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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 February | + | 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 February 26, 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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#Sprung RW Jr, Brock JW, Tanksley JP, Li M, Washington MK, Slebos RJ, Liebler DC, (2009) "Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis." <i>Mol Cell Proteomics</i> <b>8</b>(8):1988–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19467989 19467989]; doi: [https://dx.doi.org/10.1074/mcp.M800518-MCP200 10.1074/mcp.M800518-MCP200]; GPMDB: [http://gpmdb.org/data/keyword/19467989 230]. | #Sprung RW Jr, Brock JW, Tanksley JP, Li M, Washington MK, Slebos RJ, Liebler DC, (2009) "Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis." <i>Mol Cell Proteomics</i> <b>8</b>(8):1988–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19467989 19467989]; doi: [https://dx.doi.org/10.1074/mcp.M800518-MCP200 10.1074/mcp.M800518-MCP200]; GPMDB: [http://gpmdb.org/data/keyword/19467989 230]. | ||
#Burkard ME, Maciejowski J, Rodriguez-Bravo V, Repka M, Lowery DM, Clauser KR, Zhang C, Shokat KM, Carr SA, Yaffe MB, Jallepalli PV, (2009) "Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells." <i>PLoS Biol</i> <b>7</b>(5):e1000111; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19468302 19468302]; doi: [https://dx.doi.org/10.1371/journal.pbio.1000111 10.1371/journal.pbio.1000111]; GPMDB: [http://gpmdb.org/data/keyword/19468302 1]. | #Burkard ME, Maciejowski J, Rodriguez-Bravo V, Repka M, Lowery DM, Clauser KR, Zhang C, Shokat KM, Carr SA, Yaffe MB, Jallepalli PV, (2009) "Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells." <i>PLoS Biol</i> <b>7</b>(5):e1000111; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19468302 19468302]; doi: [https://dx.doi.org/10.1371/journal.pbio.1000111 10.1371/journal.pbio.1000111]; GPMDB: [http://gpmdb.org/data/keyword/19468302 1]. | ||
- | # () "" <i></i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/ ]; GPMDB: [http://gpmdb.org/data/keyword/ | + | #Samaee SM, Lahnsteiner F, Giménez G, Estévez A, Sarg B, Lindner H, (2009) "Quantitative composition of vitellogenin-derived yolk proteins and their effects on viability of embryos and larvae of common dentex (Dentex dentex), a marine pelagophil teleost." <i>J Exp Zool A Ecol Genet Physiol</i> <b>311</b>(7):504–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19492308 19492308]; doi: [https://dx.doi.org/10.1002/jez.548 10.1002/jez.548]; GPMDB: [http://gpmdb.org/data/keyword/19492308 4]. |
#Ma ZQ, Dasari S, Chambers MC, Litton MD, Sobecki SM, Zimmerman LJ, Halvey PJ, Schilling B, Drake PM, Gibson BW, Tabb DL, (2009) "IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering." <i>J Proteome Res</i> <b>8</b>(8):3872–81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19522537 19522537]; doi: [https://dx.doi.org/10.1021/pr900360j 10.1021/pr900360j]; GPMDB: [http://gpmdb.org/data/keyword/19522537 18]. | #Ma ZQ, Dasari S, Chambers MC, Litton MD, Sobecki SM, Zimmerman LJ, Halvey PJ, Schilling B, Drake PM, Gibson BW, Tabb DL, (2009) "IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering." <i>J Proteome Res</i> <b>8</b>(8):3872–81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19522537 19522537]; doi: [https://dx.doi.org/10.1021/pr900360j 10.1021/pr900360j]; GPMDB: [http://gpmdb.org/data/keyword/19522537 18]. | ||
#Shi L, Chowdhury SM, Smallwood HS, Yoon H, Mottaz-Brewer HM, Norbeck AD, McDermott JE, Clauss TR, Heffron F, Smith RD, Adkins JN, (2009) "Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica." <i>Infect Immun</i> <b>77</b>(8):3227–33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19528222 19528222]; doi: [https://dx.doi.org/10.1128/IAI.00063-09 10.1128/IAI.00063-09]; GPMDB: [http://gpmdb.org/data/keyword/19528222 29]. | #Shi L, Chowdhury SM, Smallwood HS, Yoon H, Mottaz-Brewer HM, Norbeck AD, McDermott JE, Clauss TR, Heffron F, Smith RD, Adkins JN, (2009) "Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica." <i>Infect Immun</i> <b>77</b>(8):3227–33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19528222 19528222]; doi: [https://dx.doi.org/10.1128/IAI.00063-09 10.1128/IAI.00063-09]; GPMDB: [http://gpmdb.org/data/keyword/19528222 29]. | ||
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#Nishtala K, Phong TQ, Steil L, Sauter M, Salazar MG, Kandolf R, Kroemer HK, Felix SB, Völker U, Klingel K, Hammer E, (2011) "Virus-induced dilated cardiomyopathy is characterized by increased levels of fibrotic extracellular matrix proteins and reduced amounts of energy-producing enzymes." <i>Proteomics</i> <b>11</b>(22):4310–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21954127 21954127]; doi: [https://dx.doi.org/10.1002/pmic.201100229 10.1002/pmic.201100229]; GPMDB: [http://gpmdb.org/data/keyword/21954127 91]. | #Nishtala K, Phong TQ, Steil L, Sauter M, Salazar MG, Kandolf R, Kroemer HK, Felix SB, Völker U, Klingel K, Hammer E, (2011) "Virus-induced dilated cardiomyopathy is characterized by increased levels of fibrotic extracellular matrix proteins and reduced amounts of energy-producing enzymes." <i>Proteomics</i> <b>11</b>(22):4310–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21954127 21954127]; doi: [https://dx.doi.org/10.1002/pmic.201100229 10.1002/pmic.201100229]; GPMDB: [http://gpmdb.org/data/keyword/21954127 91]. | ||
#Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M, (2012) "A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines." <i>Mol Cell Proteomics</i> <b>11</b>(3):O111.009613; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21964433 21964433]; doi: [https://dx.doi.org/10.1074/mcp.O111.009613 10.1074/mcp.O111.009613]; GPMDB: [http://gpmdb.org/data/keyword/21964433 138]. | #Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M, (2012) "A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines." <i>Mol Cell Proteomics</i> <b>11</b>(3):O111.009613; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21964433 21964433]; doi: [https://dx.doi.org/10.1074/mcp.O111.009613 10.1074/mcp.O111.009613]; GPMDB: [http://gpmdb.org/data/keyword/21964433 138]. | ||
- | # () "" <i></i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/ ]; GPMDB: [http://gpmdb.org/data/keyword/ | + | #Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, Yadav AK, Shrivastava P, Marimuthu A, Anand S, Sundaram H, Kingsbury R, Harsha HC, Nair B, Prasad TS, Chauhan DS, Katoch K, Katoch VM, Kumar P, Chaerkady R, Ramachandran S, Dash D, Pandey A, (2011) "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry." <i>Mol Cell Proteomics</i> <b>10</b>(12):M111.011627; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21969609 21969609]; doi: [https://dx.doi.org/10.1074/mcp.M111.011445 10.1074/mcp.M111.011445]; GPMDB: [http://gpmdb.org/data/keyword/21969609 52]. |
#Burgener A, Rahman S, Ahmad R, Lajoie J, Ramdahin S, Mesa C, Brunet S, Wachihi C, Kimani J, Fowke K, Carr S, Plummer F, Ball TB, (2011) "Comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers." <i>J Proteome Res</i> <b>10</b>(11):5139–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21973077 21973077]; doi: [https://dx.doi.org/10.1021/pr200596r 10.1021/pr200596r]; GPMDB: [http://gpmdb.org/data/keyword/21973077 6]. | #Burgener A, Rahman S, Ahmad R, Lajoie J, Ramdahin S, Mesa C, Brunet S, Wachihi C, Kimani J, Fowke K, Carr S, Plummer F, Ball TB, (2011) "Comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers." <i>J Proteome Res</i> <b>10</b>(11):5139–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21973077 21973077]; doi: [https://dx.doi.org/10.1021/pr200596r 10.1021/pr200596r]; GPMDB: [http://gpmdb.org/data/keyword/21973077 6]. | ||
#Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ, (2011) "Proteomic and phosphoproteomic comparison of human ES and iPS cells." <i>Nat Methods</i> <b>8</b>(10):821–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21983960 21983960]; doi: [https://dx.doi.org/10.1038/nmeth.1699 10.1038/nmeth.1699]; GPMDB: [http://gpmdb.org/data/keyword/21983960 88]. | #Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ, (2011) "Proteomic and phosphoproteomic comparison of human ES and iPS cells." <i>Nat Methods</i> <b>8</b>(10):821–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/21983960 21983960]; doi: [https://dx.doi.org/10.1038/nmeth.1699 10.1038/nmeth.1699]; GPMDB: [http://gpmdb.org/data/keyword/21983960 88]. | ||
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#Grundner-Culemann K, Dybowski JN, Klammer M, Tebbe A, Schaab C, Daub H, (2016) "Comparative proteome analysis across non-small cell lung cancer cell lines." <i>J Proteomics</i> <b>130</b>:1–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26361996 26361996]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.09.003 10.1016/j.jprot.2015.09.003]; GPMDB: [http://gpmdb.org/data/keyword/26361996 23]. | #Grundner-Culemann K, Dybowski JN, Klammer M, Tebbe A, Schaab C, Daub H, (2016) "Comparative proteome analysis across non-small cell lung cancer cell lines." <i>J Proteomics</i> <b>130</b>:1–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26361996 26361996]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.09.003 10.1016/j.jprot.2015.09.003]; GPMDB: [http://gpmdb.org/data/keyword/26361996 23]. | ||
#Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M, Obermayer B, (2015) "Extensive identification and analysis of conserved small ORFs in animals." <i>Genome Biol</i> <b>16</b>:179; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26364619 26364619]; doi: [https://dx.doi.org/10.1186/s13059-015-0742-x 10.1186/s13059-015-0742-x]; GPMDB: [http://gpmdb.org/data/keyword/26364619 19]. | #Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M, Obermayer B, (2015) "Extensive identification and analysis of conserved small ORFs in animals." <i>Genome Biol</i> <b>16</b>:179; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26364619 26364619]; doi: [https://dx.doi.org/10.1186/s13059-015-0742-x 10.1186/s13059-015-0742-x]; GPMDB: [http://gpmdb.org/data/keyword/26364619 19]. | ||
