e103852; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32227509 32227509]; doi: [https://dx.doi.org/10.15252/embj.2019103852 10.15252/embj.2019103852]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32227509 184]. | ||
- | #Reustle A, Di Marco M, Meyerhoff C, Nelde A, Walz JS, Winter S, Kandabarau S, Büttner F, Haag M, Backert L, Kowalewski DJ, Rausch S, Hennenlotter J, Stühler V, Scharpf M, Fend F, Stenzl A, Rammensee HG, Bedke J, Stevanović S, Schwab M, Schaeffeler E, (2020) "Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy." <i>Genome Med</i> <b>12</b>(1):32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32228647 32228647]; doi: [https://dx.doi.org/10.1186/s13073-020-00731-8 10.1186/s13073-020-00731-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32228647 | + | #Reustle A, Di Marco M, Meyerhoff C, Nelde A, Walz JS, Winter S, Kandabarau S, Büttner F, Haag M, Backert L, Kowalewski DJ, Rausch S, Hennenlotter J, Stühler V, Scharpf M, Fend F, Stenzl A, Rammensee HG, Bedke J, Stevanović S, Schwab M, Schaeffeler E, (2020) "Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy." <i>Genome Med</i> <b>12</b>(1):32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32228647 32228647]; doi: [https://dx.doi.org/10.1186/s13073-020-00731-8 10.1186/s13073-020-00731-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32228647 1017]. |
#Atlasi Y, Jafarnejad SM, Gkogkas CG, Vermeulen M, Sonenberg N, Stunnenberg HG, (2020) "The translational landscape of ground state pluripotency." <i>Nat Commun</i> <b>11</b>(1):1617; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32238817 32238817]; doi: [https://dx.doi.org/10.1038/s41467-020-15449-9 10.1038/s41467-020-15449-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32238817 48]. | #Atlasi Y, Jafarnejad SM, Gkogkas CG, Vermeulen M, Sonenberg N, Stunnenberg HG, (2020) "The translational landscape of ground state pluripotency." <i>Nat Commun</i> <b>11</b>(1):1617; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32238817 32238817]; doi: [https://dx.doi.org/10.1038/s41467-020-15449-9 10.1038/s41467-020-15449-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32238817 48]. | ||
+ | #Huang C, Foster SR, Shah AD, Kleifeld O, Canals M, Schittenhelm RB, Stone MJ, (2020) "Phosphoproteomic characterization of the signaling network resulting from activation of chemokine receptor CCR2." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32241914 32241914]; doi: [https://dx.doi.org/10.1074/jbc.RA119.012026 10.1074/jbc.RA119.012026]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32241914 72]. | ||
#Morishita Y, Kabil O, Young KZ, Kellogg AP, Chang A, Arvan P, (2020) "Thyrocyte cell survival and adaptation to chronic endoplasmic reticulum stress due to misfolded thyroglobulin." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32241916 32241916]; doi: [https://dx.doi.org/10.1074/jbc.RA120.012656 10.1074/jbc.RA120.012656]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32241916 1]. | #Morishita Y, Kabil O, Young KZ, Kellogg AP, Chang A, Arvan P, (2020) "Thyrocyte cell survival and adaptation to chronic endoplasmic reticulum stress due to misfolded thyroglobulin." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32241916 32241916]; doi: [https://dx.doi.org/10.1074/jbc.RA120.012656 10.1074/jbc.RA120.012656]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32241916 1]. | ||
#Mizukami H, Hathway B, Procopio N, (2020) "Aquatic Decomposition of Mammalian Corpses: A Forensic Proteomic Approach." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32242669 32242669]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00060 10.1021/acs.jproteome.0c00060]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32242669 22]. | #Mizukami H, Hathway B, Procopio N, (2020) "Aquatic Decomposition of Mammalian Corpses: A Forensic Proteomic Approach." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32242669 32242669]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00060 10.1021/acs.jproteome.0c00060]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32242669 22]. | ||
+ | #Xu G, Fromholt SE, Chakrabarty P, Zhu F, Liu X, Pace MC, Koh J, Golde TE, Levites Y, Lewis J, Borchelt DR, (2020) "Diversity in Aβ deposit morphology and secondary proteome insolubility across models of Alzheimer-type amyloidosis." <i>Acta Neuropathol Commun</i> <b>8</b>(1):43; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32252825 32252825]; doi: [https://dx.doi.org/10.1186/s40478-020-00911-y 10.1186/s40478-020-00911-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32252825 57]. | ||
#Carter SP, Moran AL, Matallanas D, McManus GJ, Blacque OE, Kennedy BN, (2020) "Genetic Deletion of Zebrafish Rab28 Causes Defective Outer Segment Shedding, but Not Retinal Degeneration." <i>Front Cell Dev Biol</i> <b>8</b>:136; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32258030 32258030]; doi: [https://dx.doi.org/10.3389/fcell.2020.00136 10.3389/fcell.2020.00136]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32258030 12]. | #Carter SP, Moran AL, Matallanas D, McManus GJ, Blacque OE, Kennedy BN, (2020) "Genetic Deletion of Zebrafish Rab28 Causes Defective Outer Segment Shedding, but Not Retinal Degeneration." <i>Front Cell Dev Biol</i> <b>8</b>:136; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32258030 32258030]; doi: [https://dx.doi.org/10.3389/fcell.2020.00136 10.3389/fcell.2020.00136]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32258030 12]. | ||
