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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 October | + | 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 October 30, 2016. |
#Scott N, Sutton J, Gray C, (1989) "Morphometric diagnosis of serous effusions: refinement of differences between benign and malignant cases by use of outlying values and larger sample size." <i>J Clin Pathol</i> <b>42</b>(6):607–12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2738165 2738165]; GPMDB: [http://gpmdb.org/data/keyword/2738165 1]. | #Scott N, Sutton J, Gray C, (1989) "Morphometric diagnosis of serous effusions: refinement of differences between benign and malignant cases by use of outlying values and larger sample size." <i>J Clin Pathol</i> <b>42</b>(6):607–12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2738165 2738165]; GPMDB: [http://gpmdb.org/data/keyword/2738165 1]. | ||
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#Reiland S, Messerli G, Baerenfaller K, Gerrits B, Endler A, Grossmann J, Gruissem W, Baginsky S, (2009) "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks." <i>Plant Physiol</i> <b>150</b>(2):889–903; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19376835 19376835]; doi: [https://dx.doi.org/10.1104/pp.109.138677 10.1104/pp.109.138677]; GPMDB: [http://gpmdb.org/data/keyword/19376835 13]. | #Reiland S, Messerli G, Baerenfaller K, Gerrits B, Endler A, Grossmann J, Gruissem W, Baginsky S, (2009) "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks." <i>Plant Physiol</i> <b>150</b>(2):889–903; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19376835 19376835]; doi: [https://dx.doi.org/10.1104/pp.109.138677 10.1104/pp.109.138677]; GPMDB: [http://gpmdb.org/data/keyword/19376835 13]. | ||
#Parker KC, Walsh RJ, Salajegheh M, Amato AA, Krastins B, Sarracino DA, Greenberg SA, (2009) "Characterization of human skeletal muscle biopsy samples using shotgun proteomics." <i>J Proteome Res</i> <b>8</b>(7):3265–77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19382779 19382779]; doi: [https://dx.doi.org/10.1021/pr800873q 10.1021/pr800873q]; GPMDB: [http://gpmdb.org/data/keyword/19382779 36]. | #Parker KC, Walsh RJ, Salajegheh M, Amato AA, Krastins B, Sarracino DA, Greenberg SA, (2009) "Characterization of human skeletal muscle biopsy samples using shotgun proteomics." <i>J Proteome Res</i> <b>8</b>(7):3265–77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19382779 19382779]; doi: [https://dx.doi.org/10.1021/pr800873q 10.1021/pr800873q]; GPMDB: [http://gpmdb.org/data/keyword/19382779 36]. | ||
- | #Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ, HUPO Test Sample Working Group, (2009) "A HUPO test sample study reveals common problems in mass spectrometry-based proteomics." <i>Nat Methods</i> <b>6</b>(6):423–30; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19448641 19448641]; doi: [https://dx.doi.org/10.1038/nmeth.1333 10.1038/nmeth.1333]; GPMDB: [http://gpmdb.org/data/keyword/19448641 14]. | + | #Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ, HUPO Test Sample Working Group., (2009) "A HUPO test sample study reveals common problems in mass spectrometry-based proteomics." <i>Nat Methods</i> <b>6</b>(6):423–30; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19448641 19448641]; doi: [https://dx.doi.org/10.1038/nmeth.1333 10.1038/nmeth.1333]; GPMDB: [http://gpmdb.org/data/keyword/19448641 14]. |
#Fernández E, Collins MO, Uren RT, Kopanitsa MV, Komiyama NH, Croning MD, Zografos L, Armstrong JD, Choudhary JS, Grant SG, (2009) "Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins." <i>Mol Syst Biol</i> <b>5</b>:269; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19455133 19455133]; doi: [https://dx.doi.org/10.1038/msb.2009.27 10.1038/msb.2009.27]; GPMDB: [http://gpmdb.org/data/keyword/19455133 70]. | #Fernández E, Collins MO, Uren RT, Kopanitsa MV, Komiyama NH, Croning MD, Zografos L, Armstrong JD, Choudhary JS, Grant SG, (2009) "Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins." <i>Mol Syst Biol</i> <b>5</b>:269; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19455133 19455133]; doi: [https://dx.doi.org/10.1038/msb.2009.27 10.1038/msb.2009.27]; GPMDB: [http://gpmdb.org/data/keyword/19455133 70]. | ||
#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]. | ||
