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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 January 1 25, 2017. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | ||
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#Carvalho AS, Ribeiro H, Voabil P, Penque D, Jensen ON, Molina H, Matthiesen R, (2014) "Global mass spectrometry and transcriptomics array based drug profiling provides novel insight into glucosamine induced endoplasmic reticulum stress." <i>Mol Cell Proteomics</i> <b>13</b>(12):3294–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25128556 25128556]; doi: [https://dx.doi.org/10.1074/mcp.M113.034363 10.1074/mcp.M113.034363]; GPMDB: [http://gpmdb.org/data/keyword/25128556 18]. | #Carvalho AS, Ribeiro H, Voabil P, Penque D, Jensen ON, Molina H, Matthiesen R, (2014) "Global mass spectrometry and transcriptomics array based drug profiling provides novel insight into glucosamine induced endoplasmic reticulum stress." <i>Mol Cell Proteomics</i> <b>13</b>(12):3294–307; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25128556 25128556]; doi: [https://dx.doi.org/10.1074/mcp.M113.034363 10.1074/mcp.M113.034363]; GPMDB: [http://gpmdb.org/data/keyword/25128556 18]. | ||
#Surmann K, Michalik S, Hildebrandt P, Gierok P, Depke M, Brinkmann L, Bernhardt J, Salazar MG, Sun Z, Shteynberg D, Kusebauch U, Moritz RL, Wollscheid B, Lalk M, Völker U, Schmidt F, (2014) "Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells." <i>Front Microbiol</i> <b>5</b>:392; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25136337 25136337]; doi: [https://dx.doi.org/10.3389/fmicb.2014.00392 10.3389/fmicb.2014.00392]; GPMDB: [http://gpmdb.org/data/keyword/25136337 71]. | #Surmann K, Michalik S, Hildebrandt P, Gierok P, Depke M, Brinkmann L, Bernhardt J, Salazar MG, Sun Z, Shteynberg D, Kusebauch U, Moritz RL, Wollscheid B, Lalk M, Völker U, Schmidt F, (2014) "Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells." <i>Front Microbiol</i> <b>5</b>:392; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25136337 25136337]; doi: [https://dx.doi.org/10.3389/fmicb.2014.00392 10.3389/fmicb.2014.00392]; GPMDB: [http://gpmdb.org/data/keyword/25136337 71]. | ||
+ | #Worboys JD, Sinclair J, Yuan Y, Jørgensen C, (2014) "Systematic evaluation of quantotypic peptides for targeted analysis of the human kinome." <i>Nat Methods</i> <b>11</b>(10):1041–4; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25152083 25152083]; doi: [https://dx.doi.org/10.1038/nmeth.3072 10.1038/nmeth.3072]; GPMDB: [http://gpmdb.org/data/keyword/25152083 12]. | ||
#Moczulska KE, Pichler P, Schutzbier M, Schleiffer A, Rumpel S, Mechtler K, (2014) "Deep and precise quantification of the mouse synaptosomal proteome reveals substantial remodeling during postnatal maturation." <i>J Proteome Res</i> <b>13</b>(10):4310–24; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25157418 25157418]; doi: [https://dx.doi.org/10.1021/pr500456t 10.1021/pr500456t]; GPMDB: [http://gpmdb.org/data/keyword/25157418 100]. | #Moczulska KE, Pichler P, Schutzbier M, Schleiffer A, Rumpel S, Mechtler K, (2014) "Deep and precise quantification of the mouse synaptosomal proteome reveals substantial remodeling during postnatal maturation." <i>J Proteome Res</i> <b>13</b>(10):4310–24; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25157418 25157418]; doi: [https://dx.doi.org/10.1021/pr500456t 10.1021/pr500456t]; GPMDB: [http://gpmdb.org/data/keyword/25157418 100]. | ||
#Han D, Jin J, Yu J, Kim K, Kim Y, (2015) "Integrated approach using multistep enzyme digestion, TiO2 enrichment, and database search for in-depth phosphoproteomic profiling." <i>Proteomics</i> <b>15</b>(2-3):618–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25159016 25159016]; doi: [https://dx.doi.org/10.1002/pmic.201400102 10.1002/pmic.201400102]; GPMDB: [http://gpmdb.org/data/keyword/25159016 36]. | #Han D, Jin J, Yu J, Kim K, Kim Y, (2015) "Integrated approach using multistep enzyme digestion, TiO2 enrichment, and database search for in-depth phosphoproteomic profiling." <i>Proteomics</i> <b>15</b>(2-3):618–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25159016 25159016]; doi: [https://dx.doi.org/10.1002/pmic.201400102 10.1002/pmic.201400102]; GPMDB: [http://gpmdb.org/data/keyword/25159016 36]. | ||
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#Zappacosta F, Scott GF, Huddleston MJ, Annan RS, (2015) "An optimized platform for hydrophilic interaction chromatography-immobilized metal affinity chromatography enables deep coverage of the rat liver phosphoproteome." <i>J Proteome Res</i> <b>14</b>(2):997–1009; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25575281 25575281]; doi: [https://dx.doi.org/10.1021/pr501025e 10.1021/pr501025e]; GPMDB: [http://gpmdb.org/data/keyword/25575281 42]. | #Zappacosta F, Scott GF, Huddleston MJ, Annan RS, (2015) "An optimized platform for hydrophilic interaction chromatography-immobilized metal affinity chromatography enables deep coverage of the rat liver phosphoproteome." <i>J Proteome Res</i> <b>14</b>(2):997–1009; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25575281 25575281]; doi: [https://dx.doi.org/10.1021/pr501025e 10.1021/pr501025e]; GPMDB: [http://gpmdb.org/data/keyword/25575281 42]. | ||
#Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ, Mann M, (2015) "Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation." <i>Mol Cell Proteomics</i> <b>14</b>(3):658–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25576301 25576301]; doi: [https://dx.doi.org/10.1074/mcp.M114.042812 10.1074/mcp.M114.042812]; GPMDB: [http://gpmdb.org/data/keyword/25576301 40]. | #Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ, Mann M, (2015) "Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation." <i>Mol Cell Proteomics</i> <b>14</b>(3):658–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25576301 25576301]; doi: [https://dx.doi.org/10.1074/mcp.M114.042812 10.1074/mcp.M114.042812]; GPMDB: [http://gpmdb.org/data/keyword/25576301 40]. | ||
