(4 intermediate revisions not shown) | |||
Line 25: | Line 25: | ||
==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 Nov. 5, 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]. | ||
Line 1,011: | Line 1,011: | ||
#Li S, Dislich B, Brakebusch CH, Lichtenthaler SF, Brocker T, (2015) "Control of Homeostasis and Dendritic Cell Survival by the GTPase RhoA." <i>J Immunol</i> <b>195</b>(9):4244–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26408665 26408665]; doi: [https://dx.doi.org/10.4049/jimmunol.1500676 10.4049/jimmunol.1500676]; GPMDB: [http://gpmdb.org/data/keyword/26408665 60]. | #Li S, Dislich B, Brakebusch CH, Lichtenthaler SF, Brocker T, (2015) "Control of Homeostasis and Dendritic Cell Survival by the GTPase RhoA." <i>J Immunol</i> <b>195</b>(9):4244–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26408665 26408665]; doi: [https://dx.doi.org/10.4049/jimmunol.1500676 10.4049/jimmunol.1500676]; GPMDB: [http://gpmdb.org/data/keyword/26408665 60]. | ||
#Beckley JR, Chen JS, Yang Y, Peng J, Gould KL, (2015) "A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival." <i>Mol Cell Proteomics</i> <b>14</b>(12):3132–41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412298 26412298]; doi: [https://dx.doi.org/10.1074/mcp.M115.050039 10.1074/mcp.M115.050039]; GPMDB: [http://gpmdb.org/data/keyword/26412298 246]. | #Beckley JR, Chen JS, Yang Y, Peng J, Gould KL, (2015) "A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival." <i>Mol Cell Proteomics</i> <b>14</b>(12):3132–41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412298 26412298]; doi: [https://dx.doi.org/10.1074/mcp.M115.050039 10.1074/mcp.M115.050039]; GPMDB: [http://gpmdb.org/data/keyword/26412298 246]. | ||
- | #Glatter T, Ahrné E, Schmidt A, (2015) "Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells." <i>J Proteome Res</i> <b>14</b>(11):4472–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412744 26412744]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00654 10.1021/acs.jproteome.5b00654]; GPMDB: [http://gpmdb.org/data/keyword/26412744 | + | #Glatter T, Ahrné E, Schmidt A, (2015) "Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells." <i>J Proteome Res</i> <b>14</b>(11):4472–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412744 26412744]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00654 10.1021/acs.jproteome.5b00654]; GPMDB: [http://gpmdb.org/data/keyword/26412744 901]. |
#Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A, (2015) "Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26418743 26418743]; doi: [https://dx.doi.org/10.7554/eLife.09579 10.7554/eLife.09579]; GPMDB: [http://gpmdb.org/data/keyword/26418743 12]. | #Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A, (2015) "Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26418743 26418743]; doi: [https://dx.doi.org/10.7554/eLife.09579 10.7554/eLife.09579]; GPMDB: [http://gpmdb.org/data/keyword/26418743 12]. | ||
#Gallart-Palau X, Serra A, Wong AS, Sandin S, Lai MK, Chen CP, Kon OL, Sze SK, (2015) "Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR)." <i>Sci Rep</i> <b>5</b>:14664; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26419333 26419333]; doi: [https://dx.doi.org/10.1038/srep14664 10.1038/srep14664]; GPMDB: [http://gpmdb.org/data/keyword/26419333 172]. | #Gallart-Palau X, Serra A, Wong AS, Sandin S, Lai MK, Chen CP, Kon OL, Sze SK, (2015) "Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR)." <i>Sci Rep</i> <b>5</b>:14664; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26419333 26419333]; doi: [https://dx.doi.org/10.1038/srep14664 10.1038/srep14664]; GPMDB: [http://gpmdb.org/data/keyword/26419333 172]. | ||
Line 1,330: | Line 1,330: | ||
#Mauri M, Kirchner M, Aharoni R, Ciolli Mattioli C, van den Bruck D, Gutkovitch N, Modepalli V, Selbach M, Moran Y, Chekulaeva M, (2016) "Conservation of miRNA-mediated silencing mechanisms across 600 million years of animal evolution." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27604873 27604873]; doi: [https://dx.doi.org/10.1093/nar/gkw792 10.1093/nar/gkw792]; GPMDB: [http://gpmdb.org/data/keyword/27604873 35]. | #Mauri M, Kirchner M, Aharoni R, Ciolli Mattioli C, van den Bruck D, Gutkovitch N, Modepalli V, Selbach M, Moran Y, Chekulaeva M, (2016) "Conservation of miRNA-mediated silencing mechanisms across 600 million years of animal evolution." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27604873 27604873]; doi: [https://dx.doi.org/10.1093/nar/gkw792 10.1093/nar/gkw792]; GPMDB: [http://gpmdb.org/data/keyword/27604873 35]. | ||
#Lee J, McKinney KQ, Pavlopoulos AJ, Han MH, Kim SH, Kim HJ, Hwang S, (2016) "Exosomal proteome analysis of cerebrospinal fluid detects biosignatures of neuromyelitis optica and multiple sclerosis." <i>Clin Chim Acta</i> <b>462</b>:118–126; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27609124 27609124]; doi: [https://dx.doi.org/10.1016/j.cca.2016.09.001 10.1016/j.cca.2016.09.001]; GPMDB: [http://gpmdb.org/data/keyword/27609124 24]. | #Lee J, McKinney KQ, Pavlopoulos AJ, Han MH, Kim SH, Kim HJ, Hwang S, (2016) "Exosomal proteome analysis of cerebrospinal fluid detects biosignatures of neuromyelitis optica and multiple sclerosis." <i>Clin Chim Acta</i> <b>462</b>:118–126; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27609124 27609124]; doi: [https://dx.doi.org/10.1016/j.cca.2016.09.001 10.1016/j.cca.2016.09.001]; GPMDB: [http://gpmdb.org/data/keyword/27609124 24]. | ||
+ | #Mulvaney KM, Matson JP, Siesser PF, Tamir TY, Goldfarb D, Jacobs TM, Cloer EW, Harrison JS, Vaziri C, Cook JG, Major MB, (2016) "Identification and Characterization of MCM3 as a Kelch-like ECH-associated Protein 1 (KEAP1) Substrate." <i>J Biol Chem</i> <b>291</b>(45):23719–23733; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27621311 27621311]; doi: [https://dx.doi.org/10.1074/jbc.M116.729418 10.1074/jbc.M116.729418]; GPMDB: [http://gpmdb.org/data/keyword/27621311 22]. | ||