+ | #Preil SA, Kristensen LP, Beck HC, Jensen PS, Nielsen PS, Steiniche T, Bjørling-Poulsen M, Larsen MR, Hansen ML, Rasmussen LM, (2015) "Quantitative Proteome Analysis Reveals Increased Content of Basement Membrane Proteins in Arteries From Patients With Type 2 Diabetes Mellitus and Lower Levels Among Metformin Users." <i>Circ Cardiovasc Genet</i> <b>8</b>(5):727–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26371159 26371159]; doi: [https://dx.doi.org/10.1161/CIRCGENETICS.115.001165 10.1161/CIRCGENETICS.115.001165]; GPMDB: [http://gpmdb.org/data/keyword/26371159 16]. | ||
#Lin MH, Sugiyama N, Ishihama Y, (2015) "Systematic profiling of the bacterial phosphoproteome reveals bacterium-specific features of phosphorylation." <i>Sci Signal</i> <b>8</b>(394):rs10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26373674 26373674]; doi: [https://dx.doi.org/10.1126/scisignal.aaa3117 10.1126/scisignal.aaa3117]; GPMDB: [http://gpmdb.org/data/keyword/26373674 73]. | #Lin MH, Sugiyama N, Ishihama Y, (2015) "Systematic profiling of the bacterial phosphoproteome reveals bacterium-specific features of phosphorylation." <i>Sci Signal</i> <b>8</b>(394):rs10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26373674 26373674]; doi: [https://dx.doi.org/10.1126/scisignal.aaa3117 10.1126/scisignal.aaa3117]; GPMDB: [http://gpmdb.org/data/keyword/26373674 73]. | ||
#Park AJ, Murphy K, Surette MD, Bandoro C, Krieger JR, Taylor P, Khursigara CM, (2015) "Tracking the Dynamic Relationship between Cellular Systems and Extracellular Subproteomes in Pseudomonas aeruginosa Biofilms." <i>J Proteome Res</i> <b>14</b>(11):4524–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26378716 26378716]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00262 10.1021/acs.jproteome.5b00262]; GPMDB: [http://gpmdb.org/data/keyword/26378716 34]. | #Park AJ, Murphy K, Surette MD, Bandoro C, Krieger JR, Taylor P, Khursigara CM, (2015) "Tracking the Dynamic Relationship between Cellular Systems and Extracellular Subproteomes in Pseudomonas aeruginosa Biofilms." <i>J Proteome Res</i> <b>14</b>(11):4524–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26378716 26378716]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00262 10.1021/acs.jproteome.5b00262]; GPMDB: [http://gpmdb.org/data/keyword/26378716 34]. | ||
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#Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S, (2016) "Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains." <i>Mol Cell</i> <b>61</b>(1):125–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26711008 26711008]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.11.016 10.1016/j.molcel.2015.11.016]; GPMDB: [http://gpmdb.org/data/keyword/26711008 44]. | #Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S, (2016) "Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains." <i>Mol Cell</i> <b>61</b>(1):125–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26711008 26711008]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.11.016 10.1016/j.molcel.2015.11.016]; GPMDB: [http://gpmdb.org/data/keyword/26711008 44]. | ||
#Vartanian S, Ma TP, Lee J, Haverty PM, Kirkpatrick DS, Yu K, Stokoe D, (2016) "Application of Mass Spectrometry Profiling to Establish Brusatol as an Inhibitor of Global Protein Synthesis." <i>Mol Cell Proteomics</i> <b>15</b>(4):1220–31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26711467 26711467]; doi: [https://dx.doi.org/10.1074/mcp.M115.055509 10.1074/mcp.M115.055509]; GPMDB: [http://gpmdb.org/data/keyword/26711467 4]. | #Vartanian S, Ma TP, Lee J, Haverty PM, Kirkpatrick DS, Yu K, Stokoe D, (2016) "Application of Mass Spectrometry Profiling to Establish Brusatol as an Inhibitor of Global Protein Synthesis." <i>Mol Cell Proteomics</i> <b>15</b>(4):1220–31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26711467 26711467]; doi: [https://dx.doi.org/10.1074/mcp.M115.055509 10.1074/mcp.M115.055509]; GPMDB: [http://gpmdb.org/data/keyword/26711467 4]. | ||
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#Bode D, Yu L, Tate P, Pardo M, Choudhary J, (2016) "Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells." <i>Mol Cell Proteomics</i> <b>15</b>(3):878–91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26714524 26714524]; doi: [https://dx.doi.org/10.1074/mcp.M115.053207 10.1074/mcp.M115.053207]; GPMDB: [http://gpmdb.org/data/keyword/26714524 179]. | #Bode D, Yu L, Tate P, Pardo M, Choudhary J, (2016) "Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells." <i>Mol Cell Proteomics</i> <b>15</b>(3):878–91; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26714524 26714524]; doi: [https://dx.doi.org/10.1074/mcp.M115.053207 10.1074/mcp.M115.053207]; GPMDB: [http://gpmdb.org/data/keyword/26714524 179]. | ||