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#Bischof S, Baerenfaller K, Wildhaber T, Troesch R, Vidi PA, Roschitzki B, Hirsch-Hoffmann M, Hennig L, Kessler F, Gruissem W, Baginsky S, (2011) "Plastid proteome assembly without Toc159: photosynthetic protein import and accumulation of N-acetylated plastid precursor proteins." <i>Plant Cell</i> <b>23</b>(11):3911–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22128122 22128122]; doi: [https://dx.doi.org/10.1105/tpc.111.092882 10.1105/tpc.111.092882]; GPMDB: [http://gpmdb.org/data/keyword/22128122 6]. | #Bischof S, Baerenfaller K, Wildhaber T, Troesch R, Vidi PA, Roschitzki B, Hirsch-Hoffmann M, Hennig L, Kessler F, Gruissem W, Baginsky S, (2011) "Plastid proteome assembly without Toc159: photosynthetic protein import and accumulation of N-acetylated plastid precursor proteins." <i>Plant Cell</i> <b>23</b>(11):3911–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22128122 22128122]; doi: [https://dx.doi.org/10.1105/tpc.111.092882 10.1105/tpc.111.092882]; GPMDB: [http://gpmdb.org/data/keyword/22128122 6]. | ||
#Prasad TS, Harsha HC, Keerthikumar S, Sekhar NR, Selvan LD, Kumar P, Pinto SM, Muthusamy B, Subbannayya Y, Renuse S, Chaerkady R, Mathur PP, Ravikumar R, Pandey A, (2012) "Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry." <i>J Proteome Res</i> <b>11</b>(1):247–60; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22129275 22129275]; doi: [https://dx.doi.org/10.1021/pr200827k 10.1021/pr200827k]; GPMDB: [http://gpmdb.org/data/keyword/22129275 70]. | #Prasad TS, Harsha HC, Keerthikumar S, Sekhar NR, Selvan LD, Kumar P, Pinto SM, Muthusamy B, Subbannayya Y, Renuse S, Chaerkady R, Mathur PP, Ravikumar R, Pandey A, (2012) "Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry." <i>J Proteome Res</i> <b>11</b>(1):247–60; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22129275 22129275]; doi: [https://dx.doi.org/10.1021/pr200827k 10.1021/pr200827k]; GPMDB: [http://gpmdb.org/data/keyword/22129275 70]. | ||
- | #Thomas L, Hodgson DA, Wentzel A, Nieselt K, Ellingsen TE, Moore J, Morrissey ER, Legaie R, STREAM Consortium, Wohlleben W, Rodríguez-García A, Martín JF, Burroughs NJ, Wellington EM, Smith MC, (2012) "Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture." <i>Mol Cell Proteomics</i> <b>11</b>(2):M111.013797; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22147733 22147733]; doi: [https://dx.doi.org/10.1074/mcp.M111.013797 10.1074/mcp.M111.013797]; GPMDB: [http://gpmdb.org/data/keyword/22147733 64]. | + | #Thomas L, Hodgson DA, Wentzel A, Nieselt K, Ellingsen TE, Moore J, Morrissey ER, Legaie R, STREAM Consortium., Wohlleben W, Rodríguez-García A, Martín JF, Burroughs NJ, Wellington EM, Smith MC, (2012) "Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture." <i>Mol Cell Proteomics</i> <b>11</b>(2):M111.013797; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22147733 22147733]; doi: [https://dx.doi.org/10.1074/mcp.M111.013797 10.1074/mcp.M111.013797]; GPMDB: [http://gpmdb.org/data/keyword/22147733 64]. |
#Choi DS, Yang JS, Choi EJ, Jang SC, Park S, Kim OY, Hwang D, Kim KP, Kim YK, Kim S, Gho YS, (2012) "The protein interaction network of extracellular vesicles derived from human colorectal cancer cells." <i>J Proteome Res</i> <b>11</b>(2):1144–51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22149170 22149170]; doi: [https://dx.doi.org/10.1021/pr200842h 10.1021/pr200842h]; GPMDB: [http://gpmdb.org/data/keyword/22149170 1]. | #Choi DS, Yang JS, Choi EJ, Jang SC, Park S, Kim OY, Hwang D, Kim KP, Kim YK, Kim S, Gho YS, (2012) "The protein interaction network of extracellular vesicles derived from human colorectal cancer cells." <i>J Proteome Res</i> <b>11</b>(2):1144–51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22149170 22149170]; doi: [https://dx.doi.org/10.1021/pr200842h 10.1021/pr200842h]; GPMDB: [http://gpmdb.org/data/keyword/22149170 1]. | ||
#Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, Hynes RO, (2012) "The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices." <i>Mol Cell Proteomics</i> <b>11</b>(4):M111.014647; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22159717 22159717]; doi: [https://dx.doi.org/10.1074/mcp.M111.014647 10.1074/mcp.M111.014647]; GPMDB: [http://gpmdb.org/data/keyword/22159717 98]. | #Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, Hynes RO, (2012) "The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices." <i>Mol Cell Proteomics</i> <b>11</b>(4):M111.014647; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/22159717 22159717]; doi: [https://dx.doi.org/10.1074/mcp.M111.014647 10.1074/mcp.M111.014647]; GPMDB: [http://gpmdb.org/data/keyword/22159717 98]. | ||