#Subramanian S, Souleimanov A, Smith DL, (2016) "Proteomic Studies on the Effects of Lipo-Chitooligosaccharide and Thuricin 17 under Unstressed and Salt Stressed Conditions in Arabidopsis thaliana." <i>Front Plant Sci</i> <b>7</b>:1314; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27625672 27625672]; doi: [https://dx.doi.org/10.3389/fpls.2016.01314 10.3389/fpls.2016.01314]; GPMDB: [http://gpmdb.org/data/keyword/27625672 36]. | #Subramanian S, Souleimanov A, Smith DL, (2016) "Proteomic Studies on the Effects of Lipo-Chitooligosaccharide and Thuricin 17 under Unstressed and Salt Stressed Conditions in Arabidopsis thaliana." <i>Front Plant Sci</i> <b>7</b>:1314; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27625672 27625672]; doi: [https://dx.doi.org/10.3389/fpls.2016.01314 10.3389/fpls.2016.01314]; GPMDB: [http://gpmdb.org/data/keyword/27625672 36]. | ||
#Stroud DA, Surgenor EE, Formosa LE, Reljic B, Frazier AE, Dibley MG, Osellame LD, Stait T, Beilharz TH, Thorburn DR, Salim A, Ryan MT, (2016) "Accessory subunits are integral for assembly and function of human mitochondrial complex I." <i>Nature</i> <b>538</b>(7623):123–126; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27626371 27626371]; doi: [https://dx.doi.org/10.1038/nature19754 10.1038/nature19754]; GPMDB: [http://gpmdb.org/data/keyword/27626371 10]. | #Stroud DA, Surgenor EE, Formosa LE, Reljic B, Frazier AE, Dibley MG, Osellame LD, Stait T, Beilharz TH, Thorburn DR, Salim A, Ryan MT, (2016) "Accessory subunits are integral for assembly and function of human mitochondrial complex I." <i>Nature</i> <b>538</b>(7623):123–126; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27626371 27626371]; doi: [https://dx.doi.org/10.1038/nature19754 10.1038/nature19754]; GPMDB: [http://gpmdb.org/data/keyword/27626371 10]. | ||
Line 1,376: | Line 1,377: | ||
#Schanzenbächer CT, Sambandan S, Langer JD, Schuman EM, (2016) "Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses." <i>Neuron</i> <b>92</b>(2):358–371; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27764671 27764671]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.09.058 10.1016/j.neuron.2016.09.058]; GPMDB: [http://gpmdb.org/data/keyword/27764671 80]. | #Schanzenbächer CT, Sambandan S, Langer JD, Schuman EM, (2016) "Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses." <i>Neuron</i> <b>92</b>(2):358–371; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27764671 27764671]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.09.058 10.1016/j.neuron.2016.09.058]; GPMDB: [http://gpmdb.org/data/keyword/27764671 80]. | ||
#Yu P, Hahne H, Wilhelm M, Kuster B, (2017) "Ethylene glycol improves electrospray ionization efficiency in bottom-up proteomics." <i>Anal Bioanal Chem</i> <b>409</b>(4):1049–1057; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27766361 27766361]; doi: [https://dx.doi.org/10.1007/s00216-016-0023-x 10.1007/s00216-016-0023-x]; GPMDB: [http://gpmdb.org/data/keyword/27766361 147]. | #Yu P, Hahne H, Wilhelm M, Kuster B, (2017) "Ethylene glycol improves electrospray ionization efficiency in bottom-up proteomics." <i>Anal Bioanal Chem</i> <b>409</b>(4):1049–1057; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27766361 27766361]; doi: [https://dx.doi.org/10.1007/s00216-016-0023-x 10.1007/s00216-016-0023-x]; GPMDB: [http://gpmdb.org/data/keyword/27766361 147]. | ||
+ | #Isogai T, van der Kammen R, Bleijerveld OB, Goerdayal SS, Argenzio E, Altelaar AF, Innocenti M, (2016) "Quantitative Proteomics Illuminates a Functional Interaction between mDia2 and the Proteasome." <i>J Proteome Res</i> <b>15</b>(12):4624–4637; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27769112 27769112]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00718 10.1021/acs.jproteome.6b00718]; GPMDB: [http://gpmdb.org/data/keyword/27769112 44]. | ||
#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]. | #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]. | #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]. | ||
Line 1,466: | Line 1,468: | ||
#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]. | ||
#Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B, (2017) "Building ProteomeTools based on a complete synthetic human proteome." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28135259 28135259]; doi: [https://dx.doi.org/10.1038/nmeth.4153 10.1038/nmeth.4153]; GPMDB: [http://gpmdb.org/data/keyword/28135259 1095]. | #Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B, (2017) "Building ProteomeTools based on a complete synthetic human proteome." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28135259 28135259]; doi: [https://dx.doi.org/10.1038/nmeth.4153 10.1038/nmeth.4153]; GPMDB: [http://gpmdb.org/data/keyword/28135259 1095]. | ||
+ | #Abe Y, Nagano M, Tada A, Adachi J, Tomonaga T, (2017) "Deep Phosphotyrosine Proteomics by Optimization of Phosphotyrosine Enrichment and MS/MS Parameters." <i>J Proteome Res</i> <b>16</b>(2):1077–1086; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28152594 28152594]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00576 10.1021/acs.jproteome.6b00576]; GPMDB: [http://gpmdb.org/data/keyword/28152594 41]. | ||
#Jung SY, Choi JM, Rousseaux MW, Malovannaya A, Kim JJ, Kutzera J, Wang Y, Huang Y, Zhu W, Maity S, Zoghbi HY, Qin J, (2017) "An anatomically resolved mouse brain proteome reveals Parkinson disease-relevant pathways." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28153913 28153913]; doi: [https://dx.doi.org/10.1074/mcp.M116.061440 10.1074/mcp.M116.061440]; GPMDB: [http://gpmdb.org/data/keyword/28153913 610]. | #Jung SY, Choi JM, Rousseaux MW, Malovannaya A, Kim JJ, Kutzera J, Wang Y, Huang Y, Zhu W, Maity S, Zoghbi HY, Qin J, (2017) "An anatomically resolved mouse brain proteome reveals Parkinson disease-relevant pathways." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28153913 28153913]; doi: [https://dx.doi.org/10.1074/mcp.M116.061440 10.1074/mcp.M116.061440]; GPMDB: [http://gpmdb.org/data/keyword/28153913 610]. | ||