#McAfee A, Harpur BA, Michaud S, Beavis RC, Kent CF, Zayed A, Foster LJ, (2016) "Toward an Upgraded Honey Bee (Apis mellifera L.) Genome Annotation Using Proteogenomics." <i>J Proteome Res</i> <b>15</b>(2):411–21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26718741 26718741]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00589 10.1021/acs.jproteome.5b00589]; GPMDB: [http://gpmdb.org/data/keyword/26718741 27]. | #McAfee A, Harpur BA, Michaud S, Beavis RC, Kent CF, Zayed A, Foster LJ, (2016) "Toward an Upgraded Honey Bee (Apis mellifera L.) Genome Annotation Using Proteogenomics." <i>J Proteome Res</i> <b>15</b>(2):411–21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26718741 26718741]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00589 10.1021/acs.jproteome.5b00589]; GPMDB: [http://gpmdb.org/data/keyword/26718741 27]. | ||
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#Kristensen TN, Kjeldal H, Schou MF, Nielsen JL, (2016) "Proteomic data reveal a physiological basis for costs and benefits associated with thermal acclimation." <i>J Exp Biol</i> <b>219</b>(Pt 7):969–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26823104 26823104]; doi: [https://dx.doi.org/10.1242/jeb.132696 10.1242/jeb.132696]; GPMDB: [http://gpmdb.org/data/keyword/26823104 9]. | #Kristensen TN, Kjeldal H, Schou MF, Nielsen JL, (2016) "Proteomic data reveal a physiological basis for costs and benefits associated with thermal acclimation." <i>J Exp Biol</i> <b>219</b>(Pt 7):969–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26823104 26823104]; doi: [https://dx.doi.org/10.1242/jeb.132696 10.1242/jeb.132696]; GPMDB: [http://gpmdb.org/data/keyword/26823104 9]. | ||
#Steger M, Tonelli F, Ito G, Davies P, Trost M, Vetter M, Wachter S, Lorentzen E, Duddy G, Wilson S, Baptista MA, Fiske BK, Fell MJ, Morrow JA, Reith AD, Alessi DR, Mann M, (2016) "Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26824392 26824392]; doi: [https://dx.doi.org/10.7554/eLife.12813 10.7554/eLife.12813]; GPMDB: [http://gpmdb.org/data/keyword/26824392 216]. | #Steger M, Tonelli F, Ito G, Davies P, Trost M, Vetter M, Wachter S, Lorentzen E, Duddy G, Wilson S, Baptista MA, Fiske BK, Fell MJ, Morrow JA, Reith AD, Alessi DR, Mann M, (2016) "Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26824392 26824392]; doi: [https://dx.doi.org/10.7554/eLife.12813 10.7554/eLife.12813]; GPMDB: [http://gpmdb.org/data/keyword/26824392 216]. | ||
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#Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE, (2016) "Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases." <i>Cell Rep</i> <b>14</b>(5):1049–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832403 26832403]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.01.009 10.1016/j.celrep.2016.01.009]; GPMDB: [http://gpmdb.org/data/keyword/26832403 486]. | #Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE, (2016) "Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases." <i>Cell Rep</i> <b>14</b>(5):1049–61; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832403 26832403]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.01.009 10.1016/j.celrep.2016.01.009]; GPMDB: [http://gpmdb.org/data/keyword/26832403 486]. | ||
#Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE, (2016) "miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells." <i>Cancer Cell</i> <b>29</b>(2):214–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832662 26832662]; doi: [https://dx.doi.org/10.1016/j.ccell.2015.12.011 10.1016/j.ccell.2015.12.011]; GPMDB: [http://gpmdb.org/data/keyword/26832662 72]. | #Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE, (2016) "miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells." <i>Cancer Cell</i> <b>29</b>(2):214–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26832662 26832662]; doi: [https://dx.doi.org/10.1016/j.ccell.2015.12.011 10.1016/j.ccell.2015.12.011]; GPMDB: [http://gpmdb.org/data/keyword/26832662 72]. | ||
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#Xu B, Gao Y, Zhan S, Xiong F, Qiu W, Qian X, Wang T, Wang N, Zhang D, Yang Q, Wang R, Bao X, Dou W, Tian R, Meng S, Gai WP, Huang Y, Yan XX, Ge W, Ma C, (2016) "Quantitative protein profiling of hippocampus during human aging." <i>Neurobiol Aging</i> <b>39</b>:46–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26923401 26923401]; doi: [https://dx.doi.org/10.1016/j.neurobiolaging.2015.11.029 10.1016/j.neurobiolaging.2015.11.029]; GPMDB: [http://gpmdb.org/data/keyword/26923401 20]. | #Xu B, Gao Y, Zhan S, Xiong F, Qiu W, Qian X, Wang T, Wang N, Zhang D, Yang Q, Wang R, Bao X, Dou W, Tian R, Meng S, Gai WP, Huang Y, Yan XX, Ge W, Ma C, (2016) "Quantitative protein profiling of hippocampus during human aging." <i>Neurobiol Aging</i> <b>39</b>:46–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26923401 26923401]; doi: [https://dx.doi.org/10.1016/j.neurobiolaging.2015.11.029 10.1016/j.neurobiolaging.2015.11.029]; GPMDB: [http://gpmdb.org/data/keyword/26923401 20]. | ||
#Reddy RJ, Gajadhar AS, Swenson EJ, Rothenberg DA, Curran TG, White FM, (2016) "Early signaling dynamics of the epidermal growth factor receptor." <i>Proc Natl Acad Sci U S A</i> <b>113</b>(11):3114–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26929352 26929352]; doi: [https://dx.doi.org/10.1073/pnas.1521288113 10.1073/pnas.1521288113]; GPMDB: [http://gpmdb.org/data/keyword/26929352 30]. | #Reddy RJ, Gajadhar AS, Swenson EJ, Rothenberg DA, Curran TG, White FM, (2016) "Early signaling dynamics of the epidermal growth factor receptor." <i>Proc Natl Acad Sci U S A</i> <b>113</b>(11):3114–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26929352 26929352]; doi: [https://dx.doi.org/10.1073/pnas.1521288113 10.1073/pnas.1521288113]; GPMDB: [http://gpmdb.org/data/keyword/26929352 30]. | ||