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#Guldbrandsen A, Vethe H, Farag Y, Oveland E, Garberg H, Berle M, Myhr KM, Opsahl JA, Barsnes H, Berven FS, (2014) "In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR)." <i>Mol Cell Proteomics</i> <b>13</b>(11):3152–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25038066 25038066]; doi: [https://dx.doi.org/10.1074/mcp.M114.038554 10.1074/mcp.M114.038554]; GPMDB: [http://gpmdb.org/data/keyword/25038066 88]. | #Guldbrandsen A, Vethe H, Farag Y, Oveland E, Garberg H, Berle M, Myhr KM, Opsahl JA, Barsnes H, Berven FS, (2014) "In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR)." <i>Mol Cell Proteomics</i> <b>13</b>(11):3152–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25038066 25038066]; doi: [https://dx.doi.org/10.1074/mcp.M114.038554 10.1074/mcp.M114.038554]; GPMDB: [http://gpmdb.org/data/keyword/25038066 88]. | ||
#Chen YJ, Ching WC, Chen JS, Lee TY, Lu CT, Chou HC, Lin PY, Khoo KH, Chen JH, Chen YJ, (2014) "Decoding the s-nitrosoproteomic atlas in individualized human colorectal cancer tissues using a label-free quantitation strategy." <i>J Proteome Res</i> <b>13</b>(11):4942–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25040305 25040305]; doi: [https://dx.doi.org/10.1021/pr5002675 10.1021/pr5002675]; GPMDB: [http://gpmdb.org/data/keyword/25040305 54]. | #Chen YJ, Ching WC, Chen JS, Lee TY, Lu CT, Chou HC, Lin PY, Khoo KH, Chen JH, Chen YJ, (2014) "Decoding the s-nitrosoproteomic atlas in individualized human colorectal cancer tissues using a label-free quantitation strategy." <i>J Proteome Res</i> <b>13</b>(11):4942–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25040305 25040305]; doi: [https://dx.doi.org/10.1021/pr5002675 10.1021/pr5002675]; GPMDB: [http://gpmdb.org/data/keyword/25040305 54]. | ||
- | #Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC, NCI CPTAC, (2014) "Proteogenomic characterization of human colon and rectal cancer." <i>Nature</i> <b>513</b>(7518):382–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25043054 25043054]; doi: [https://dx.doi.org/10.1038/nature13438 10.1038/nature13438]; GPMDB: [http://gpmdb.org/data/keyword/25043054 1381]. | + | #Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC, NCI CPTAC., (2014) "Proteogenomic characterization of human colon and rectal cancer." <i>Nature</i> <b>513</b>(7518):382–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25043054 25043054]; doi: [https://dx.doi.org/10.1038/nature13438 10.1038/nature13438]; GPMDB: [http://gpmdb.org/data/keyword/25043054 1381]. |
#An E, Narayanan M, Manes NP, Nita-Lazar A, (2014) "Characterization of functional reprogramming during osteoclast development using quantitative proteomics and mRNA profiling." <i>Mol Cell Proteomics</i> <b>13</b>(10):2687–704; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25044017 25044017]; doi: [https://dx.doi.org/10.1074/mcp.M113.034371 10.1074/mcp.M113.034371]; GPMDB: [http://gpmdb.org/data/keyword/25044017 73]. | #An E, Narayanan M, Manes NP, Nita-Lazar A, (2014) "Characterization of functional reprogramming during osteoclast development using quantitative proteomics and mRNA profiling." <i>Mol Cell Proteomics</i> <b>13</b>(10):2687–704; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25044017 25044017]; doi: [https://dx.doi.org/10.1074/mcp.M113.034371 10.1074/mcp.M113.034371]; GPMDB: [http://gpmdb.org/data/keyword/25044017 73]. | ||
#Végh MJ, Rausell A, Loos M, Heldring CM, Jurkowski W, van Nierop P, Paliukhovich I, Li KW, del Sol A, Smit AB, Spijker S, van Kesteren RE, (2014) "Hippocampal extracellular matrix levels and stochasticity in synaptic protein expression increase with age and are associated with age-dependent cognitive decline." <i>Mol Cell Proteomics</i> <b>13</b>(11):2975–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25044018 25044018]; doi: [https://dx.doi.org/10.1074/mcp.M113.032086 10.1074/mcp.M113.032086]; GPMDB: [http://gpmdb.org/data/keyword/25044018 8]. | #Végh MJ, Rausell A, Loos M, Heldring CM, Jurkowski W, van Nierop P, Paliukhovich I, Li KW, del Sol A, Smit AB, Spijker S, van Kesteren RE, (2014) "Hippocampal extracellular matrix levels and stochasticity in synaptic protein expression increase with age and are associated with age-dependent cognitive decline." <i>Mol Cell Proteomics</i> <b>13</b>(11):2975–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25044018 25044018]; doi: [https://dx.doi.org/10.1074/mcp.M113.032086 10.1074/mcp.M113.032086]; GPMDB: [http://gpmdb.org/data/keyword/25044018 8]. | ||