#Diering GH, Nirujogi RS, Roth RH, Worley PF, Pandey A, Huganir RL, (2017) "Homer1a drives homeostatic scaling-down of excitatory synapses during sleep." <i>Science</i> <b>355</b>(6324):511–515; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28154077 28154077]; doi: [https://dx.doi.org/10.1126/science.aai8355 10.1126/science.aai8355]; GPMDB: [http://gpmdb.org/data/keyword/28154077 25]. | #Diering GH, Nirujogi RS, Roth RH, Worley PF, Pandey A, Huganir RL, (2017) "Homer1a drives homeostatic scaling-down of excitatory synapses during sleep." <i>Science</i> <b>355</b>(6324):511–515; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28154077 28154077]; doi: [https://dx.doi.org/10.1126/science.aai8355 10.1126/science.aai8355]; GPMDB: [http://gpmdb.org/data/keyword/28154077 25]. | ||
Line 1,635: | Line 1,638: | ||
#Ayre DC, Chute IC, Joy AP, Barnett DA, Hogan AM, Grüll MP, Peña-Castillo L, Lang AS, Lewis SM, Christian SL, (2017) "CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo." <i>Sci Rep</i> <b>7</b>(1):8642; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28819186 28819186]; doi: [https://dx.doi.org/10.1038/s41598-017-08094-8 10.1038/s41598-017-08094-8]; GPMDB: [http://gpmdb.org/data/keyword/28819186 146]. | #Ayre DC, Chute IC, Joy AP, Barnett DA, Hogan AM, Grüll MP, Peña-Castillo L, Lang AS, Lewis SM, Christian SL, (2017) "CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo." <i>Sci Rep</i> <b>7</b>(1):8642; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28819186 28819186]; doi: [https://dx.doi.org/10.1038/s41598-017-08094-8 10.1038/s41598-017-08094-8]; GPMDB: [http://gpmdb.org/data/keyword/28819186 146]. | ||
#Hung CL, Pan SH, Han CL, Chang CW, Hsu YL, Su CH, Shih SC, Lai YJ, Chiang Chiau JS, Yeh HI, Liu CY, Lee HC, Lam CSP, (2017) "Membrane Proteomics of Impaired Energetics and Cytoskeletal Disorganization in Elderly Diet-Induced Diabetic Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28823169 28823169]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00148 10.1021/acs.jproteome.7b00148]; GPMDB: [http://gpmdb.org/data/keyword/28823169 14]. | #Hung CL, Pan SH, Han CL, Chang CW, Hsu YL, Su CH, Shih SC, Lai YJ, Chiang Chiau JS, Yeh HI, Liu CY, Lee HC, Lam CSP, (2017) "Membrane Proteomics of Impaired Energetics and Cytoskeletal Disorganization in Elderly Diet-Induced Diabetic Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28823169 28823169]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00148 10.1021/acs.jproteome.7b00148]; GPMDB: [http://gpmdb.org/data/keyword/28823169 14]. | ||
- | #Fu L, Liu KK, Sun MA, Tian CP, Sun R, Morales Betanzos C, Tallman KA, Porter NA, Yang Y, Guo DJ, Liebler DC, Yang J, (2017) "Systematic and quantitative assessment of hydrogen peroxide reactivity with cysteines across human proteomes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28827280 28827280]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000108 10.1074/mcp.RA117.000108]; GPMDB: [http://gpmdb.org/data/keyword/28827280 | + | #Fu L, Liu KK, Sun MA, Tian CP, Sun R, Morales Betanzos C, Tallman KA, Porter NA, Yang Y, Guo DJ, Liebler DC, Yang J, (2017) "Systematic and quantitative assessment of hydrogen peroxide reactivity with cysteines across human proteomes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28827280 28827280]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000108 10.1074/mcp.RA117.000108]; GPMDB: [http://gpmdb.org/data/keyword/28827280 12]. |
#Phillips TJ, Scott H, Menassa DA, Bignell AL, Sood A, Morton JS, Akagi T, Azuma K, Rogers MF, Gilmore CE, Inman GJ, Grant S, Chung Y, Aljunaidy MM, Cooke CL, Steinkraus BR, Pocklington A, Logan A, Collett GP, Kemp H, Holmans PA, Murphy MP, Fulga TA, Coney AM, Akashi M, Davidge ST, Case CP, (2017) "Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development." <i>Sci Rep</i> <b>7</b>(1):9079; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28831049 28831049]; doi: [https://dx.doi.org/10.1038/s41598-017-06300-1 10.1038/s41598-017-06300-1]; GPMDB: [http://gpmdb.org/data/keyword/28831049 1]. | #Phillips TJ, Scott H, Menassa DA, Bignell AL, Sood A, Morton JS, Akagi T, Azuma K, Rogers MF, Gilmore CE, Inman GJ, Grant S, Chung Y, Aljunaidy MM, Cooke CL, Steinkraus BR, Pocklington A, Logan A, Collett GP, Kemp H, Holmans PA, Murphy MP, Fulga TA, Coney AM, Akashi M, Davidge ST, Case CP, (2017) "Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development." <i>Sci Rep</i> <b>7</b>(1):9079; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28831049 28831049]; doi: [https://dx.doi.org/10.1038/s41598-017-06300-1 10.1038/s41598-017-06300-1]; GPMDB: [http://gpmdb.org/data/keyword/28831049 1]. | ||
#Vyse S, McCarthy F, Broncel M, Paul A, Wong JP, Bhamra A, Huang PH, (2017) "Quantitative phosphoproteomic analysis of acquired cancer drug resistance to pazopanib and dasatinib." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28842319 28842319]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.08.015 10.1016/j.jprot.2017.08.015]; GPMDB: [http://gpmdb.org/data/keyword/28842319 42]. | #Vyse S, McCarthy F, Broncel M, Paul A, Wong JP, Bhamra A, Huang PH, (2017) "Quantitative phosphoproteomic analysis of acquired cancer drug resistance to pazopanib and dasatinib." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28842319 28842319]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.08.015 10.1016/j.jprot.2017.08.015]; GPMDB: [http://gpmdb.org/data/keyword/28842319 42]. | ||
Line 1,641: | Line 1,644: | ||