+ | #Hong JH, Kaustov L, Coyaud E, Srikumar T, Wan J, Arrowsmith C, Raught B, (2015) "KCMF1 (potassium channel modulatory factor 1) Links RAD6 to UBR4 (ubiquitin N-recognin domain-containing E3 ligase 4) and lysosome-mediated degradation." <i>Mol Cell Proteomics</i> <b>14</b>(3):674–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25582440 25582440]; doi: [https://dx.doi.org/10.1074/mcp.M114.042168 10.1074/mcp.M114.042168]; GPMDB: [http://gpmdb.org/data/keyword/25582440 58]. | ||
#Chiang DY, Lebesgue N, Beavers DL, Alsina KM, Damen JM, Voigt N, Dobrev D, Wehrens XH, Scholten A, (2015) "Alterations in the interactome of serine/threonine protein phosphatase type-1 in atrial fibrillation patients." <i>J Am Coll Cardiol</i> <b>65</b>(2):163–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25593058 25593058]; doi: [https://dx.doi.org/10.1016/j.jacc.2014.10.042 10.1016/j.jacc.2014.10.042]; GPMDB: [http://gpmdb.org/data/keyword/25593058 22]. | #Chiang DY, Lebesgue N, Beavers DL, Alsina KM, Damen JM, Voigt N, Dobrev D, Wehrens XH, Scholten A, (2015) "Alterations in the interactome of serine/threonine protein phosphatase type-1 in atrial fibrillation patients." <i>J Am Coll Cardiol</i> <b>65</b>(2):163–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25593058 25593058]; doi: [https://dx.doi.org/10.1016/j.jacc.2014.10.042 10.1016/j.jacc.2014.10.042]; GPMDB: [http://gpmdb.org/data/keyword/25593058 22]. | ||
#Kasvandik S, Sillaste G, Velthut-Meikas A, Mikelsaar AV, Hallap T, Padrik P, Tenson T, Jaakma Ü, Kõks S, Salumets A, (2015) "Bovine sperm plasma membrane proteomics through biotinylation and subcellular enrichment." <i>Proteomics</i> <b>15</b>(11):1906–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25603787 25603787]; doi: [https://dx.doi.org/10.1002/pmic.201400297 10.1002/pmic.201400297]; GPMDB: [http://gpmdb.org/data/keyword/25603787 16]. | #Kasvandik S, Sillaste G, Velthut-Meikas A, Mikelsaar AV, Hallap T, Padrik P, Tenson T, Jaakma Ü, Kõks S, Salumets A, (2015) "Bovine sperm plasma membrane proteomics through biotinylation and subcellular enrichment." <i>Proteomics</i> <b>15</b>(11):1906–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25603787 25603787]; doi: [https://dx.doi.org/10.1002/pmic.201400297 10.1002/pmic.201400297]; GPMDB: [http://gpmdb.org/data/keyword/25603787 16]. | ||
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#Osinalde N, Sánchez-Quiles V, Blagoev B, Kratchmarova I, (2016) "Changes in Gab2 phosphorylation and interaction partners in response to interleukin (IL)-2 stimulation in T-lymphocytes." <i>Sci Rep</i> <b>6</b>:23530; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27025927 27025927]; doi: [https://dx.doi.org/10.1038/srep23530 10.1038/srep23530]; GPMDB: [http://gpmdb.org/data/keyword/27025927 22]. | #Osinalde N, Sánchez-Quiles V, Blagoev B, Kratchmarova I, (2016) "Changes in Gab2 phosphorylation and interaction partners in response to interleukin (IL)-2 stimulation in T-lymphocytes." <i>Sci Rep</i> <b>6</b>:23530; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27025927 27025927]; doi: [https://dx.doi.org/10.1038/srep23530 10.1038/srep23530]; GPMDB: [http://gpmdb.org/data/keyword/27025927 22]. | ||
#Xu G, Pattamatta A, Hildago R, Pace MC, Brown H, Borchelt DR, (2016) "Vulnerability of newly synthesized proteins to proteostasis stress." <i>J Cell Sci</i> <b>129</b>(9):1892–901; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27026526 27026526]; doi: [https://dx.doi.org/10.1242/jcs.176479 10.1242/jcs.176479]; GPMDB: [http://gpmdb.org/data/keyword/27026526 55]. | #Xu G, Pattamatta A, Hildago R, Pace MC, Brown H, Borchelt DR, (2016) "Vulnerability of newly synthesized proteins to proteostasis stress." <i>J Cell Sci</i> <b>129</b>(9):1892–901; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27026526 27026526]; doi: [https://dx.doi.org/10.1242/jcs.176479 10.1242/jcs.176479]; GPMDB: [http://gpmdb.org/data/keyword/27026526 55]. | ||
+ | #Lo Sasso G, Titz B, Nury C, Boué S, Phillips B, Belcastro V, Schneider T, Dijon S, Baumer K, Peric D, Dulize R, Elamin A, Guedj E, Buettner A, Leroy P, Kleinhans S, Vuillaume G, Veljkovic E, Ivanov NV, Martin F, Vanscheeuwijck P, Peitsch MC, Hoeng J, (2016) "Effects of cigarette smoke, cessation and switching to a candidate modified risk tobacco product on the liver in Apoe -/- mice--a systems toxicology analysis." <i>Inhal Toxicol</i> <b>28</b>(5):226–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27027324 27027324]; doi: [https://dx.doi.org/10.3109/08958378.2016.1150368 10.3109/08958378.2016.1150368]; GPMDB: [http://gpmdb.org/data/keyword/27027324 80]. | ||
#Goldman-Pinkovich A, Balno C, Strasser R, Zeituni-Molad M, Bendelak K, Rentsch D, Ephros M, Wiese M, Jardim A, Myler PJ, Zilberstein D, (2016) "An Arginine Deprivation Response Pathway Is Induced in Leishmania during Macrophage Invasion." <i>PLoS Pathog</i> <b>12</b>(4):e1005494; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27043018 27043018]; doi: [https://dx.doi.org/10.1371/journal.ppat.1005494 10.1371/journal.ppat.1005494]; GPMDB: [http://gpmdb.org/data/keyword/27043018 8]. | #Goldman-Pinkovich A, Balno C, Strasser R, Zeituni-Molad M, Bendelak K, Rentsch D, Ephros M, Wiese M, Jardim A, Myler PJ, Zilberstein D, (2016) "An Arginine Deprivation Response Pathway Is Induced in Leishmania during Macrophage Invasion." <i>PLoS Pathog</i> <b>12</b>(4):e1005494; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27043018 27043018]; doi: [https://dx.doi.org/10.1371/journal.ppat.1005494 10.1371/journal.ppat.1005494]; GPMDB: [http://gpmdb.org/data/keyword/27043018 8]. | ||