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#Madeira JP, Alpha-Bazin B, Armengaud J, Duport C, (2015) "Time dynamics of the Bacillus cereus exoproteome are shaped by cellular oxidation." <i>Front Microbiol</i> <b>6</b>:342; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25954265 25954265]; doi: [https://dx.doi.org/10.3389/fmicb.2015.00342 10.3389/fmicb.2015.00342]; GPMDB: [http://gpmdb.org/data/keyword/25954265 30]. | #Madeira JP, Alpha-Bazin B, Armengaud J, Duport C, (2015) "Time dynamics of the Bacillus cereus exoproteome are shaped by cellular oxidation." <i>Front Microbiol</i> <b>6</b>:342; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25954265 25954265]; doi: [https://dx.doi.org/10.3389/fmicb.2015.00342 10.3389/fmicb.2015.00342]; GPMDB: [http://gpmdb.org/data/keyword/25954265 30]. | ||
#Walther DM, Kasturi P, Zheng M, Pinkert S, Vecchi G, Ciryam P, Morimoto RI, Dobson CM, Vendruscolo M, Mann M, Hartl FU, (2015) "Widespread Proteome Remodeling and Aggregation in Aging C. elegans." <i>Cell</i> <b>161</b>(4):919–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25957690 25957690]; doi: [https://dx.doi.org/10.1016/j.cell.2015.03.032 10.1016/j.cell.2015.03.032]; GPMDB: [http://gpmdb.org/data/keyword/25957690 278]. | #Walther DM, Kasturi P, Zheng M, Pinkert S, Vecchi G, Ciryam P, Morimoto RI, Dobson CM, Vendruscolo M, Mann M, Hartl FU, (2015) "Widespread Proteome Remodeling and Aggregation in Aging C. elegans." <i>Cell</i> <b>161</b>(4):919–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25957690 25957690]; doi: [https://dx.doi.org/10.1016/j.cell.2015.03.032 10.1016/j.cell.2015.03.032]; GPMDB: [http://gpmdb.org/data/keyword/25957690 278]. | ||
- | #Hosp F, Vossfeldt H, Heinig M, Vasiljevic D, Arumughan A, Wyler E, Genetic and Environmental Risk for Alzheimer’s Disease GERAD1 Consortium, Landthaler M, Hubner N, Wanker EE, Lannfelt L, Ingelsson M, Lalowski M, Voigt A, Selbach M, (2015) "Quantitative interaction proteomics of neurodegenerative disease proteins." <i>Cell Rep</i> <b>11</b>(7):1134–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25959826 25959826]; doi: [https://dx.doi.org/10.1016/j.celrep.2015.04.030 10.1016/j.celrep.2015.04.030]; GPMDB: [http://gpmdb.org/data/keyword/25959826 122]. | + | #Hosp F, Vossfeldt H, Heinig M, Vasiljevic D, Arumughan A, Wyler E, Genetic and Environmental Risk for Alzheimer’s Disease GERAD1 Consortium., Landthaler M, Hubner N, Wanker EE, Lannfelt L, Ingelsson M, Lalowski M, Voigt A, Selbach M, (2015) "Quantitative interaction proteomics of neurodegenerative disease proteins." <i>Cell Rep</i> <b>11</b>(7):1134–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25959826 25959826]; doi: [https://dx.doi.org/10.1016/j.celrep.2015.04.030 10.1016/j.celrep.2015.04.030]; GPMDB: [http://gpmdb.org/data/keyword/25959826 122]. |
#Tay AP, Pang CN, Twine NA, Hart-Smith G, Harkness L, Kassem M, Wilkins MR, (2015) "Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data." <i>J Proteome Res</i> <b>14</b>(9):3541–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25961807 25961807]; doi: [https://dx.doi.org/10.1021/pr5011394 10.1021/pr5011394]; GPMDB: [http://gpmdb.org/data/keyword/25961807 77]. | #Tay AP, Pang CN, Twine NA, Hart-Smith G, Harkness L, Kassem M, Wilkins MR, (2015) "Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data." <i>J Proteome Res</i> <b>14</b>(9):3541–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25961807 25961807]; doi: [https://dx.doi.org/10.1021/pr5011394 10.1021/pr5011394]; GPMDB: [http://gpmdb.org/data/keyword/25961807 77]. | ||
#Koch H, Busto ME, Kramer K, Médard G, Kuster B, (2015) "Chemical Proteomics Uncovers EPHA2 as a Mechanism of Acquired Resistance to Small Molecule EGFR Kinase Inhibition." <i>J Proteome Res</i> <b>14</b>(6):2617–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25963923 25963923]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00161 10.1021/acs.jproteome.5b00161]; GPMDB: [http://gpmdb.org/data/keyword/25963923 18]. | #Koch H, Busto ME, Kramer K, Médard G, Kuster B, (2015) "Chemical Proteomics Uncovers EPHA2 as a Mechanism of Acquired Resistance to Small Molecule EGFR Kinase Inhibition." <i>J Proteome Res</i> <b>14</b>(6):2617–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25963923 25963923]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00161 10.1021/acs.jproteome.5b00161]; GPMDB: [http://gpmdb.org/data/keyword/25963923 18]. | ||