+ | #Bigenzahn JW, Fauster A, Rebsamen M, Kandasamy RK, Scorzoni S, Vladimer GI, Müller AC, Gstaiger M, Zuber J, Bennett KL, Superti-Furga G, (2016) "An Inducible Retroviral Expression System for Tandem Affinity Purification Mass-Spectrometry-Based Proteomics Identifies Mixed Lineage Kinase Domain-like Protein (MLKL) as an Heat Shock Protein 90 (HSP90) Client." <i>Mol Cell Proteomics</i> <b>15</b>(3):1139–50; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26933192 26933192]; doi: [https://dx.doi.org/10.1074/mcp.O115.055350 10.1074/mcp.O115.055350 ]; GPMDB: [http://gpmdb.org/data/keyword/26933192 16]. | ||
#de Torre-Minguela C, Barberà-Cremades M, Gómez AI, Martín-Sánchez F, Pelegrín P, (2016) "Macrophage activation and polarization modify P2X7 receptor secretome influencing the inflammatory process." <i>Sci Rep</i> <b>6</b>:22586; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26935289 26935289]; doi: [https://dx.doi.org/10.1038/srep22586 10.1038/srep22586]; GPMDB: [http://gpmdb.org/data/keyword/26935289 118]. | #de Torre-Minguela C, Barberà-Cremades M, Gómez AI, Martín-Sánchez F, Pelegrín P, (2016) "Macrophage activation and polarization modify P2X7 receptor secretome influencing the inflammatory process." <i>Sci Rep</i> <b>6</b>:22586; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26935289 26935289]; doi: [https://dx.doi.org/10.1038/srep22586 10.1038/srep22586]; GPMDB: [http://gpmdb.org/data/keyword/26935289 118]. | ||
#Ly A, Merl-Pham J, Priller M, Gruhn F, Senninger N, Ueffing M, Hauck SM, (2016) "Proteomic Profiling Suggests Central Role Of STAT Signaling during Retinal Degeneration in the rd10 Mouse Model." <i>J Proteome Res</i> <b>15</b>(4):1350–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26939627 26939627]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00111 10.1021/acs.jproteome.6b00111]; GPMDB: [http://gpmdb.org/data/keyword/26939627 24]. | #Ly A, Merl-Pham J, Priller M, Gruhn F, Senninger N, Ueffing M, Hauck SM, (2016) "Proteomic Profiling Suggests Central Role Of STAT Signaling during Retinal Degeneration in the rd10 Mouse Model." <i>J Proteome Res</i> <b>15</b>(4):1350–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26939627 26939627]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00111 10.1021/acs.jproteome.6b00111]; GPMDB: [http://gpmdb.org/data/keyword/26939627 24]. | ||
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#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]. | #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]. | ||
+ | #Chen Z, Tran M, Tang M, Wang W, Gong Z, Chen J, (2016) "Proteomic Analysis Reveals a Novel Mutator S (MutS) Partner Involved in Mismatch Repair Pathway." <i>Mol Cell Proteomics</i> <b>15</b>(4):1299–308; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27037360 27037360]; doi: [https://dx.doi.org/10.1074/mcp.M115.056093 10.1074/mcp.M115.056093 ]; GPMDB: [http://gpmdb.org/data/keyword/27037360 22]. | ||
#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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#St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JD, Rajendran D, Couzens AL, Currie KW, Tkach JM, Cheung SW, Pelletier L, Gingras AC, (2016) "Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators." <i>Cell Rep</i> <b>17</b>(9):2488–2501; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27880917 27880917]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.10.078 10.1016/j.celrep.2016.10.078]; GPMDB: [http://gpmdb.org/data/keyword/27880917 315]. | #St-Denis N, Gupta GD, Lin ZY, Gonzalez-Badillo B, Veri AO, Knight JD, Rajendran D, Couzens AL, Currie KW, Tkach JM, Cheung SW, Pelletier L, Gingras AC, (2016) "Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators." <i>Cell Rep</i> <b>17</b>(9):2488–2501; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27880917 27880917]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.10.078 10.1016/j.celrep.2016.10.078]; GPMDB: [http://gpmdb.org/data/keyword/27880917 315]. | ||
#Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." <i>Nat Commun</i> <b>7</b>:13595; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27882920 27882920]; doi: [https://dx.doi.org/10.1038/ncomms13595 10.1038/ncomms13595]; GPMDB: [http://gpmdb.org/data/keyword/27882920 9]. | #Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." <i>Nat Commun</i> <b>7</b>:13595; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27882920 27882920]; doi: [https://dx.doi.org/10.1038/ncomms13595 10.1038/ncomms13595]; GPMDB: [http://gpmdb.org/data/keyword/27882920 9]. | ||