#Salvetti A, Couté Y, Epstein A, Arata L, Kraut A, Navratil V, Bouvet P, Greco A, (2016) "Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches." <i>J Proteome Res</i> <b>15</b>(5):1659–69; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27049334 27049334]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00126 10.1021/acs.jproteome.6b00126]; GPMDB: [http://gpmdb.org/data/keyword/27049334 7]. | #Salvetti A, Couté Y, Epstein A, Arata L, Kraut A, Navratil V, Bouvet P, Greco A, (2016) "Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches." <i>J Proteome Res</i> <b>15</b>(5):1659–69; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27049334 27049334]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00126 10.1021/acs.jproteome.6b00126]; GPMDB: [http://gpmdb.org/data/keyword/27049334 7]. | ||
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#Tape CJ, Ling S, Dimitriadi M, McMahon KM, Worboys JD, Leong HS, Norrie IC, Miller CJ, Poulogiannis G, Lauffenburger DA, Jørgensen C, (2016) "Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation." <i>Cell</i> <b>165</b>(4):910–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27087446 27087446]; doi: [https://dx.doi.org/10.1016/j.cell.2016.03.029 10.1016/j.cell.2016.03.029]; GPMDB: [http://gpmdb.org/data/keyword/27087446 374]. | #Tape CJ, Ling S, Dimitriadi M, McMahon KM, Worboys JD, Leong HS, Norrie IC, Miller CJ, Poulogiannis G, Lauffenburger DA, Jørgensen C, (2016) "Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation." <i>Cell</i> <b>165</b>(4):910–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27087446 27087446]; doi: [https://dx.doi.org/10.1016/j.cell.2016.03.029 10.1016/j.cell.2016.03.029]; GPMDB: [http://gpmdb.org/data/keyword/27087446 374]. | ||
#Stoehr A, Yang Y, Patel S, Evangelista AM, Aponte A, Wang G, Liu P, Boylston J, Kloner PH, Lin Y, Gucek M, Zhu J, Murphy E, (2016) "Prolyl hydroxylation regulates protein degradation, synthesis, and splicing in human induced pluripotent stem cell-derived cardiomyocytes." <i>Cardiovasc Res</i> <b>110</b>(3):346–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27095734 27095734]; doi: [https://dx.doi.org/10.1093/cvr/cvw081 10.1093/cvr/cvw081]; GPMDB: [http://gpmdb.org/data/keyword/27095734 12]. | #Stoehr A, Yang Y, Patel S, Evangelista AM, Aponte A, Wang G, Liu P, Boylston J, Kloner PH, Lin Y, Gucek M, Zhu J, Murphy E, (2016) "Prolyl hydroxylation regulates protein degradation, synthesis, and splicing in human induced pluripotent stem cell-derived cardiomyocytes." <i>Cardiovasc Res</i> <b>110</b>(3):346–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27095734 27095734]; doi: [https://dx.doi.org/10.1093/cvr/cvw081 10.1093/cvr/cvw081]; GPMDB: [http://gpmdb.org/data/keyword/27095734 12]. | ||
+ | #Grassl N, Kulak NA, Pichler G, Geyer PE, Jung J, Schubert S, Sinitcyn P, Cox J, Mann M, (2016) "Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome." <i>Genome Med</i> <b>8</b>(1):44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27102203 27102203]; doi: [https://dx.doi.org/10.1186/s13073-016-0293-0 10.1186/s13073-016-0293-0]; GPMDB: [http://gpmdb.org/data/keyword/27102203 89]. | ||
#Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M, (2016) "Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows." <i>J Proteomics</i> <b>145</b>:214–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27107777 27107777]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.03.049 10.1016/j.jprot.2016.03.049]; GPMDB: [http://gpmdb.org/data/keyword/27107777 163]. | #Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M, (2016) "Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows." <i>J Proteomics</i> <b>145</b>:214–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27107777 27107777]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.03.049 10.1016/j.jprot.2016.03.049]; GPMDB: [http://gpmdb.org/data/keyword/27107777 163]. | ||
#Larance M, Kirkwood KJ, Tinti M, Brenes Murillo A, Ferguson MA, Lamond AI, (2016) "Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(7):2476–90; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27114452 27114452]; doi: [https://dx.doi.org/10.1074/mcp.O115.055467 10.1074/mcp.O115.055467]; GPMDB: [http://gpmdb.org/data/keyword/27114452 396]. | #Larance M, Kirkwood KJ, Tinti M, Brenes Murillo A, Ferguson MA, Lamond AI, (2016) "Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(7):2476–90; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27114452 27114452]; doi: [https://dx.doi.org/10.1074/mcp.O115.055467 10.1074/mcp.O115.055467]; GPMDB: [http://gpmdb.org/data/keyword/27114452 396]. | ||
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#Kempf SJ, Metaxas A, Ibáñez-Vea M, Darvesh S, Finsen B, Larsen MR, (2016) "An integrated proteomics approach shows synaptic plasticity changes in an APP/PS1 Alzheimer's mouse model." <i>Oncotarget</i> <b>7</b>(23):33627–48; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27144524 27144524]; doi: [https://dx.doi.org/10.18632/oncotarget.9092 10.18632/oncotarget.9092]; GPMDB: [http://gpmdb.org/data/keyword/27144524 104]. | #Kempf SJ, Metaxas A, Ibáñez-Vea M, Darvesh S, Finsen B, Larsen MR, (2016) "An integrated proteomics approach shows synaptic plasticity changes in an APP/PS1 Alzheimer's mouse model." <i>Oncotarget</i> <b>7</b>(23):33627–48; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27144524 27144524]; doi: [https://dx.doi.org/10.18632/oncotarget.9092 10.18632/oncotarget.9092]; GPMDB: [http://gpmdb.org/data/keyword/27144524 104]. | ||
#Dørum S, Steinsbø Ø, Bergseng E, Arntzen MØ, de Souza GA, Sollid LM, (2016) "Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes." <i>Sci Rep</i> <b>6</b>:25565; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27146306 27146306]; doi: [https://dx.doi.org/10.1038/srep25565 10.1038/srep25565]; GPMDB: [http://gpmdb.org/data/keyword/27146306 27]. | #Dørum S, Steinsbø Ø, Bergseng E, Arntzen MØ, de Souza GA, Sollid LM, (2016) "Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes." <i>Sci Rep</i> <b>6</b>:25565; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27146306 27146306]; doi: [https://dx.doi.org/10.1038/srep25565 10.1038/srep25565]; GPMDB: [http://gpmdb.org/data/keyword/27146306 27]. | ||