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#Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L, (2016) "Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome." <i>Proteomics</i> <b>16</b>(4):554–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26702875 26702875]; doi: [https://dx.doi.org/10.1002/pmic.201500187 10.1002/pmic.201500187]; GPMDB: [http://gpmdb.org/data/keyword/26702875 2]. | #Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L, (2016) "Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome." <i>Proteomics</i> <b>16</b>(4):554–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26702875 26702875]; doi: [https://dx.doi.org/10.1002/pmic.201500187 10.1002/pmic.201500187]; GPMDB: [http://gpmdb.org/data/keyword/26702875 2]. | ||
#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]. | ||
- | # | + | # () "" <i></i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/ ]; GPMDB: [http://gpmdb.org/data/keyword/26714523 16]. |
#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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#Fang Y, Zhang Q, Wang X, Yang X, Wang X, Huang Z, Jiao Y, Wang J, (2016) "Quantitative phosphoproteomics reveals genistein as a modulator of cell cycle and DNA damage response pathways in triple-negative breast cancer cells." <i>Int J Oncol</i> <b>48</b>(3):1016–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26783066 26783066]; doi: [https://dx.doi.org/10.3892/ijo.2016.3327 10.3892/ijo.2016.3327]; GPMDB: [http://gpmdb.org/data/keyword/26783066 2]. | #Fang Y, Zhang Q, Wang X, Yang X, Wang X, Huang Z, Jiao Y, Wang J, (2016) "Quantitative phosphoproteomics reveals genistein as a modulator of cell cycle and DNA damage response pathways in triple-negative breast cancer cells." <i>Int J Oncol</i> <b>48</b>(3):1016–28; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26783066 26783066]; doi: [https://dx.doi.org/10.3892/ijo.2016.3327 10.3892/ijo.2016.3327]; GPMDB: [http://gpmdb.org/data/keyword/26783066 2]. | ||
#Cheng Z, Teo G, Krueger S, Rock TM, Koh HW, Choi H, Vogel C, (2016) "Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress." <i>Mol Syst Biol</i> <b>12</b>(1):855; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26792871 26792871]; GPMDB: [http://gpmdb.org/data/keyword/26792871 138]. | #Cheng Z, Teo G, Krueger S, Rock TM, Koh HW, Choi H, Vogel C, (2016) "Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress." <i>Mol Syst Biol</i> <b>12</b>(1):855; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26792871 26792871]; GPMDB: [http://gpmdb.org/data/keyword/26792871 138]. | ||
- | #Vincent D, Ezernieks V, Elkins A, Nguyen N, Moate PJ, Cocks BG, Rochfort S, ( | + | #Vincent D, Ezernieks V, Elkins A, Nguyen N, Moate PJ, Cocks BG, Rochfort S, (2016) "Milk Bottom-Up Proteomics: Method Optimization." <i>Front Genet</i> <b>6</b>:360; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26793233 26793233]; doi: [https://dx.doi.org/10.3389/fgene.2015.00360 10.3389/fgene.2015.00360]; GPMDB: [http://gpmdb.org/data/keyword/26793233 262]. |
#Li Q, Lex RK, Chung H, Giovanetti SM, Ji Z, Ji H, Person MD, Kim J, Vokes SA, (2016) "The Pluripotency Factor NANOG Binds to GLI Proteins and Represses Hedgehog-mediated Transcription." <i>J Biol Chem</i> <b>291</b>(13):7171–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26797124 26797124]; doi: [https://dx.doi.org/10.1074/jbc.M116.714857 10.1074/jbc.M116.714857]; GPMDB: [http://gpmdb.org/data/keyword/26797124 10]. | #Li Q, Lex RK, Chung H, Giovanetti SM, Ji Z, Ji H, Person MD, Kim J, Vokes SA, (2016) "The Pluripotency Factor NANOG Binds to GLI Proteins and Represses Hedgehog-mediated Transcription." <i>J Biol Chem</i> <b>291</b>(13):7171–82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26797124 26797124]; doi: [https://dx.doi.org/10.1074/jbc.M116.714857 10.1074/jbc.M116.714857]; GPMDB: [http://gpmdb.org/data/keyword/26797124 10]. | ||
#Schüller R, Forné I, Straub T, Schreieck A, Texier Y, Shah N, Decker TM, Cramer P, Imhof A, Eick D, (2016) "Heptad-Specific Phosphorylation of RNA Polymerase II CTD." <i>Mol Cell</i> <b>61</b>(2):305–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26799765 26799765]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.12.003 10.1016/j.molcel.2015.12.003]; GPMDB: [http://gpmdb.org/data/keyword/26799765 209]. | #Schüller R, Forné I, Straub T, Schreieck A, Texier Y, Shah N, Decker TM, Cramer P, Imhof A, Eick D, (2016) "Heptad-Specific Phosphorylation of RNA Polymerase II CTD." <i>Mol Cell</i> <b>61</b>(2):305–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26799765 26799765]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.12.003 10.1016/j.molcel.2015.12.003]; GPMDB: [http://gpmdb.org/data/keyword/26799765 209]. | ||