+ | #Hurwitz SN, Rider MA, Bundy JL, Liu X, Singh RK, Meckes DG Jr, (2016) "Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers." <i>Oncotarget</i> <b>7</b>(52):86999–87015; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27894104 27894104]; doi: [https://dx.doi.org/10.18632/oncotarget.13569 10.18632/oncotarget.13569]; GPMDB: [http://gpmdb.org/data/keyword/27894104 898]. | ||
#Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT, (2016) "A proteomic approach to analyse the aspirin-mediated lysine acetylome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27913581 27913581]; doi: [https://dx.doi.org/10.1074/mcp.O116.065219 10.1074/mcp.O116.065219]; GPMDB: [http://gpmdb.org/data/keyword/27913581 40]. | #Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT, (2016) "A proteomic approach to analyse the aspirin-mediated lysine acetylome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27913581 27913581]; doi: [https://dx.doi.org/10.1074/mcp.O116.065219 10.1074/mcp.O116.065219]; GPMDB: [http://gpmdb.org/data/keyword/27913581 40]. | ||
#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]. | ||
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#Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ, (2017) "Interactome disassembly during apoptosis occurs independent of caspase cleavage." <i>Mol Syst Biol</i> <b>13</b>(1):906; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28082348 28082348]; GPMDB: [http://gpmdb.org/data/keyword/28082348 521]. | #Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ, (2017) "Interactome disassembly during apoptosis occurs independent of caspase cleavage." <i>Mol Syst Biol</i> <b>13</b>(1):906; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28082348 28082348]; GPMDB: [http://gpmdb.org/data/keyword/28082348 521]. | ||
#Emmott E, Sorgeloos F, Caddy SL, Vashist S, Sosnovtsev S, Lloyd R, Heesom K, Locker N, Goodfellow I, (2017) "Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087593 28087593]; doi: [https://dx.doi.org/10.1074/mcp.M116.062448 10.1074/mcp.M116.062448]; GPMDB: [http://gpmdb.org/data/keyword/28087593 3]. | #Emmott E, Sorgeloos F, Caddy SL, Vashist S, Sosnovtsev S, Lloyd R, Heesom K, Locker N, Goodfellow I, (2017) "Norovirus-mediated modification of the translational landscape via virus and host-induced cleavage of translation initiation factors." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087593 28087593]; doi: [https://dx.doi.org/10.1074/mcp.M116.062448 10.1074/mcp.M116.062448]; GPMDB: [http://gpmdb.org/data/keyword/28087593 3]. | ||
+ | #Niklasson M, Maddalo G, Sramkova Z, Mutlu E, Wee S, Sekyrova P, Schmidt L, Fritz N, Dehnisch I, Kyriatzis G, Krafcikova M, Carson BB, Feenstra J, Marinescu VD, Segerman A, Haraldsson M, Gustavsson AL, Hammarström LG, Jenmalm-Jensen A, Uhrbom L, Altelaar AF, Linnarsson S, Uhlén P, Trantirek L, Vincent CT, Nelander S, Enger PØ, Andäng M, (2017) "Membrane-depolarizing channel blockers induce selective glioma cell death by impairing nutrient transport and unfolded protein/amino acid responses." <i>Cancer Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28087597 28087597]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-16-2274 10.1158/0008-5472.CAN-16-2274]; GPMDB: [http://gpmdb.org/data/keyword/28087597 2]. | ||
#Riesner K, Shi Y, Jacobi A, Kraeter M, Kalupa M, McGearey A, Mertlitz S, Cordes S, Schrezenmeier JF, Mengwasser J, Westphal S, Perez-Hernandez D, Schmitt C, Dittmar G, Guck J, Penack O, (2017) "Initiation of acute graft-versus-host disease by angiogenesis." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096092 28096092]; doi: [https://dx.doi.org/10.1182/blood-2016-08-736314 10.1182/blood-2016-08-736314]; GPMDB: [http://gpmdb.org/data/keyword/28096092 1]. | #Riesner K, Shi Y, Jacobi A, Kraeter M, Kalupa M, McGearey A, Mertlitz S, Cordes S, Schrezenmeier JF, Mengwasser J, Westphal S, Perez-Hernandez D, Schmitt C, Dittmar G, Guck J, Penack O, (2017) "Initiation of acute graft-versus-host disease by angiogenesis." <i>Blood</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096092 28096092]; doi: [https://dx.doi.org/10.1182/blood-2016-08-736314 10.1182/blood-2016-08-736314]; GPMDB: [http://gpmdb.org/data/keyword/28096092 1]. | ||
#Princz LN, Wild P, Bittmann J, Aguado FJ, Blanco MG, Matos J, Pfander B, (2017) "Dbf4-dependent kinase and the Rtt107 scaffold promote Mus81-Mms4 resolvase activation during mitosis." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096179 28096179]; doi: [https://dx.doi.org/10.15252/embj.201694831 10.15252/embj.201694831]; GPMDB: [http://gpmdb.org/data/keyword/28096179 130]. | #Princz LN, Wild P, Bittmann J, Aguado FJ, Blanco MG, Matos J, Pfander B, (2017) "Dbf4-dependent kinase and the Rtt107 scaffold promote Mus81-Mms4 resolvase activation during mitosis." <i>EMBO J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096179 28096179]; doi: [https://dx.doi.org/10.15252/embj.201694831 10.15252/embj.201694831]; GPMDB: [http://gpmdb.org/data/keyword/28096179 130]. | ||
#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: [http://gpmdb.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: [http://gpmdb.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: [http://gpmdb.org/data/keyword/28111465 10]. | ||