+ | #Chen R, Zou H, Figeys D, (2016) "Detergent-Assisted Glycoprotein Capture: A Versatile Tool for In-Depth N-Glycoproteome Analysis." <i>J Proteome Res</i> <b>15</b>(6):2080–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27147131 27147131]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00056 10.1021/acs.jproteome.6b00056]; GPMDB: [http://gpmdb.org/data/keyword/27147131 36]. | ||
#Packialakshmi B, Liyanage R, Lay JO Jr, Okimoto R, Rath NC, (2016) "Proteomic Changes in the Plasma of Broiler Chickens with Femoral Head Necrosis." <i>Biomark Insights</i> <b>11</b>:55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27147818 27147818]; doi: [https://dx.doi.org/10.4137/BMI.S38291 10.4137/BMI.S38291]; GPMDB: [http://gpmdb.org/data/keyword/27147818 6]. | #Packialakshmi B, Liyanage R, Lay JO Jr, Okimoto R, Rath NC, (2016) "Proteomic Changes in the Plasma of Broiler Chickens with Femoral Head Necrosis." <i>Biomark Insights</i> <b>11</b>:55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27147818 27147818]; doi: [https://dx.doi.org/10.4137/BMI.S38291 10.4137/BMI.S38291]; GPMDB: [http://gpmdb.org/data/keyword/27147818 6]. | ||
#Jhingan GD, Kumari S, Jamwal SV, Kalam H, Arora D, Jain N, Kumaar LK, Samal A, Rao KV, Kumar D, Nandicoori VK, (2016) "Comparative Proteomic Analyses of Avirulent, Virulent, and Clinical Strains of Mycobacterium tuberculosis Identify Strain-specific Patterns." <i>J Biol Chem</i> <b>291</b>(27):14257–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27151218 27151218]; doi: [https://dx.doi.org/10.1074/jbc.M115.666123 10.1074/jbc.M115.666123]; GPMDB: [http://gpmdb.org/data/keyword/27151218 16]. | #Jhingan GD, Kumari S, Jamwal SV, Kalam H, Arora D, Jain N, Kumaar LK, Samal A, Rao KV, Kumar D, Nandicoori VK, (2016) "Comparative Proteomic Analyses of Avirulent, Virulent, and Clinical Strains of Mycobacterium tuberculosis Identify Strain-specific Patterns." <i>J Biol Chem</i> <b>291</b>(27):14257–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27151218 27151218]; doi: [https://dx.doi.org/10.1074/jbc.M115.666123 10.1074/jbc.M115.666123]; GPMDB: [http://gpmdb.org/data/keyword/27151218 16]. | ||
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#Shraibman B, Kadosh DM, Barnea E, Admon A, (2016) "Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy." <i>Mol Cell Proteomics</i> <b>15</b>(9):3058–70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27412690 27412690]; doi: [https://dx.doi.org/10.1074/mcp.M116.060350 10.1074/mcp.M116.060350]; GPMDB: [http://gpmdb.org/data/keyword/27412690 60]. | #Shraibman B, Kadosh DM, Barnea E, Admon A, (2016) "Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy." <i>Mol Cell Proteomics</i> <b>15</b>(9):3058–70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27412690 27412690]; doi: [https://dx.doi.org/10.1074/mcp.M116.060350 10.1074/mcp.M116.060350]; GPMDB: [http://gpmdb.org/data/keyword/27412690 60]. | ||
#Müller S, Balaz M, Stefanicka P, Varga L, Amri EZ, Ukropec J, Wollscheid B, Wolfrum C, (2016) "Proteomic Analysis of Human Brown Adipose Tissue Reveals Utilization of Coupled and Uncoupled Energy Expenditure Pathways." <i>Sci Rep</i> <b>6</b>:30030; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418403 27418403]; doi: [https://dx.doi.org/10.1038/srep30030 10.1038/srep30030]; GPMDB: [http://gpmdb.org/data/keyword/27418403 32]. | #Müller S, Balaz M, Stefanicka P, Varga L, Amri EZ, Ukropec J, Wollscheid B, Wolfrum C, (2016) "Proteomic Analysis of Human Brown Adipose Tissue Reveals Utilization of Coupled and Uncoupled Energy Expenditure Pathways." <i>Sci Rep</i> <b>6</b>:30030; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418403 27418403]; doi: [https://dx.doi.org/10.1038/srep30030 10.1038/srep30030]; GPMDB: [http://gpmdb.org/data/keyword/27418403 32]. | ||
+ | #Rice RH, Durbin-Johnson BP, Ishitsuka Y, Salemi M, Phinney BS, Rocke DM, Roop DR, (2016) "Proteomic Analysis of Loricrin Knockout Mouse Epidermis." <i>J Proteome Res</i> <b>15</b>(8):2560–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418529 27418529]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00108 10.1021/acs.jproteome.6b00108]; GPMDB: [http://gpmdb.org/data/keyword/27418529 42]. | ||
#Petrera A, Kern U, Linz D, Gomez-Auli A, Hohl M, Gassenhuber J, Sadowski T, Schilling O, (2016) "Proteomic Profiling of Cardiomyocyte-Specific Cathepsin A Overexpression Links Cathepsin A to the Oxidative Stress Response." <i>J Proteome Res</i> <b>15</b>(9):3188–95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432266 27432266]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00413 10.1021/acs.jproteome.6b00413]; GPMDB: [http://gpmdb.org/data/keyword/27432266 3]. | #Petrera A, Kern U, Linz D, Gomez-Auli A, Hohl M, Gassenhuber J, Sadowski T, Schilling O, (2016) "Proteomic Profiling of Cardiomyocyte-Specific Cathepsin A Overexpression Links Cathepsin A to the Oxidative Stress Response." <i>J Proteome Res</i> <b>15</b>(9):3188–95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432266 27432266]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00413 10.1021/acs.jproteome.6b00413]; GPMDB: [http://gpmdb.org/data/keyword/27432266 3]. | ||
#Zhou Y, Xiong L, Zhang Y, Yu R, Jiang X, Xu G, (2016) "Quantitative proteomics identifies myoferlin as a novel regulator of A Disintegrin and Metalloproteinase 12 in HeLa cells." <i>J Proteomics</i> <b>148</b>:94–104; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432471 27432471]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.07.015 10.1016/j.jprot.2016.07.015]; GPMDB: [http://gpmdb.org/data/keyword/27432471 14]. | #Zhou Y, Xiong L, Zhang Y, Yu R, Jiang X, Xu G, (2016) "Quantitative proteomics identifies myoferlin as a novel regulator of A Disintegrin and Metalloproteinase 12 in HeLa cells." <i>J Proteomics</i> <b>148</b>:94–104; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432471 27432471]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.07.015 10.1016/j.jprot.2016.07.015]; GPMDB: [http://gpmdb.org/data/keyword/27432471 14]. | ||