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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]. | ||
- | # | + | # () "" <i></i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/ ]; GPMDB: [http://gpmdb.org/data/keyword/26828036 22]. |
#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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#Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C, (2016) "Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration." <i>Sci Signal</i> <b>9</b>(414):ra15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861043 26861043]; doi: [https://dx.doi.org/10.1126/scisignal.aac5820 10.1126/scisignal.aac5820]; GPMDB: [http://gpmdb.org/data/keyword/26861043 76]. | #Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, van Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C, (2016) "Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration." <i>Sci Signal</i> <b>9</b>(414):ra15; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861043 26861043]; doi: [https://dx.doi.org/10.1126/scisignal.aac5820 10.1126/scisignal.aac5820]; GPMDB: [http://gpmdb.org/data/keyword/26861043 76]. | ||
#Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-Dürr P, Shah AM, Brandes RP, (2016) "The Endoplasmic Reticulum Chaperone Calnexin Is a NADPH Oxidase NOX4 Interacting Protein." <i>J Biol Chem</i> <b>291</b>(13):7045–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861875 26861875]; doi: [https://dx.doi.org/10.1074/jbc.M115.710772 10.1074/jbc.M115.710772]; GPMDB: [http://gpmdb.org/data/keyword/26861875 80]. | #Prior KK, Wittig I, Leisegang MS, Groenendyk J, Weissmann N, Michalak M, Jansen-Dürr P, Shah AM, Brandes RP, (2016) "The Endoplasmic Reticulum Chaperone Calnexin Is a NADPH Oxidase NOX4 Interacting Protein." <i>J Biol Chem</i> <b>291</b>(13):7045–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26861875 26861875]; doi: [https://dx.doi.org/10.1074/jbc.M115.710772 10.1074/jbc.M115.710772]; GPMDB: [http://gpmdb.org/data/keyword/26861875 80]. | ||
- | #Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssié D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianférani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Couté Y, Gonzalez de Peredo A, ( | + | #Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssié D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianférani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Couté Y, Gonzalez de Peredo A, (2015) "Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods." <i>Data Brief</i> <b>6</b>:286–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26862574 26862574]; doi: [https://dx.doi.org/10.1016/j.dib.2015.11.063 10.1016/j.dib.2015.11.063]; GPMDB: [http://gpmdb.org/data/keyword/26862574 27]. |
#Sahebekhtiari N, Thomsen MM, Sloth JJ, Stenbroen V, Zeviani M, Gregersen N, Viscomi C, Palmfeldt J, (2016) "Quantitative proteomics suggests metabolic reprogramming during ETHE1 deficiency." <i>Proteomics</i> <b>16</b>(7):1166–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26867521 26867521]; doi: [https://dx.doi.org/10.1002/pmic.201500336 10.1002/pmic.201500336]; GPMDB: [http://gpmdb.org/data/keyword/26867521 50]. | #Sahebekhtiari N, Thomsen MM, Sloth JJ, Stenbroen V, Zeviani M, Gregersen N, Viscomi C, Palmfeldt J, (2016) "Quantitative proteomics suggests metabolic reprogramming during ETHE1 deficiency." <i>Proteomics</i> <b>16</b>(7):1166–76; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26867521 26867521]; doi: [https://dx.doi.org/10.1002/pmic.201500336 10.1002/pmic.201500336]; GPMDB: [http://gpmdb.org/data/keyword/26867521 50]. | ||
#Lamberti Y, Cafiero JH, Surmann K, Valdez H, Holubova J, Večerek B, Sebo P, Schmidt F, Völker U, Rodriguez ME, (2016) "Proteome analysis of Bordetella pertussis isolated from human macrophages." <i>J Proteomics</i> <b>136</b>:55–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26873878 26873878]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.002 10.1016/j.jprot.2016.02.002]; GPMDB: [http://gpmdb.org/data/keyword/26873878 9]. | #Lamberti Y, Cafiero JH, Surmann K, Valdez H, Holubova J, Večerek B, Sebo P, Schmidt F, Völker U, Rodriguez ME, (2016) "Proteome analysis of Bordetella pertussis isolated from human macrophages." <i>J Proteomics</i> <b>136</b>:55–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26873878 26873878]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.02.002 10.1016/j.jprot.2016.02.002]; GPMDB: [http://gpmdb.org/data/keyword/26873878 9]. | ||