#Andersen PR, Tirian L, Vunjak M, Brennecke J, (2017) "A heterochromatin-dependent transcription machinery drives piRNA expression." <i>Nature</i> <b>549</b>(7670):54–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28847004 28847004]; doi: [https://dx.doi.org/10.1038/nature23482 10.1038/nature23482]; GPMDB: [http://gpmdb.org/data/keyword/28847004 46]. | #Andersen PR, Tirian L, Vunjak M, Brennecke J, (2017) "A heterochromatin-dependent transcription machinery drives piRNA expression." <i>Nature</i> <b>549</b>(7670):54–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28847004 28847004]; doi: [https://dx.doi.org/10.1038/nature23482 10.1038/nature23482]; GPMDB: [http://gpmdb.org/data/keyword/28847004 46]. | ||
#Mohl BP, Emmott E, Roy P, (2017) "Phosphoproteomic analysis reveals the importance of kinase regulation during orbivirus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28851738 28851738]; doi: [https://dx.doi.org/10.1074/mcp.M117.067355 10.1074/mcp.M117.067355]; GPMDB: [http://gpmdb.org/data/keyword/28851738 6]. | #Mohl BP, Emmott E, Roy P, (2017) "Phosphoproteomic analysis reveals the importance of kinase regulation during orbivirus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28851738 28851738]; doi: [https://dx.doi.org/10.1074/mcp.M117.067355 10.1074/mcp.M117.067355]; GPMDB: [http://gpmdb.org/data/keyword/28851738 6]. | ||
+ | #Merkley ED, Sego LH, Lin A, Leiser OP, Kaiser BLD, Adkins JN, Keim PS, Wagner DM, Kreuzer HW, (2017) "Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague." <i>PLoS One</i> <b>12</b>(8):e0183478; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28854255 28854255]; doi: [https://dx.doi.org/10.1371/journal.pone.0183478 10.1371/journal.pone.0183478]; GPMDB: [http://gpmdb.org/data/keyword/28854255 343]. | ||
#Peng X, Xu F, Liu S, Li S, Huang Q, Chang L, Wang L, Ma X, He F, Xu P, (2017) "Identification of Missing Proteins in the Phosphoproteome of Kidney Cancer." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28857561 28857561]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00332 10.1021/acs.jproteome.7b00332]; GPMDB: [http://gpmdb.org/data/keyword/28857561 17]. | #Peng X, Xu F, Liu S, Li S, Huang Q, Chang L, Wang L, Ma X, He F, Xu P, (2017) "Identification of Missing Proteins in the Phosphoproteome of Kidney Cancer." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28857561 28857561]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00332 10.1021/acs.jproteome.7b00332]; GPMDB: [http://gpmdb.org/data/keyword/28857561 17]. | ||
#Subramanian K, Rauniyar N, Lavalleé-Adam M, Yates JR 3rd, Balch WE, (2017) "Quantitative Analysis of the Proteome Response to the Histone Deacetylase Inhibitor (HDACi) Vorinostat in Niemann-Pick Type C1 disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28860124 28860124]; doi: [https://dx.doi.org/10.1074/mcp.M116.064949 10.1074/mcp.M116.064949]; GPMDB: [http://gpmdb.org/data/keyword/28860124 7]. | #Subramanian K, Rauniyar N, Lavalleé-Adam M, Yates JR 3rd, Balch WE, (2017) "Quantitative Analysis of the Proteome Response to the Histone Deacetylase Inhibitor (HDACi) Vorinostat in Niemann-Pick Type C1 disease." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28860124 28860124]; doi: [https://dx.doi.org/10.1074/mcp.M116.064949 10.1074/mcp.M116.064949]; GPMDB: [http://gpmdb.org/data/keyword/28860124 7]. | ||
#Rossello J, Lima A, Gil M, Rodríguez Duarte J, Correa A, Carvalho PC, Kierbel A, Durán R, (2017) "The EAL-domain protein FcsR regulates flagella, chemotaxis and type III secretion system in Pseudomonas aeruginosa by a phosphodiesterase independent mechanism." <i>Sci Rep</i> <b>7</b>(1):10281; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28860517 28860517]; doi: [https://dx.doi.org/10.1038/s41598-017-09926-3 10.1038/s41598-017-09926-3]; GPMDB: [http://gpmdb.org/data/keyword/28860517 21]. | #Rossello J, Lima A, Gil M, Rodríguez Duarte J, Correa A, Carvalho PC, Kierbel A, Durán R, (2017) "The EAL-domain protein FcsR regulates flagella, chemotaxis and type III secretion system in Pseudomonas aeruginosa by a phosphodiesterase independent mechanism." <i>Sci Rep</i> <b>7</b>(1):10281; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28860517 28860517]; doi: [https://dx.doi.org/10.1038/s41598-017-09926-3 10.1038/s41598-017-09926-3]; GPMDB: [http://gpmdb.org/data/keyword/28860517 21]. | ||
- | #Mendes M, Peláez-García A, López-Lucendo M, Bartolomé RA, Calviño E, Barderas R, Casal JI, (2017) "Mapping the spatial proteome of metastatic cells in colorectal cancer." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28861940 28861940]; doi: [https://dx.doi.org/10.1002/pmic.201700094 10.1002/pmic.201700094]; GPMDB: [http://gpmdb.org/data/keyword/28861940 | + | #Mendes M, Peláez-García A, López-Lucendo M, Bartolomé RA, Calviño E, Barderas R, Casal JI, (2017) "Mapping the spatial proteome of metastatic cells in colorectal cancer." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28861940 28861940]; doi: [https://dx.doi.org/10.1002/pmic.201700094 10.1002/pmic.201700094]; GPMDB: [http://gpmdb.org/data/keyword/28861940 200]. |
#Tanabe Y, Naito Y, Vasuta C, Lee AK, Soumounou Y, Linhoff MW, Takahashi H, (2017) "IgSF21 promotes differentiation of inhibitory synapses via binding to neurexin2α." <i>Nat Commun</i> <b>8</b>(1):408; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28864826 28864826]; doi: [https://dx.doi.org/10.1038/s41467-017-00333-w 10.1038/s41467-017-00333-w]; GPMDB: [http://gpmdb.org/data/keyword/28864826 32]. | #Tanabe Y, Naito Y, Vasuta C, Lee AK, Soumounou Y, Linhoff MW, Takahashi H, (2017) "IgSF21 promotes differentiation of inhibitory synapses via binding to neurexin2α." <i>Nat Commun</i> <b>8</b>(1):408; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28864826 28864826]; doi: [https://dx.doi.org/10.1038/s41467-017-00333-w 10.1038/s41467-017-00333-w]; GPMDB: [http://gpmdb.org/data/keyword/28864826 32]. | ||