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#Marino F, Mommen GP, Jeko A, Meiring HD, van Gaans-van den Brink JA, Scheltema RA, van Els CA, Heck AJ, (2016) "Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27503676 27503676]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00528 10.1021/acs.jproteome.6b00528]; GPMDB: [http://gpmdb.org/data/keyword/27503676 31]. | #Marino F, Mommen GP, Jeko A, Meiring HD, van Gaans-van den Brink JA, Scheltema RA, van Els CA, Heck AJ, (2016) "Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27503676 27503676]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00528 10.1021/acs.jproteome.6b00528]; GPMDB: [http://gpmdb.org/data/keyword/27503676 31]. | ||
#Budayeva HG, Cristea IM, (2016) "Human Sirtuin 2 Localization, Transient Interactions, and Impact on the Proteome Point to Its Role in Intracellular Trafficking." <i>Mol Cell Proteomics</i> <b>15</b>(10):3107–3125; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27503897 27503897]; doi: [https://dx.doi.org/10.1074/mcp.M116.061333 10.1074/mcp.M116.061333]; GPMDB: [http://gpmdb.org/data/keyword/27503897 15]. | #Budayeva HG, Cristea IM, (2016) "Human Sirtuin 2 Localization, Transient Interactions, and Impact on the Proteome Point to Its Role in Intracellular Trafficking." <i>Mol Cell Proteomics</i> <b>15</b>(10):3107–3125; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27503897 27503897]; doi: [https://dx.doi.org/10.1074/mcp.M116.061333 10.1074/mcp.M116.061333]; GPMDB: [http://gpmdb.org/data/keyword/27503897 15]. | ||
+ | #Gat-Yablonski G, Finka A, Pinto G, Quadroni M, Shtaif B, Goloubinoff P, (2016) "Quantitative proteomics of rat livers shows that unrestricted feeding is stressful for proteostasis with implications on life span." <i>Aging (Albany NY)</i> <b>8</b>(8):1735–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27508340 27508340]; doi: [https://dx.doi.org/10.18632/aging.101009 10.18632/aging.101009]; GPMDB: [http://gpmdb.org/data/keyword/27508340 18]. | ||
#Swenson JM, Colmenares SU, Strom AR, Costes SV, Karpen GH, (2016) "The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27514026 27514026]; doi: [https://dx.doi.org/10.7554/eLife.16096 10.7554/eLife.16096]; GPMDB: [http://gpmdb.org/data/keyword/27514026 4]. | #Swenson JM, Colmenares SU, Strom AR, Costes SV, Karpen GH, (2016) "The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27514026 27514026]; doi: [https://dx.doi.org/10.7554/eLife.16096 10.7554/eLife.16096]; GPMDB: [http://gpmdb.org/data/keyword/27514026 4]. | ||
#Naboulsi W, Bracht T, Megger DA, Reis H, Ahrens M, Turewicz M, Eisenacher M, Tautges S, Canbay AE, Meyer HE, Weber F, Baba HA, Sitek B, (2016) "Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation." <i>Biochim Biophys Acta</i> <b>1864</b>(11):1579–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27519163 27519163]; doi: [https://dx.doi.org/10.1016/j.bbapap.2016.08.005 10.1016/j.bbapap.2016.08.005]; GPMDB: [http://gpmdb.org/data/keyword/27519163 36]. | #Naboulsi W, Bracht T, Megger DA, Reis H, Ahrens M, Turewicz M, Eisenacher M, Tautges S, Canbay AE, Meyer HE, Weber F, Baba HA, Sitek B, (2016) "Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation." <i>Biochim Biophys Acta</i> <b>1864</b>(11):1579–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27519163 27519163]; doi: [https://dx.doi.org/10.1016/j.bbapap.2016.08.005 10.1016/j.bbapap.2016.08.005]; GPMDB: [http://gpmdb.org/data/keyword/27519163 36]. | ||
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#Sarvaiya HA, Lazar IM, (2016) "Insulin stimulated MCF7 breast cancer cells: Proteome dataset." <i>Data Brief</i> <b>9</b>:579–584; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27761513 27761513]; doi: [https://dx.doi.org/10.1016/j.dib.2016.09.025 10.1016/j.dib.2016.09.025]; GPMDB: [http://gpmdb.org/data/keyword/27761513 1]. | #Sarvaiya HA, Lazar IM, (2016) "Insulin stimulated MCF7 breast cancer cells: Proteome dataset." <i>Data Brief</i> <b>9</b>:579–584; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27761513 27761513]; doi: [https://dx.doi.org/10.1016/j.dib.2016.09.025 10.1016/j.dib.2016.09.025]; GPMDB: [http://gpmdb.org/data/keyword/27761513 1]. | ||
#Assoni A, Coatti G, Valadares MC, Beccari M, Gomes J, Pelatti M, Mitne-Neto M, Carvalho VM, Zatz M, (2016) "Different Donors Mesenchymal Stromal Cells Secretomes Reveal Heterogeneous Profile of Relevance for Therapeutic Use." <i>Stem Cells Dev</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27762666 27762666]; doi: [https://dx.doi.org/10.1089/scd.2016.0218 10.1089/scd.2016.0218]; GPMDB: [http://gpmdb.org/data/keyword/27762666 48]. | #Assoni A, Coatti G, Valadares MC, Beccari M, Gomes J, Pelatti M, Mitne-Neto M, Carvalho VM, Zatz M, (2016) "Different Donors Mesenchymal Stromal Cells Secretomes Reveal Heterogeneous Profile of Relevance for Therapeutic Use." <i>Stem Cells Dev</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27762666 27762666]; doi: [https://dx.doi.org/10.1089/scd.2016.0218 10.1089/scd.2016.0218]; GPMDB: [http://gpmdb.org/data/keyword/27762666 48]. | ||
- | #Peng J, Cao J, Ng FM, Hill J, (2016) "Pseudomonas aeruginosa develops Ciprofloxacin resistance from low to high level with distinctive proteome changes." <i>J Proteomics</i> <b>152</b>:75–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27771372 27771372]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.10.005 10.1016/j.jprot.2016.10.005]; GPMDB: [http://gpmdb.org/data/keyword/27771372 | + | #Peng J, Cao J, Ng FM, Hill J, (2016) "Pseudomonas aeruginosa develops Ciprofloxacin resistance from low to high level with distinctive proteome changes." <i>J Proteomics</i> <b>152</b>:75–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27771372 27771372]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.10.005 10.1016/j.jprot.2016.10.005]; GPMDB: [http://gpmdb.org/data/keyword/27771372 25]. |
+ | #Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J, (2016) "Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins." <i>Mol Cell</i> <b>64</b>(3):624–635; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27773674 27773674]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.09.019 10.1016/j.molcel.2016.09.019]; GPMDB: [http://gpmdb.org/data/keyword/27773674 13]. | ||