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#Packialakshmi B, Liyanage R, Lay JO Jr, Okimoto R, Rath NC, (2016) "Proteomic Changes in the Plasma of Broiler Chickens with Femoral Head Necrosis." <i>Biomark Insights</i> <b>11</b>:55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27147818 27147818]; doi: [https://dx.doi.org/10.4137/BMI.S38291 10.4137/BMI.S38291]; GPMDB: [http://gpmdb.org/data/keyword/27147818 6]. | #Packialakshmi B, Liyanage R, Lay JO Jr, Okimoto R, Rath NC, (2016) "Proteomic Changes in the Plasma of Broiler Chickens with Femoral Head Necrosis." <i>Biomark Insights</i> <b>11</b>:55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27147818 27147818]; doi: [https://dx.doi.org/10.4137/BMI.S38291 10.4137/BMI.S38291]; GPMDB: [http://gpmdb.org/data/keyword/27147818 6]. | ||
#Jhingan GD, Kumari S, Jamwal SV, Kalam H, Arora D, Jain N, Kumaar LK, Samal A, Rao KV, Kumar D, Nandicoori VK, (2016) "Comparative Proteomic Analyses of Avirulent, Virulent, and Clinical Strains of Mycobacterium tuberculosis Identify Strain-specific Patterns." <i>J Biol Chem</i> <b>291</b>(27):14257–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27151218 27151218]; doi: [https://dx.doi.org/10.1074/jbc.M115.666123 10.1074/jbc.M115.666123]; GPMDB: [http://gpmdb.org/data/keyword/27151218 16]. | #Jhingan GD, Kumari S, Jamwal SV, Kalam H, Arora D, Jain N, Kumaar LK, Samal A, Rao KV, Kumar D, Nandicoori VK, (2016) "Comparative Proteomic Analyses of Avirulent, Virulent, and Clinical Strains of Mycobacterium tuberculosis Identify Strain-specific Patterns." <i>J Biol Chem</i> <b>291</b>(27):14257–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27151218 27151218]; doi: [https://dx.doi.org/10.1074/jbc.M115.666123 10.1074/jbc.M115.666123]; GPMDB: [http://gpmdb.org/data/keyword/27151218 16]. | ||
- | #Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun DA, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-Lami HA, Yeung Y, Choi YJ, University of Washington Center for Mendelian Genomics, Duffourd Y, Faivre L, Rivière JB, Chen J, Liu KJ, Marcotte EM, Hildebrandt F, Thauvin-Robinet C, Krakow D, Jackson PK, Wallingford JB, (2016) "The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery." <i>Nat Genet</i> <b>48</b>(6):648–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27158779 27158779]; doi: [https://dx.doi.org/10.1038/ng.3558 10.1038/ng.3558]; GPMDB: [http://gpmdb.org/data/keyword/27158779 44]. | + | #Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun DA, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-Lami HA, Yeung Y, Choi YJ, University of Washington Center for Mendelian Genomics., Duffourd Y, Faivre L, Rivière JB, Chen J, Liu KJ, Marcotte EM, Hildebrandt F, Thauvin-Robinet C, Krakow D, Jackson PK, Wallingford JB, (2016) "The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery." <i>Nat Genet</i> <b>48</b>(6):648–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27158779 27158779]; doi: [https://dx.doi.org/10.1038/ng.3558 10.1038/ng.3558]; GPMDB: [http://gpmdb.org/data/keyword/27158779 44]. |
#Hsu CH, Hsu CW, Hsueh C, Wang CL, Wu YC, Wu CC, Liu CC, Yu JS, Chang YS, Yu CJ, (2016) "Identification and Characterization of Potential Biomarkers by Quantitative Tissue Proteomics of Primary Lung Adenocarcinoma." <i>Mol Cell Proteomics</i> <b>15</b>(7):2396–410; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27161446 27161446]; doi: [https://dx.doi.org/10.1074/mcp.M115.057026 10.1074/mcp.M115.057026]; GPMDB: [http://gpmdb.org/data/keyword/27161446 60]. | #Hsu CH, Hsu CW, Hsueh C, Wang CL, Wu YC, Wu CC, Liu CC, Yu JS, Chang YS, Yu CJ, (2016) "Identification and Characterization of Potential Biomarkers by Quantitative Tissue Proteomics of Primary Lung Adenocarcinoma." <i>Mol Cell Proteomics</i> <b>15</b>(7):2396–410; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27161446 27161446]; doi: [https://dx.doi.org/10.1074/mcp.M115.057026 10.1074/mcp.M115.057026]; GPMDB: [http://gpmdb.org/data/keyword/27161446 60]. | ||