- | #Edupuganti RR, Geiger S, Lindeboom RGH, Shi H, Hsu PJ, Lu Z, Wang SY, Baltissen MPA, Jansen PWTC, Rossa M, Müller M, Stunnenberg HG, He C, Carell T, Vermeulen M, (2017) "N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) recruits and repels proteins to regulate mRNA homeostasis." <i>Nat Struct Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28869609 28869609]; doi: [https://dx.doi.org/10.1038/nsmb.3462 10.1038/nsmb.3462]; GPMDB: [http://gpmdb.org/data/keyword/28869609 | + | #Kraner ME, Müller C, Sonnewald U, (2017) "Comparative proteomic profiling of the Choline transporter-like1 (CHER1) mutant provides insights into plasmodesmata composition of fully developed Arabidopsis thaliana leaves." <i>Plant J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28865150 28865150]; doi: [https://dx.doi.org/10.1111/tpj.13702 10.1111/tpj.13702]; GPMDB: [http://gpmdb.org/data/keyword/28865150 1]. |
+ | #Edupuganti RR, Geiger S, Lindeboom RGH, Shi H, Hsu PJ, Lu Z, Wang SY, Baltissen MPA, Jansen PWTC, Rossa M, Müller M, Stunnenberg HG, He C, Carell T, Vermeulen M, (2017) "N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) recruits and repels proteins to regulate mRNA homeostasis." <i>Nat Struct Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28869609 28869609]; doi: [https://dx.doi.org/10.1038/nsmb.3462 10.1038/nsmb.3462]; GPMDB: [http://gpmdb.org/data/keyword/28869609 40]. | ||
+ | #Liu MQ, Zeng WF, Fang P, Cao WQ, Liu C, Yan GQ, Zhang Y, Peng C, Wu JQ, Zhang XJ, Tu HJ, Chi H, Sun RX, Cao Y, Dong MQ, Jiang BY, Huang JM, Shen HL, Wong CCL, He SM, Yang PY, (2017) "pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification." <i>Nat Commun</i> <b>8</b>(1):438; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28874712 28874712]; doi: [https://dx.doi.org/10.1038/s41467-017-00535-2 10.1038/s41467-017-00535-2]; GPMDB: [http://gpmdb.org/data/keyword/28874712 4]. | ||
+ | #Dittus L, Werner T, Muelbaier M, Bantscheff M, (2017) "Differential Kinobeads Profiling for Target Identification of Irreversible Kinase Inhibitors." <i>ACS Chem Biol</i> <b>12</b>(10):2515–2521; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28876896 28876896]; doi: [https://dx.doi.org/10.1021/acschembio.7b00617 10.1021/acschembio.7b00617]; GPMDB: [http://gpmdb.org/data/keyword/28876896 154]. | ||
#Kälin S, Becker M, Ott VB, Serr I, Hosp F, Mollah MMH, Keipert S, Lamp D, Rohner-Jeanrenaud F, Flynn VK, Scherm MG, Nascimento LFR, Gerlach K, Popp V, Dietzen S, Bopp T, Krishnamurthy P, Kaplan MH, Serrano M, Woods SC, Tripal P, Palmisano R, Jastroch M, Blüher M, Wolfrum C, Weigmann B, Ziegler AG, Mann M, Tschöp MH, Daniel C, (2017) "A Stat6/Pten Axis Links Regulatory T Cells with Adipose Tissue Function." <i>Cell Metab</i> <b>26</b>(3):475–492.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28877454 28877454]; doi: [https://dx.doi.org/10.1016/j.cmet.2017.08.008 10.1016/j.cmet.2017.08.008]; GPMDB: [http://gpmdb.org/data/keyword/28877454 31]. | #Kälin S, Becker M, Ott VB, Serr I, Hosp F, Mollah MMH, Keipert S, Lamp D, Rohner-Jeanrenaud F, Flynn VK, Scherm MG, Nascimento LFR, Gerlach K, Popp V, Dietzen S, Bopp T, Krishnamurthy P, Kaplan MH, Serrano M, Woods SC, Tripal P, Palmisano R, Jastroch M, Blüher M, Wolfrum C, Weigmann B, Ziegler AG, Mann M, Tschöp MH, Daniel C, (2017) "A Stat6/Pten Axis Links Regulatory T Cells with Adipose Tissue Function." <i>Cell Metab</i> <b>26</b>(3):475–492.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28877454 28877454]; doi: [https://dx.doi.org/10.1016/j.cmet.2017.08.008 10.1016/j.cmet.2017.08.008]; GPMDB: [http://gpmdb.org/data/keyword/28877454 31]. | ||
+ | #Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IY, Yeh YM, Chen CD, Li HP, Luo JD, Tan BC, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP, Chang YS, (2017) "APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism." <i>Nat Commun</i> <b>8</b>(1):465; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28878238 28878238]; doi: [https://dx.doi.org/10.1038/s41467-017-00493-9 10.1038/s41467-017-00493-9]; GPMDB: [http://gpmdb.org/data/keyword/28878238 1]. | ||
+ | #Han B, Fang Y, Feng M, Hu H, Hao Y, Ma C, Huo X, Meng L, Zhang X, Wu F, Li J, (2017) "Brain Membrane Proteome and Phosphoproteome Reveal Molecular Basis Associating with Nursing and Foraging Behaviors of Honeybee Workers." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28879772 28879772]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00371 10.1021/acs.jproteome.7b00371]; GPMDB: [http://gpmdb.org/data/keyword/28879772 47]. | ||
#Phillips B, Titz B, Kogel U, Sharma D, Leroy P, Xiang Y, Vuillaume G, Lebrun S, Sciuscio D, Ho J, Nury C, Guedj E, Elamin A, Esposito M, Krishnan S, Schlage WK, Veljkovic E, Ivanov NV, Martin F, Peitsch MC, Hoeng J, Vanscheeuwijck P, (2017) "Toxicity of the main electronic cigarette components, propylene glycol, glycerin, and nicotine, in Sprague-Dawley rats in a 90-day OECD inhalation study complemented by molecular endpoints." <i>Food Chem Toxicol</i> <b>109</b>(Pt 1):315–332; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28882640 28882640]; doi: [https://dx.doi.org/10.1016/j.fct.2017.09.001 10.1016/j.fct.2017.09.001]; GPMDB: [http://gpmdb.org/data/keyword/28882640 36]. | #Phillips B, Titz B, Kogel U, Sharma D, Leroy P, Xiang Y, Vuillaume G, Lebrun S, Sciuscio D, Ho J, Nury C, Guedj E, Elamin A, Esposito M, Krishnan S, Schlage WK, Veljkovic E, Ivanov NV, Martin F, Peitsch MC, Hoeng J, Vanscheeuwijck P, (2017) "Toxicity of the main electronic cigarette components, propylene glycol, glycerin, and nicotine, in Sprague-Dawley rats in a 90-day OECD inhalation study complemented by molecular endpoints." <i>Food Chem Toxicol</i> <b>109</b>(Pt 1):315–332; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28882640 28882640]; doi: [https://dx.doi.org/10.1016/j.fct.2017.09.001 10.1016/j.fct.2017.09.001]; GPMDB: [http://gpmdb.org/data/keyword/28882640 36]. | ||