#Duncan O, Trösch J, Fenske R, Taylor NL, Millar AH, (2016) "Mapping the Triticum aestivum proteome." <i>Plant J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27775198 27775198]; doi: [https://dx.doi.org/10.1111/tpj.13402 10.1111/tpj.13402]; GPMDB: [http://gpmdb.org/data/keyword/27775198 28]. | #Duncan O, Trösch J, Fenske R, Taylor NL, Millar AH, (2016) "Mapping the Triticum aestivum proteome." <i>Plant J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27775198 27775198]; doi: [https://dx.doi.org/10.1111/tpj.13402 10.1111/tpj.13402]; GPMDB: [http://gpmdb.org/data/keyword/27775198 28]. | ||
+ | #Maleki S, Kjellqvist S, Paloschi V, Magné J, Branca RM, Du L, Hultenby K, Petrini J, Fuxe J, MIBAVA Leducq Consortium., Lehtiö J, Franco-Cereceda A, Eriksson P, Björck HM, (2016) "Mesenchymal state of intimal cells may explain higher propensity to ascending aortic aneurysm in bicuspid aortic valves." <i>Sci Rep</i> <b>6</b>:35712; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27779199 27779199]; doi: [https://dx.doi.org/10.1038/srep35712 10.1038/srep35712]; GPMDB: [http://gpmdb.org/data/keyword/27779199 5]. | ||
#Cunsolo V, Fasoli E, Di Francesco A, Saletti R, Muccilli V, Gallina S, Righetti PG, Foti S, (2016) "Polyphemus, Odysseus and the ovine milk proteome." <i>J Proteomics</i> <b>152</b>:58–74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27784645 27784645]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.10.007 10.1016/j.jprot.2016.10.007]; GPMDB: [http://gpmdb.org/data/keyword/27784645 40]. | #Cunsolo V, Fasoli E, Di Francesco A, Saletti R, Muccilli V, Gallina S, Righetti PG, Foti S, (2016) "Polyphemus, Odysseus and the ovine milk proteome." <i>J Proteomics</i> <b>152</b>:58–74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27784645 27784645]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.10.007 10.1016/j.jprot.2016.10.007]; GPMDB: [http://gpmdb.org/data/keyword/27784645 40]. | ||
#Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS, (2016) "Flexible Data Analysis Pipeline for High-Confidence Proteogenomics." <i>J Proteome Res</i> <b>15</b>(12):4686–4695; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27786492 27786492]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00765 10.1021/acs.jproteome.6b00765]; GPMDB: [http://gpmdb.org/data/keyword/27786492 35]. | #Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS, (2016) "Flexible Data Analysis Pipeline for High-Confidence Proteogenomics." <i>J Proteome Res</i> <b>15</b>(12):4686–4695; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27786492 27786492]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00765 10.1021/acs.jproteome.6b00765]; GPMDB: [http://gpmdb.org/data/keyword/27786492 35]. | ||
#Shishkova E, Hebert AS, Coon JJ, (2016) "Now, More Than Ever, Proteomics Needs Better Chromatography." <i>Cell Syst</i> <b>3</b>(4):321–324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27788355 27788355]; doi: [https://dx.doi.org/10.1016/j.cels.2016.10.007 10.1016/j.cels.2016.10.007]; GPMDB: [http://gpmdb.org/data/keyword/27788355 35]. | #Shishkova E, Hebert AS, Coon JJ, (2016) "Now, More Than Ever, Proteomics Needs Better Chromatography." <i>Cell Syst</i> <b>3</b>(4):321–324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27788355 27788355]; doi: [https://dx.doi.org/10.1016/j.cels.2016.10.007 10.1016/j.cels.2016.10.007]; GPMDB: [http://gpmdb.org/data/keyword/27788355 35]. | ||
+ | #Lundquist PK, Mantegazza O, Stefanski A, Stühler K, Weber AP, (2016) "Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts." <i>Mol Plant</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27794502 27794502]; doi: [https://dx.doi.org/10.1016/j.molp.2016.10.011 10.1016/j.molp.2016.10.011]; GPMDB: [http://gpmdb.org/data/keyword/27794502 42]. | ||
#Fournier M, Orpinell M, Grauffel C, Scheer E, Garnier JM, Ye T, Chavant V, Joint M, Esashi F, Dejaegere A, Gönczy P, Tora L, (2016) "KAT2A/KAT2B-targeted acetylome reveals a role for PLK4 acetylation in preventing centrosome amplification." <i>Nat Commun</i> <b>7</b>:13227; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27796307 27796307]; doi: [https://dx.doi.org/10.1038/ncomms13227 10.1038/ncomms13227]; GPMDB: [http://gpmdb.org/data/keyword/27796307 114]. | #Fournier M, Orpinell M, Grauffel C, Scheer E, Garnier JM, Ye T, Chavant V, Joint M, Esashi F, Dejaegere A, Gönczy P, Tora L, (2016) "KAT2A/KAT2B-targeted acetylome reveals a role for PLK4 acetylation in preventing centrosome amplification." <i>Nat Commun</i> <b>7</b>:13227; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27796307 27796307]; doi: [https://dx.doi.org/10.1038/ncomms13227 10.1038/ncomms13227]; GPMDB: [http://gpmdb.org/data/keyword/27796307 114]. | ||
#Mardakheh FK, Self A, Marshall CJ, (2016) "RHO binding to FAM65A regulates Golgi reorientation during cell migration." <i>J Cell Sci</i> <b>129</b>(24):4466–4479; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807006 27807006]; doi: [https://dx.doi.org/10.1242/jcs.198614 10.1242/jcs.198614]; GPMDB: [http://gpmdb.org/data/keyword/27807006 18]. | #Mardakheh FK, Self A, Marshall CJ, (2016) "RHO binding to FAM65A regulates Golgi reorientation during cell migration." <i>J Cell Sci</i> <b>129</b>(24):4466–4479; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807006 27807006]; doi: [https://dx.doi.org/10.1242/jcs.198614 10.1242/jcs.198614]; GPMDB: [http://gpmdb.org/data/keyword/27807006 18]. | ||
#Leach MD, Kim T, DiGregorio S, Collins C, Zhang Z, Duennwald ML, Cowen LE, (2016) "Candida albicans Is Resistant to Polyglutamine Aggregation and Toxicity." <i>G3 (Bethesda)</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807047 27807047]; doi: [https://dx.doi.org/10.1534/g3.116.035675 10.1534/g3.116.035675]; GPMDB: [http://gpmdb.org/data/keyword/27807047 6]. | #Leach MD, Kim T, DiGregorio S, Collins C, Zhang Z, Duennwald ML, Cowen LE, (2016) "Candida albicans Is Resistant to Polyglutamine Aggregation and Toxicity." <i>G3 (Bethesda)</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27807047 27807047]; doi: [https://dx.doi.org/10.1534/g3.116.035675 10.1534/g3.116.035675]; GPMDB: [http://gpmdb.org/data/keyword/27807047 6]. | ||