#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: [http://gpmdb.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: [http://gpmdb.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: [http://gpmdb.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: [http://gpmdb.org/data/keyword/28114419 24]. | ||
#Glisovic-Aplenc T, Gill S, Spruce LA, Smith IR, Fazelinia H, Shestova O, Ding H, Tasian SK, Aplenc R, Seeholzer SH, (2017) "Improved plasma membrane proteome coverage with a label-free non-affinity-purified workflow." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28116781 28116781]; doi: [https://dx.doi.org/10.1002/pmic.201600344 10.1002/pmic.201600344]; GPMDB: [http://gpmdb.org/data/keyword/28116781 41]. | #Glisovic-Aplenc T, Gill S, Spruce LA, Smith IR, Fazelinia H, Shestova O, Ding H, Tasian SK, Aplenc R, Seeholzer SH, (2017) "Improved plasma membrane proteome coverage with a label-free non-affinity-purified workflow." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28116781 28116781]; doi: [https://dx.doi.org/10.1002/pmic.201600344 10.1002/pmic.201600344]; GPMDB: [http://gpmdb.org/data/keyword/28116781 41]. | ||
- | #Kulak NA, Geyer PE, Mann M, (2017) "Loss-less nano-fractionator for high sensitivity, high coverage proteomics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28126900 28126900]; doi: [https://dx.doi.org/10.1074/mcp.O116.065136 10.1074/mcp.O116.065136]; GPMDB: [http://gpmdb.org/data/keyword/28126900 | + | #Kulak NA, Geyer PE, Mann M, (2017) "Loss-less nano-fractionator for high sensitivity, high coverage proteomics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28126900 28126900]; doi: [https://dx.doi.org/10.1074/mcp.O116.065136 10.1074/mcp.O116.065136]; GPMDB: [http://gpmdb.org/data/keyword/28126900 60]. |
#Yu Y, Kwon K, Tsitrin T, Bekele S, Sikorski P, Nelson KE, Pieper R, (2017) "Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections." <i>PLoS Pathog</i> <b>13</b>(1):e1006151; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28129394 28129394]; doi: [https://dx.doi.org/10.1371/journal.ppat.1006151 10.1371/journal.ppat.1006151]; GPMDB: [http://gpmdb.org/data/keyword/28129394 72]. | #Yu Y, Kwon K, Tsitrin T, Bekele S, Sikorski P, Nelson KE, Pieper R, (2017) "Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections." <i>PLoS Pathog</i> <b>13</b>(1):e1006151; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28129394 28129394]; doi: [https://dx.doi.org/10.1371/journal.ppat.1006151 10.1371/journal.ppat.1006151]; GPMDB: [http://gpmdb.org/data/keyword/28129394 72]. | ||
#Godfrey M, Touati SA, Kataria M, Jones A, Snijders AP, Uhlmann F, (2017) "PP2A<sup>Cdc55</sup> Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation." <i>Mol Cell</i> <b>65</b>(3):393–402.e3; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132839 28132839]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.12.018 10.1016/j.molcel.2016.12.018]; GPMDB: [http://gpmdb.org/data/keyword/28132839 120]. | #Godfrey M, Touati SA, Kataria M, Jones A, Snijders AP, Uhlmann F, (2017) "PP2A<sup>Cdc55</sup> Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation." <i>Mol Cell</i> <b>65</b>(3):393–402.e3; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132839 28132839]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.12.018 10.1016/j.molcel.2016.12.018]; GPMDB: [http://gpmdb.org/data/keyword/28132839 120]. | ||
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#Park YJ, Koh J, Kwon JT, Park YS, Yang L, Cha S, (2017) "Uncovering stem cell differentiation factors for salivary gland regeneration by quantitative analysis of differential proteomes." <i>PLoS One</i> <b>12</b>(2):e0169677; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28158262 28158262]; doi: [https://dx.doi.org/10.1371/journal.pone.0169677 10.1371/journal.pone.0169677]; GPMDB: [http://gpmdb.org/data/keyword/28158262 2]. | #Park YJ, Koh J, Kwon JT, Park YS, Yang L, Cha S, (2017) "Uncovering stem cell differentiation factors for salivary gland regeneration by quantitative analysis of differential proteomes." <i>PLoS One</i> <b>12</b>(2):e0169677; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28158262 28158262]; doi: [https://dx.doi.org/10.1371/journal.pone.0169677 10.1371/journal.pone.0169677]; GPMDB: [http://gpmdb.org/data/keyword/28158262 2]. | ||
#Davis S, Charles PD, He L, Mowlds P, Kessler BM, Fischer R, (2017) "Expanding proteome coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) combined with broad specificity proteolysis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28164708 28164708]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00915 10.1021/acs.jproteome.6b00915]; GPMDB: [http://gpmdb.org/data/keyword/28164708 7]. | #Davis S, Charles PD, He L, Mowlds P, Kessler BM, Fischer R, (2017) "Expanding proteome coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) combined with broad specificity proteolysis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28164708 28164708]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00915 10.1021/acs.jproteome.6b00915]; GPMDB: [http://gpmdb.org/data/keyword/28164708 7]. | ||