+ | #Pawellek A, Ryder U, Tammsalu T, King LJ, Kreinin H, Ly T, Hay RT, Hartley RC, Lamond AI, (2017) "Characterisation of the biflavonoid hinokiflavone as a pre-mRNA splicing modulator that inhibits SENP." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28884683 28884683]; doi: [https://dx.doi.org/10.7554/eLife.27402 10.7554/eLife.27402]; GPMDB: [http://gpmdb.org/data/keyword/28884683 6]. | ||
+ | #Kishazi E, Dor M, Eperon S, Oberic A, Hamedani M, Turck N, (2017) "Thyroid-associated orbitopathy and tears: A proteomics study." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28887209 28887209]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.09.001 10.1016/j.jprot.2017.09.001]; GPMDB: [http://gpmdb.org/data/keyword/28887209 8]. | ||
#Rijkers M, van den Eshof BL, van der Meer PF, van Alphen FPJ, de Korte D, Leebeek FWG, Meijer AB, Voorberg J, Jansen AJG, (2017) "Monitoring storage induced changes in the platelet proteome employing label free quantitative mass spectrometry." <i>Sci Rep</i> <b>7</b>(1):11045; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28887518 28887518]; doi: [https://dx.doi.org/10.1038/s41598-017-11643-w 10.1038/s41598-017-11643-w]; GPMDB: [http://gpmdb.org/data/keyword/28887518 21]. | #Rijkers M, van den Eshof BL, van der Meer PF, van Alphen FPJ, de Korte D, Leebeek FWG, Meijer AB, Voorberg J, Jansen AJG, (2017) "Monitoring storage induced changes in the platelet proteome employing label free quantitative mass spectrometry." <i>Sci Rep</i> <b>7</b>(1):11045; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28887518 28887518]; doi: [https://dx.doi.org/10.1038/s41598-017-11643-w 10.1038/s41598-017-11643-w]; GPMDB: [http://gpmdb.org/data/keyword/28887518 21]. | ||
#Bachofner M, Speicher T, Bogorad RL, Muzumdar S, Derrer CP, Hürlimann F, Böhm F, Nanni P, Kockmann T, Kachaylo E, Meyer M, Padrissa-Altés S, Graf R, Anderson DG, Koteliansky V, Auf dem Keller U, Werner S, (2017) "Large-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration." <i>Dev Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28890072 28890072]; doi: [https://dx.doi.org/10.1016/j.devcel.2017.07.025 10.1016/j.devcel.2017.07.025]; GPMDB: [http://gpmdb.org/data/keyword/28890072 20]. | #Bachofner M, Speicher T, Bogorad RL, Muzumdar S, Derrer CP, Hürlimann F, Böhm F, Nanni P, Kockmann T, Kachaylo E, Meyer M, Padrissa-Altés S, Graf R, Anderson DG, Koteliansky V, Auf dem Keller U, Werner S, (2017) "Large-Scale Quantitative Proteomics Identifies the Ubiquitin Ligase Nedd4-1 as an Essential Regulator of Liver Regeneration." <i>Dev Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28890072 28890072]; doi: [https://dx.doi.org/10.1016/j.devcel.2017.07.025 10.1016/j.devcel.2017.07.025]; GPMDB: [http://gpmdb.org/data/keyword/28890072 20]. | ||
+ | #Lapek JD Jr, Greninger P, Morris R, Amzallag A, Pruteanu-Malinici I, Benes CH, Haas W, (2017) "Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28892078 28892078]; doi: [https://dx.doi.org/10.1038/nbt.3955 10.1038/nbt.3955]; GPMDB: [http://gpmdb.org/data/keyword/28892078 11]. | ||
+ | #Guccione EJ, Kendall JJ, Hitchcock A, Garg N, White MA, Mulholland F, Poole RK, Kelly DJ, (2017) "Transcriptome and proteome dynamics in chemostat culture reveal how Campylobacter jejuni modulates metabolism, stress responses and virulence factors upon changes in oxygen availability." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28892295 28892295]; doi: [https://dx.doi.org/10.1111/1462-2920.13930 10.1111/1462-2920.13930]; GPMDB: [http://gpmdb.org/data/keyword/28892295 54]. | ||
+ | #Bardot P, Vincent SD, Fournier M, Hubaud A, Joint M, Tora L, Pourquié O, (2017) "The TAF10-containing TFIID and SAGA transcriptional complexes are dispensable for early somitogenesis in the mouse embryo." <i>Development</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28893950 28893950]; doi: [https://dx.doi.org/10.1242/dev.146902 10.1242/dev.146902]; GPMDB: [http://gpmdb.org/data/keyword/28893950 30]. | ||
#Avenarius MR, Krey JF, Dumont RA, Morgan CP, Benson CB, Vijayakumar S, Cunningham CL, Scheffer DI, Corey DP, Müller U, Jones SM, Barr-Gillespie PG, (2017) "Heterodimeric capping protein is required for stereocilia length and width regulation." <i>J Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28899994 28899994]; doi: [https://dx.doi.org/10.1083/jcb.201704171 10.1083/jcb.201704171]; GPMDB: [http://gpmdb.org/data/keyword/28899994 52]. | #Avenarius MR, Krey JF, Dumont RA, Morgan CP, Benson CB, Vijayakumar S, Cunningham CL, Scheffer DI, Corey DP, Müller U, Jones SM, Barr-Gillespie PG, (2017) "Heterodimeric capping protein is required for stereocilia length and width regulation." <i>J Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28899994 28899994]; doi: [https://dx.doi.org/10.1083/jcb.201704171 10.1083/jcb.201704171]; GPMDB: [http://gpmdb.org/data/keyword/28899994 52]. | ||
- | #Hospital MA, Jacquel A, Mazed F, Saland E, Larrue C, Mondesir J, Birsen R, Green AS, Lambert M, Sujobert P, Gautier EF, Salnot V, Le Gall M, Decroocq J, Poulain L, Jacque N, Fontenay M, Kosmider O, Récher C, Auberger P, Mayeux P, Bouscary D, Sarry JE, Tamburini J, (2017) "RSK2 is a new Pim2 target with pro-survival functions in FLT3-ITD-positive acute myeloid leukemia." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28914261 28914261]; doi: [https://dx.doi.org/10.1038/leu.2017.284 10.1038/leu.2017.284]; GPMDB: [http://gpmdb.org/data/keyword/28914261 | + | #Rowland EA, Greco TM, Snowden CK, McCabe AL, Silhavy TJ, Cristea IM, (2017) "Sirtuin Lipoamidase Activity Is Conserved in Bacteria as a Regulator of Metabolic Enzyme Complexes." <i>MBio</i> <b>8</b>(5):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28900027 28900027]; doi: [https://dx.doi.org/10.1128/mBio.01096-17 10.1128/mBio.01096-17]; GPMDB: [http://gpmdb.org/data/keyword/28900027 2]. |