#Chen Y, Xie Y, Xu L, Zhan S, Xiao Y, Gao Y, Wu B, Ge W, (2017) "Protein content and functional characteristics of serum-purified exosomes from patients with colorectal cancer revealed by quantitative proteomics." <i>Int J Cancer</i> <b>140</b>(4):900–913; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27813080 27813080]; doi: [https://dx.doi.org/10.1002/ijc.30496 10.1002/ijc.30496]; GPMDB: [http://gpmdb.org/data/keyword/27813080 1]. | #Chen Y, Xie Y, Xu L, Zhan S, Xiao Y, Gao Y, Wu B, Ge W, (2017) "Protein content and functional characteristics of serum-purified exosomes from patients with colorectal cancer revealed by quantitative proteomics." <i>Int J Cancer</i> <b>140</b>(4):900–913; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27813080 27813080]; doi: [https://dx.doi.org/10.1002/ijc.30496 10.1002/ijc.30496]; GPMDB: [http://gpmdb.org/data/keyword/27813080 1]. | ||
- | #Wang J, Mauvoisin D, Martin E, Atger F, Galindo AN, Dayon L, Sizzano F, Palini A, Kussmann M, Waridel P, Quadroni M, Dulić V, Naef F, Gachon F, (2016) "Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver." <i>Cell Metab</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27818260 27818260]; doi: [https://dx.doi.org/10.1016/j.cmet.2016.10.003 10.1016/j.cmet.2016.10.003]; GPMDB: [http://gpmdb.org/data/keyword/27818260 | + | #Wang J, Mauvoisin D, Martin E, Atger F, Galindo AN, Dayon L, Sizzano F, Palini A, Kussmann M, Waridel P, Quadroni M, Dulić V, Naef F, Gachon F, (2016) "Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver." <i>Cell Metab</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27818260 27818260]; doi: [https://dx.doi.org/10.1016/j.cmet.2016.10.003 10.1016/j.cmet.2016.10.003]; GPMDB: [http://gpmdb.org/data/keyword/27818260 28]. |
- | #Kogel U, Titz B, Schlage WK, Nury C, Martin F, Oviedo A, Lebrun S, Elamin A, Guedj E, Trivedi K, Ivanov NV, Vanscheeuwijck P, Peitsch MC, Hoeng J, (2016) "Evaluation of the Tobacco Heating System 2.2. Part 7: Systems toxicological assessment of a mentholated version revealed reduced cellular and molecular exposure effects compared with mentholated and non-mentholated cigarette smoke." <i>Regul Toxicol Pharmacol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27818347 27818347]; doi: [https://dx.doi.org/10.1016/j.yrtph.2016.11.001 10.1016/j.yrtph.2016.11.001]; GPMDB: [http://gpmdb.org/data/keyword/27818347 36]. | + | #Kogel U, Titz B, Schlage WK, Nury C, Martin F, Oviedo A, Lebrun S, Elamin A, Guedj E, Trivedi K, Ivanov NV, Vanscheeuwijck P, Peitsch MC, Hoeng J, (2016) "Evaluation of the Tobacco Heating System 2.2. Part 7: Systems toxicological assessment of a mentholated version revealed reduced cellular and molecular exposure effects compared with mentholated and non-mentholated cigarette smoke." <i>Regul Toxicol Pharmacol</i> <b>81 Suppl 2</b>:S123–S138; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27818347 27818347]; doi: [https://dx.doi.org/10.1016/j.yrtph.2016.11.001 10.1016/j.yrtph.2016.11.001]; GPMDB: [http://gpmdb.org/data/keyword/27818347 36]. |
#Schmitt K, Smolinski N, Neumann P, Schmaul S, Hofer-Pretz V, Braus GH, Valerius O, (2016) "Asc1p/RACK1 connects ribosomes to eukaryotic phospho-signaling." <i>Mol Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27821475 27821475]; doi: [https://dx.doi.org/10.1128/MCB.00279-16 10.1128/MCB.00279-16]; GPMDB: [http://gpmdb.org/data/keyword/27821475 274]. | #Schmitt K, Smolinski N, Neumann P, Schmaul S, Hofer-Pretz V, Braus GH, Valerius O, (2016) "Asc1p/RACK1 connects ribosomes to eukaryotic phospho-signaling." <i>Mol Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27821475 27821475]; doi: [https://dx.doi.org/10.1128/MCB.00279-16 10.1128/MCB.00279-16]; GPMDB: [http://gpmdb.org/data/keyword/27821475 274]. | ||
+ | #Mardakheh FK, Sailem HZ, Kümper S, Tape CJ, McCully RR, Paul A, Anjomani-Virmouni S, Jørgensen C, Poulogiannis G, Marshall CJ, Bakal C, (2016) "Proteomics profiling of interactome dynamics by colocalisation analysis (COLA)." <i>Mol Biosyst</i> <b>13</b>(1):92–105; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27824369 27824369]; doi: [https://dx.doi.org/10.1039/c6mb00701e 10.1039/c6mb00701e]; GPMDB: [http://gpmdb.org/data/keyword/27824369 16]. | ||
+ | #Liu Y, Sellegounder D, Sun J, (2016) "Neuronal GPCR OCTR-1 regulates innate immunity by controlling protein synthesis in Caenorhabditis elegans." <i>Sci Rep</i> <b>6</b>:36832; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27833098 27833098]; doi: [https://dx.doi.org/10.1038/srep36832 10.1038/srep36832]; GPMDB: [http://gpmdb.org/data/keyword/27833098 20]. | ||
+ | #Valdés A, García-Cañas V, Artemenko KA, Simó C, Bergquist J, Cifuentes A, (2016) "Nano-liquid chromatography-orbitrap MS -based quantitative proteomics reveals differences between the mechanisms of action of carnosic acid and carnosol in colon cancer cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27834734 27834734]; doi: [https://dx.doi.org/10.1074/mcp.M116.061481 10.1074/mcp.M116.061481]; GPMDB: [http://gpmdb.org/data/keyword/27834734 54]. | ||
#Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR, (2016) "Multiparameter functional diversity of human C2H2 zinc finger proteins." <i>Genome Res</i> <b>26</b>(12):1742–1752; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27852650 27852650]; doi: [https://dx.doi.org/10.1101/gr.209643.116 10.1101/gr.209643.116]; GPMDB: [http://gpmdb.org/data/keyword/27852650 224]. | #Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR, (2016) "Multiparameter functional diversity of human C2H2 zinc finger proteins." <i>Genome Res</i> <b>26</b>(12):1742–1752; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27852650 27852650]; doi: [https://dx.doi.org/10.1101/gr.209643.116 10.1101/gr.209643.116]; GPMDB: [http://gpmdb.org/data/keyword/27852650 224]. | ||