+ | #Djomehri SI, Gonzalez ME, da Veiga Leprevost F, Tekula SR, Chang HY, White MJ, Cimino-Mathews A, Burman B, Basrur V, Argani P, Nesvizhskii AI, Kleer CG, (2020) "Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors." <i>Nat Commun</i> <b>11</b>(1):1723; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32265444 32265444]; doi: [https://dx.doi.org/10.1038/s41467-020-15283-z 10.1038/s41467-020-15283-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32265444 4]. | ||
+ | #Busso CS, Guidry JJ, Gonzalez JJ, Zorba V, Son LS, Winsauer PJ, Walvekar RR, (2020) "A comprehensive analysis of sialolith proteins and the clinical implications." <i>Clin Proteomics</i> <b>17</b>:12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32265614 32265614]; doi: [https://dx.doi.org/10.1186/s12014-020-09275-w 10.1186/s12014-020-09275-w]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32265614 1]. | ||
#Rohlenova K, Goveia J, García-Caballero M, Subramanian A, Kalucka J, Treps L, Falkenberg KD, de Rooij LPMH, Zheng Y, Lin L, Sokol L, Teuwen LA, Geldhof V, Taverna F, Pircher A, Conradi LC, Khan S, Stegen S, Panovska D, De Smet F, Staal FJT, Mclaughlin RJ, Vinckier S, Van Bergen T, Ectors N, De Haes P, Wang J, Bolund L, Schoonjans L, Karakach TK, Yang H, Carmeliet G, Liu Y, Thienpont B, Dewerchin M, Eelen G, Li X, Luo Y, Carmeliet P, (2020) "Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis." <i>Cell Metab</i> <b>31</b>(4):862–877.e14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32268117 32268117]; doi: [https://dx.doi.org/10.1016/j.cmet.2020.03.009 10.1016/j.cmet.2020.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32268117 15]. | #Rohlenova K, Goveia J, García-Caballero M, Subramanian A, Kalucka J, Treps L, Falkenberg KD, de Rooij LPMH, Zheng Y, Lin L, Sokol L, Teuwen LA, Geldhof V, Taverna F, Pircher A, Conradi LC, Khan S, Stegen S, Panovska D, De Smet F, Staal FJT, Mclaughlin RJ, Vinckier S, Van Bergen T, Ectors N, De Haes P, Wang J, Bolund L, Schoonjans L, Karakach TK, Yang H, Carmeliet G, Liu Y, Thienpont B, Dewerchin M, Eelen G, Li X, Luo Y, Carmeliet P, (2020) "Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis." <i>Cell Metab</i> <b>31</b>(4):862–877.e14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32268117 32268117]; doi: [https://dx.doi.org/10.1016/j.cmet.2020.03.009 10.1016/j.cmet.2020.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32268117 15]. | ||
+ | #Hoesl C, Zanuttigh E, Fröhlich T, Philippou-Massier J, Krebs S, Blum H, Dahlhoff M, (2020) "The secretome of skin cancer cells activates the mTOR/MYC pathway in healthy keratinocytes and induces tumorigenic properties." <i>Biochim Biophys Acta Mol Cell Res</i> <b>1867</b>(8):118717; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32283126 32283126]; doi: [https://dx.doi.org/10.1016/j.bbamcr.2020.118717 10.1016/j.bbamcr.2020.118717]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32283126 12]. | ||
+ | #Jarzab A, Kurzawa N, Hopf T, Moerch M, Zecha J, Leijten N, Bian Y, Musiol E, Maschberger M, Stoehr G, Becher I, Daly C, Samaras P, Mergner J, Spanier B, Angelov A, Werner T, Bantscheff M, Wilhelm M, Klingenspor M, Lemeer S, Liebl W, Hahne H, Savitski MM, Kuster B, (2020) "Meltome atlas-thermal proteome stability across the tree of life." <i>Nat Methods</i> <b>17</b>(5):495–503; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32284610 32284610]; doi: [https://dx.doi.org/10.1038/s41592-020-0801-4 10.1038/s41592-020-0801-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32284610 31]. | ||
+ | #Goebel T, Mausbach S, Tuermer A, Eltahir H, Winter D, Gieselmann V, Thelen M, (2020) "Proteaphagy in mammalian cells can function independent of ATG5/ATG7." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32299840 32299840]; doi: [https://dx.doi.org/10.1074/mcp.RA120.001983 10.1074/mcp.RA120.001983]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32299840 149]. | ||
+ | #Chen Z, Wang C, Lei C, Feng X, Li C, Jung SY, Qin J, Chen J, (2020) "Phosphoproteomics Analysis Reveals a Potential Role of CHK1 in Regulation of Innate Immunity through IRF3." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32314919 32314919]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00829 10.1021/acs.jproteome.9b00829]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32314919 48]. | ||
+ | #Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A, (2020) "BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain." <i>Cell Syst</i> <b>10</b>(4):333–350.e14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32325033 32325033]; doi: [https://dx.doi.org/10.1016/j.cels.2020.03.003 10.1016/j.cels.2020.03.003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32325033 578]. |
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 10, 2020.