+ | #Hospital MA, Jacquel A, Mazed F, Saland E, Larrue C, Mondesir J, Birsen R, Green AS, Lambert M, Sujobert P, Gautier EF, Salnot V, Le Gall M, Decroocq J, Poulain L, Jacque N, Fontenay M, Kosmider O, Récher C, Auberger P, Mayeux P, Bouscary D, Sarry JE, Tamburini J, (2017) "RSK2 is a new Pim2 target with pro-survival functions in FLT3-ITD-positive acute myeloid leukemia." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28914261 28914261]; doi: [https://dx.doi.org/10.1038/leu.2017.284 10.1038/leu.2017.284]; GPMDB: [http://gpmdb.org/data/keyword/28914261 17]. | ||
#Tain LS, Sehlke R, Jain C, Chokkalingam M, Nagaraj N, Essers P, Rassner M, Grönke S, Froelich J, Dieterich C, Mann M, Alic N, Beyer A, Partridge L, (2017) "A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance." <i>Mol Syst Biol</i> <b>13</b>(9):939; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28916541 28916541]; GPMDB: [http://gpmdb.org/data/keyword/28916541 92]. | #Tain LS, Sehlke R, Jain C, Chokkalingam M, Nagaraj N, Essers P, Rassner M, Grönke S, Froelich J, Dieterich C, Mann M, Alic N, Beyer A, Partridge L, (2017) "A proteomic atlas of insulin signalling reveals tissue-specific mechanisms of longevity assurance." <i>Mol Syst Biol</i> <b>13</b>(9):939; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28916541 28916541]; GPMDB: [http://gpmdb.org/data/keyword/28916541 92]. | ||
+ | #Martin-Perez M, Villén J, (2017) "Determinants and Regulation of Protein Turnover in Yeast." <i>Cell Syst</i> <b>5</b>(3):283–294.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28918244 28918244]; doi: [https://dx.doi.org/10.1016/j.cels.2017.08.008 10.1016/j.cels.2017.08.008]; GPMDB: [http://gpmdb.org/data/keyword/28918244 12]. | ||
+ | #Weber A, Elliott PR, Pinto-Fernandez A, Bonham S, Kessler BM, Komander D, El Oualid F, Krappmann D, (2017) "A Linear Diubiquitin-Based Probe for Efficient and Selective Detection of the Deubiquitinating Enzyme OTULIN." <i>Cell Chem Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28919039 28919039]; doi: [https://dx.doi.org/10.1016/j.chembiol.2017.08.006 10.1016/j.chembiol.2017.08.006]; GPMDB: [http://gpmdb.org/data/keyword/28919039 16]. | ||
+ | #Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ, (2017) "Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection." <i>Nat Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28924191 28924191]; doi: [https://dx.doi.org/10.1038/s41564-017-0021-6 10.1038/s41564-017-0021-6]; GPMDB: [http://gpmdb.org/data/keyword/28924191 15]. | ||
+ | #Lum KM, Sato Y, Beyer BA, Plaisted WC, Anglin JL, Lairson LL, Cravatt BF, (2017) "Mapping Protein Targets of Bioactive Small Molecules Using Lipid-Based Chemical Proteomics." <i>ACS Chem Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28930429 28930429]; doi: [https://dx.doi.org/10.1021/acschembio.7b00581 10.1021/acschembio.7b00581]; GPMDB: [http://gpmdb.org/data/keyword/28930429 43]. | ||
+ | #Whiteley AM, Prado MA, Peng I, Abbas AR, Haley B, Paulo JA, Reichelt M, Katakam A, Sagolla M, Modrusan Z, Lee DY, Roose-Girma M, Kirkpatrick DS, McKenzie BS, Gygi SP, Finley D, Brown EJ, (2017) "Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28933694 28933694]; doi: [https://dx.doi.org/10.7554/eLife.26435 10.7554/eLife.26435]; GPMDB: [http://gpmdb.org/data/keyword/28933694 4]. | ||
+ | #Velásquez E, Nogueira FCS, Velásquez I, Schmitt A, Falkai P, Domont GB, Martins de Souza D, (2017) "Synaptosomal proteome of the orbitofrontal cortex from schizophrenia patients using quantitative label-free and iTRAQ-based shotgun proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28949146 28949146]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00422 10.1021/acs.jproteome.7b00422]; GPMDB: [http://gpmdb.org/data/keyword/28949146 3]. | ||
+ | #Cuijpers SAG, Willemstein E, Vertegaal ACO, (2017) "<b>Converging SUMO and ubiquitin signaling: improved methodology identifies co-modified target proteins</b>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28951443 28951443]; doi: [https://dx.doi.org/10.1074/mcp.TIR117.000152 10.1074/mcp.TIR117.000152]; GPMDB: [http://gpmdb.org/data/keyword/28951443 102]. | ||
+ | #Seddigh P, Bracht T, Molinier-Frenkel V, Castellano F, Kniemeyer O, Schuster M, Weski J, Hasenberg A, Kraus A, Poschet G, Hager T, Theegarte D, Opitz C, Brakhage AA, Sitek B, Hasenberg M, Gunzer M, (2017) "Quantitative Analysis of Proteome Modulations in Alveolar Epithelial Type II Cells in Response to Pulmonary <i>Aspergillus fumigatus</i> Infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28951444 28951444]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000072 10.1074/mcp.RA117.000072]; GPMDB: [http://gpmdb.org/data/keyword/28951444 18]. | ||
+ | #Wang Q, Lu Q, (2017) "Plasma membrane-derived extracellular microvesicles mediate non-canonical intercellular NOTCH signaling." <i>Nat Commun</i> <b>8</b>(1):709; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28955033 28955033]; doi: [https://dx.doi.org/10.1038/s41467-017-00767-2 10.1038/s41467-017-00767-2]; GPMDB: [http://gpmdb.org/data/keyword/28955033 2]. | ||
+ | #Triana S, de Cock H, Ohm RA, Danies G, Wösten HAB, Restrepo S, González Barrios AF, Celis A, (2017) "Lipid Metabolic Versatility in <i>Malassezia</i> spp. Yeasts Studied through Metabolic Modeling." <i>Front Microbiol</i> <b>8</b>:1772; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28959251 28959251]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01772 10.3389/fmicb.2017.01772]; GPMDB: [http://gpmdb.org/data/keyword/28959251 37]. | ||
+ | #Wang Y, Chen Y, Zhang Y, Wei W, Li Y, Zhang T, He F, Gao Y, Xu P, (2017) "Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28959888 28959888]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00340 10.1021/acs.jproteome.7b00340]; GPMDB: [http://gpmdb.org/data/keyword/28959888 63]. | ||
+ | #Stadlmann J, Taubenschmid J, Wenzel D, Gattinger A, Dürnberger G, Dusberger F, Elling U, Mach L, Mechtler K, Penninger JM, (2017) "Comparative glycoproteomics of stem cells identifies new players in ricin toxicity." <i>Nature</i> <b>549</b>(7673):538–542; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28959962 28959962]; doi: [https://dx.doi.org/10.1038/nature24015 10.1038/nature24015]; GPMDB: [http://gpmdb.org/data/keyword/28959962 1]. | ||