#Bassani-Sternberg M, Bräunlein E, Klar R, Engleitner T, Sinitcyn P, Audehm S, Straub M, Weber J, Slotta-Huspenina J, Specht K, Martignoni ME, Werner A, Hein R, H Busch D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM, (2016) "Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry." <i>Nat Commun</i> <b>7</b>:13404; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27869121 27869121]; doi: [https://dx.doi.org/10.1038/ncomms13404 10.1038/ncomms13404]; GPMDB: [http://gpmdb.org/data/keyword/27869121 138]. | #Bassani-Sternberg M, Bräunlein E, Klar R, Engleitner T, Sinitcyn P, Audehm S, Straub M, Weber J, Slotta-Huspenina J, Specht K, Martignoni ME, Werner A, Hein R, H Busch D, Peschel C, Rad R, Cox J, Mann M, Krackhardt AM, (2016) "Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry." <i>Nat Commun</i> <b>7</b>:13404; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27869121 27869121]; doi: [https://dx.doi.org/10.1038/ncomms13404 10.1038/ncomms13404]; GPMDB: [http://gpmdb.org/data/keyword/27869121 138]. | ||
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#Beaumont V, Zhong S, Lin H, Xu W, Bradaia A, Steidl E, Gleyzes M, Wadel K, Buisson B, Padovan-Neto FE, Chakroborty S, Ward KM, Harms JF, Beltran J, Kwan M, Ghavami A, Häggkvist J, Tóth M, Halldin C, Varrone A, Schaab C, Dybowski JN, Elschenbroich S, Lehtimäki K, Heikkinen T, Park L, Rosinski J, Mrzljak L, Lavery D, West AR, Schmidt CJ, Zaleska MM, Munoz-Sanjuan I, (2016) "Phosphodiesterase 10A Inhibition Improves Cortico-Basal Ganglia Function in Huntington's Disease Models." <i>Neuron</i> <b>92</b>(6):1220–1237; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27916455 27916455]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.10.064 10.1016/j.neuron.2016.10.064]; GPMDB: [http://gpmdb.org/data/keyword/27916455 377]. | #Beaumont V, Zhong S, Lin H, Xu W, Bradaia A, Steidl E, Gleyzes M, Wadel K, Buisson B, Padovan-Neto FE, Chakroborty S, Ward KM, Harms JF, Beltran J, Kwan M, Ghavami A, Häggkvist J, Tóth M, Halldin C, Varrone A, Schaab C, Dybowski JN, Elschenbroich S, Lehtimäki K, Heikkinen T, Park L, Rosinski J, Mrzljak L, Lavery D, West AR, Schmidt CJ, Zaleska MM, Munoz-Sanjuan I, (2016) "Phosphodiesterase 10A Inhibition Improves Cortico-Basal Ganglia Function in Huntington's Disease Models." <i>Neuron</i> <b>92</b>(6):1220–1237; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27916455 27916455]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.10.064 10.1016/j.neuron.2016.10.064]; GPMDB: [http://gpmdb.org/data/keyword/27916455 377]. | ||
#Tiberti N, Latham SL, Bush S, Cohen A, Opoka RO, John CC, Juillard A, Grau GE, Combes V, (2016) "Exploring experimental cerebral malaria pathogenesis through the characterisation of host-derived plasma microparticle protein content." <i>Sci Rep</i> <b>6</b>:37871; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27917875 27917875]; doi: [https://dx.doi.org/10.1038/srep37871 10.1038/srep37871]; GPMDB: [http://gpmdb.org/data/keyword/27917875 4]. | #Tiberti N, Latham SL, Bush S, Cohen A, Opoka RO, John CC, Juillard A, Grau GE, Combes V, (2016) "Exploring experimental cerebral malaria pathogenesis through the characterisation of host-derived plasma microparticle protein content." <i>Sci Rep</i> <b>6</b>:37871; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27917875 27917875]; doi: [https://dx.doi.org/10.1038/srep37871 10.1038/srep37871]; GPMDB: [http://gpmdb.org/data/keyword/27917875 4]. | ||
- | #Zhao H, Konzer A, Mi J, Chen M, Pettersson U, Lind SB, (2016) "Posttranscriptional Regulation in Adenovirus Infected Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27959563 27959563]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00834 10.1021/acs.jproteome.6b00834]; GPMDB: [http://gpmdb.org/data/keyword/27959563 | + | #Sharma R, Fedorenko I, Spence PT, Sondak VK, Smalley KS, Koomen JM, (2016) "Activity-Based Protein Profiling Shows Heterogeneous Signaling Adaptations to BRAF Inhibition." <i>J Proteome Res</i> <b>15</b>(12):4476–4489; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27934295 27934295]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00613 10.1021/acs.jproteome.6b00613]; GPMDB: [http://gpmdb.org/data/keyword/27934295 18]. |
+ | #Zhao H, Konzer A, Mi J, Chen M, Pettersson U, Lind SB, (2016) "Posttranscriptional Regulation in Adenovirus Infected Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27959563 27959563]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00834 10.1021/acs.jproteome.6b00834]; GPMDB: [http://gpmdb.org/data/keyword/27959563 6]. | ||
+ | #Dauden MI, Kosinski J, Kolaj-Robin O, Desfosses A, Ori A, Faux C, Hoffmann NA, Onuma OF, Breunig KD, Beck M, Sachse C, Séraphin B, Glatt S, Müller CW, (2016) "Architecture of the yeast Elongator complex." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27974378 27974378]; doi: [https://dx.doi.org/10.15252/embr.201643353 10.15252/embr.201643353]; GPMDB: [http://gpmdb.org/data/keyword/27974378 44]. | ||
#Choi M, Eren-Dogu ZF, Colangelo CM, Cottrell JS, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O, (2016) "ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experiments." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27990823 27990823]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00881 10.1021/acs.jproteome.6b00881]; GPMDB: [http://gpmdb.org/data/keyword/27990823 12]. | #Choi M, Eren-Dogu ZF, Colangelo CM, Cottrell JS, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O, (2016) "ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experiments." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27990823 27990823]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00881 10.1021/acs.jproteome.6b00881]; GPMDB: [http://gpmdb.org/data/keyword/27990823 12]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a 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 January 1 25, 2017.