+ | #Kalkan T, Olova N, Roode M, Mulas C, Lee HJ, Nett I, Marks H, Walker R, Stunnenberg HG, Lilley KS, Nichols J, Reik W, Bertone P, Smith A, (2017) "Tracking the embryonic stem cell transition from ground state pluripotency." <i>Development</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28174249 28174249]; doi: [https://dx.doi.org/10.1242/dev.142711 10.1242/dev.142711]; GPMDB: [http://gpmdb.org/data/keyword/28174249 6]. | ||
+ | #Massafra V, Milona A, Vos HR, Burgering BM, van Mil SW, (2017) "Quantitative liver proteomics identifies FGF19 targets that couple metabolism and proliferation." <i>PLoS One</i> <b>12</b>(2):e0171185; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28178326 28178326]; doi: [https://dx.doi.org/10.1371/journal.pone.0171185 10.1371/journal.pone.0171185]; GPMDB: [http://gpmdb.org/data/keyword/28178326 9]. | ||
+ | #Kulej K, Avgousti DC, Sidoli S, Herrmann C, Della Fera AN, Kim ET, Garcia BA, Weitzman MD, (2017) "Time-resolved global and chromatin proteomics during herpes simplex virus (HSV-1) infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28179408 28179408]; doi: [https://dx.doi.org/10.1074/mcp.M116.065987 10.1074/mcp.M116.065987]; GPMDB: [http://gpmdb.org/data/keyword/28179408 32]. | ||
#Schm Oumllders J, Manske C, Otto A, Hoffmann C, Steiner B, Welin A, Becher DO, Hilbi H, (2017) "Comparative proteomics of purified pathogen vacuoles correlates intracellular replication of <i>Legionella pneumophila</i> with the small GTPase Rap1." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28183814 28183814]; doi: [https://dx.doi.org/10.1074/mcp.M116.063453 10.1074/mcp.M116.063453]; GPMDB: [http://gpmdb.org/data/keyword/28183814 118]. | #Schm Oumllders J, Manske C, Otto A, Hoffmann C, Steiner B, Welin A, Becher DO, Hilbi H, (2017) "Comparative proteomics of purified pathogen vacuoles correlates intracellular replication of <i>Legionella pneumophila</i> with the small GTPase Rap1." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28183814 28183814]; doi: [https://dx.doi.org/10.1074/mcp.M116.063453 10.1074/mcp.M116.063453]; GPMDB: [http://gpmdb.org/data/keyword/28183814 118]. | ||
- | #Fielding CA, Weekes MP, Nobre LV, Ruckova E, Wilkie GS, Paulo JA, Chang C, Suárez NM, Davies JA, Antrobus R, Stanton RJ, Aicheler RJ, Nichols H, Vojtesek B, Trowsdale J, Davison AJ, Gygi SP, Tomasec P, Lehner PJ, Wilkinson GW, (2017) "Control of immune ligands by members of a cytomegalovirus gene expansion suppresses natural killer cell activation." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28186488 28186488]; doi: [https://dx.doi.org/10.7554/eLife.22206 10.7554/eLife.22206]; GPMDB: [http://gpmdb.org/data/keyword/28186488 | + | #Fielding CA, Weekes MP, Nobre LV, Ruckova E, Wilkie GS, Paulo JA, Chang C, Suárez NM, Davies JA, Antrobus R, Stanton RJ, Aicheler RJ, Nichols H, Vojtesek B, Trowsdale J, Davison AJ, Gygi SP, Tomasec P, Lehner PJ, Wilkinson GW, (2017) "Control of immune ligands by members of a cytomegalovirus gene expansion suppresses natural killer cell activation." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28186488 28186488]; doi: [https://dx.doi.org/10.7554/eLife.22206 10.7554/eLife.22206]; GPMDB: [http://gpmdb.org/data/keyword/28186488 9]. |
- | #Barnea E, Melamed Kadosh D, Haimovich Y, Satumtira N, Dorris ML, Nguyen MT, Hammer RE, Tran TM, Colbert RA, Taurog JD, Admon A, (2017) "The HLA-B27 peptidome in vivo in spondyloarthritis-susceptible HLA-B27 transgenic rats and the effect of ERAP1 deletion." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28188227 28188227]; doi: [https://dx.doi.org/10.1074/mcp.M116.066241 10.1074/mcp.M116.066241]; GPMDB: [http://gpmdb.org/data/keyword/28188227 | + | #Barnea E, Melamed Kadosh D, Haimovich Y, Satumtira N, Dorris ML, Nguyen MT, Hammer RE, Tran TM, Colbert RA, Taurog JD, Admon A, (2017) "The HLA-B27 peptidome in vivo in spondyloarthritis-susceptible HLA-B27 transgenic rats and the effect of ERAP1 deletion." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28188227 28188227]; doi: [https://dx.doi.org/10.1074/mcp.M116.066241 10.1074/mcp.M116.066241]; GPMDB: [http://gpmdb.org/data/keyword/28188227 49]. |
+ | #Howie D, Cobbold SP, Adams E, Ten Bokum A, Necula AS, Zhang W, Huang H, Roberts DJ, Thomas B, Hester SS, Vaux DJ, Betz AG, Waldmann H, (2017) "Foxp3 drives oxidative phosphorylation and protection from lipotoxicity." <i>JCI Insight</i> <b>2</b>(3):e89160; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28194435 28194435]; doi: [https://dx.doi.org/10.1172/jci.insight.89160 10.1172/jci.insight.89160]; GPMDB: [http://gpmdb.org/data/keyword/28194435 1]. | ||
+ | #Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM, (2017) "Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28195392 28195392]; doi: [https://dx.doi.org/10.1002/pmic.201600300 10.1002/pmic.201600300]; GPMDB: [http://gpmdb.org/data/keyword/28195392 36]. |
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.
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 February 26, 2017.