+ | #Li S, He Y, Lin Z, Xu S, Zhou R, Liang F, Wang J, Yang H, Liu S, Ren Y, (2017) "Digging more missing proteins using an enrichment approach with ProteoMiner™." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28960076 28960076]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00353 10.1021/acs.jproteome.7b00353]; GPMDB: [http://gpmdb.org/data/keyword/28960076 199]. | ||
+ | #Hauser DN, Mamais A, Conti MM, Primiani CT, Kumaran R, Dillman AA, Langston RG, Beilina A, Garcia JH, Diaz-Ruiz A, Bernier M, Fiesel FC, Hou X, Springer W, Li Y, de Cabo R, Cookson MR, (2017) "Hexokinases link DJ-1 to the PINK1/parkin pathway." <i>Mol Neurodegener</i> <b>12</b>(1):70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28962651 28962651]; doi: [https://dx.doi.org/10.1186/s13024-017-0212-x 10.1186/s13024-017-0212-x]; GPMDB: [http://gpmdb.org/data/keyword/28962651 6]. | ||
+ | #Zhang W, Chen X, Yan Z, Chen Y, Cui Y, Chen B, Huang C, Zhang W, Yin X, He QY, He F, Wang T, (2017) "Detergent-insoluble proteome analysis revealed aberrantly aggregated proteins in human preeclampsia placentas." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28965414 28965414]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00352 10.1021/acs.jproteome.7b00352]; GPMDB: [http://gpmdb.org/data/keyword/28965414 4]. | ||
+ | #Reyes ED, Kulej K, Pancholi NJ, Akhtar LN, Avgousti DC, Kim ET, Bricker DK, Spruce LA, Koniski SA, Seeholzer SH, Isaacs SN, Garcia BA, Weitzman MD, (2017) "Identifying host factors associated with DNA replicated during virus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28972080 28972080]; doi: [https://dx.doi.org/10.1074/mcp.M117.067116 10.1074/mcp.M117.067116]; GPMDB: [http://gpmdb.org/data/keyword/28972080 164]. | ||
+ | #Kollipara L, Buchkremer S, Coraspe JAG, Hathazi D, Senderek J, Weis J, Zahedi RP, Roos A, (2017) "In-depth phenotyping of lymphoblastoid cells suggests selective cellular vulnerability in Marinesco-Sjögren syndrome." <i>Oncotarget</i> <b>8</b>(40):68493–68516; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28978133 28978133]; doi: [https://dx.doi.org/10.18632/oncotarget.19663 10.18632/oncotarget.19663]; GPMDB: [http://gpmdb.org/data/keyword/28978133 23]. | ||
+ | #Opitz N, Schmitt K, Hofer-Pretz V, Neumann B, Krebber H, Braus GH, Valerius O, (2017) "Capturing the Asc1p/RACK1 microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982715 28982715]; doi: [https://dx.doi.org/10.1074/mcp.M116.066654 10.1074/mcp.M116.066654]; GPMDB: [http://gpmdb.org/data/keyword/28982715 268]. | ||
+ | #Saravanan R, Adav SS, Choong YK, van der Plas MJA, Petrlova J, Kjellström S, Sze SK, Schmidtchen A, (2017) "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo." <i>Sci Rep</i> <b>7</b>(1):13136; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29030565 29030565]; doi: [https://dx.doi.org/10.1038/s41598-017-13197-3 10.1038/s41598-017-13197-3]; GPMDB: [http://gpmdb.org/data/keyword/29030565 43]. | ||
+ | #Grenga L, Chandra G, Saalbach G, Galmozzi CV, Kramer G, Malone JG, (2017) "Analyzing the Complex Regulatory Landscape of Hfq - an Integrative, Multi-Omics Approach." <i>Front Microbiol</i> <b>8</b>:1784; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29033902 29033902]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01784 10.3389/fmicb.2017.01784]; GPMDB: [http://gpmdb.org/data/keyword/29033902 1]. | ||
+ | #Kugeratski FG, Batista M, Lima CVP, Neilson LJ, da Cunha ES, de Godoy LMF, Zanivan S, Krieger MA, Marchini FK, (2017) "The mitogen-activated protein kinase kinase 5 regulates the proliferation and biosynthetic processes in procyclic forms of Trypanosoma brucei." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29043805 29043805]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00415 10.1021/acs.jproteome.7b00415]; GPMDB: [http://gpmdb.org/data/keyword/29043805 15]. | ||
+ | #Fabrik I, Link M, Putzova D, Plzakova L, Lubovska Z, Philimonenko V, Pavkova I, Rehulka P, Krocova Z, Hozak P, Santic M, Stulik J, (2017) "<b>The early dendritic cell signaling induced by virulent <i>Francisella</i><i>tularensis</i> strain occurs in phases and involves the activation of ERKs and p38 in the later stage.</b>" <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29046388 29046388]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000160 10.1074/mcp.RA117.000160]; GPMDB: [http://gpmdb.org/data/keyword/29046388 358]. | ||
+ | #Raschdorf O, Bonn F, Zeytuni N, Zarivach R, Becher D, Schüler D, (2017) "A quantitative assessment of the membrane-integral sub-proteome of a bacterial magnetic organelle." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29054541 29054541]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.10.007 10.1016/j.jprot.2017.10.007]; GPMDB: [http://gpmdb.org/data/keyword/29054541 127]. | ||
+ | #Karg E, Smets M, Ryan J, Forné I, Qin W, Mulholland CB, Kalideris G, Imhof A, Bultmann S, Leonhardt H, (2017) "Ubiquitome analysis reveals PCNA-associated factor 15 (PAF15) as a specific ubiquitination target of UHRF1 in embryonic stem cells." <i>J Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29055779 29055779]; doi: [https://dx.doi.org/10.1016/j.jmb.2017.10.014 10.1016/j.jmb.2017.10.014]; GPMDB: [http://gpmdb.org/data/keyword/29055779 32]. | ||
+ | #Hartl M, Füßl M, Boersema PJ, Jost JO, Kramer K, Bakirbas A, Sindlinger J, Plöchinger M, Leister D, Uhrig G, Moorhead GB, Cox J, Salvucci ME, Schwarzer D, Mann M, Finkemeier I, (2017) "Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in <i>Arabidopsis</i>." <i>Mol Syst Biol</i> <b>13</b>(10):949; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29061669 29061669]; GPMDB: [http://gpmdb.org/data/keyword/29061669 44]. |
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 Nov. 5, 2017.