#Taha MK, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane AE, Frosch M, Hellenbrand W, Hong E, Parent du Châtelet I, Prior K, Harmsen D, Vogel U, (2016) "Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men." <i>PLoS One</i> <b>11</b>(5):e0154047; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27167067 27167067]; doi: [https://dx.doi.org/10.1371/journal.pone.0154047 10.1371/journal.pone.0154047]; GPMDB: [http://gpmdb.org/data/keyword/27167067 12]. | #Taha MK, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane AE, Frosch M, Hellenbrand W, Hong E, Parent du Châtelet I, Prior K, Harmsen D, Vogel U, (2016) "Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men." <i>PLoS One</i> <b>11</b>(5):e0154047; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27167067 27167067]; doi: [https://dx.doi.org/10.1371/journal.pone.0154047 10.1371/journal.pone.0154047]; GPMDB: [http://gpmdb.org/data/keyword/27167067 12]. | ||
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#Bullen JW, Tchernyshyov I, Holewinski RJ, DeVine L, Wu F, Venkatraman V, Kass DL, Cole RN, Van Eyk J, Semenza GL, (2016) "Protein kinase A-dependent phosphorylation stimulates the transcriptional activity of hypoxia-inducible factor 1." <i>Sci Signal</i> <b>9</b>(430):ra56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27245613 27245613]; doi: [https://dx.doi.org/10.1126/scisignal.aaf0583 10.1126/scisignal.aaf0583]; GPMDB: [http://gpmdb.org/data/keyword/27245613 14]. | #Bullen JW, Tchernyshyov I, Holewinski RJ, DeVine L, Wu F, Venkatraman V, Kass DL, Cole RN, Van Eyk J, Semenza GL, (2016) "Protein kinase A-dependent phosphorylation stimulates the transcriptional activity of hypoxia-inducible factor 1." <i>Sci Signal</i> <b>9</b>(430):ra56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27245613 27245613]; doi: [https://dx.doi.org/10.1126/scisignal.aaf0583 10.1126/scisignal.aaf0583]; GPMDB: [http://gpmdb.org/data/keyword/27245613 14]. | ||
#Patella F, Neilson LJ, Athineos D, Erami Z, Anderson KI, Blyth K, Ryan KM, Zanivan S, (2016) "In-Depth Proteomics Identifies a Role for Autophagy in Controlling Reactive Oxygen Species Mediated Endothelial Permeability." <i>J Proteome Res</i> <b>15</b>(7):2187–97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27246970 27246970]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00166 10.1021/acs.jproteome.6b00166]; GPMDB: [http://gpmdb.org/data/keyword/27246970 25]. | #Patella F, Neilson LJ, Athineos D, Erami Z, Anderson KI, Blyth K, Ryan KM, Zanivan S, (2016) "In-Depth Proteomics Identifies a Role for Autophagy in Controlling Reactive Oxygen Species Mediated Endothelial Permeability." <i>J Proteome Res</i> <b>15</b>(7):2187–97; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27246970 27246970]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00166 10.1021/acs.jproteome.6b00166]; GPMDB: [http://gpmdb.org/data/keyword/27246970 25]. | ||
- | #Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC, (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [http://gpmdb.org/data/keyword/27251275 1265]. | + | #Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC., (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [http://gpmdb.org/data/keyword/27251275 1265]. |
#Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(8):2671–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [http://gpmdb.org/data/keyword/27259358 112]. | #Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(8):2671–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [http://gpmdb.org/data/keyword/27259358 112]. | ||
#Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W, (2016) "Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2]. | #Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W, (2016) "Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer." <i>Oncotarget</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2]. | ||
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#Dobó J, Szakács D, Oroszlán G, Kortvely E, Kiss B, Boros E, Szász R, Závodszky P, Gál P, Pál G, (2016) "MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked." <i>Sci Rep</i> <b>6</b>:31877; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535802 27535802]; doi: [https://dx.doi.org/10.1038/srep31877 10.1038/srep31877]; GPMDB: [http://gpmdb.org/data/keyword/27535802 6]. | #Dobó J, Szakács D, Oroszlán G, Kortvely E, Kiss B, Boros E, Szász R, Závodszky P, Gál P, Pál G, (2016) "MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked." <i>Sci Rep</i> <b>6</b>:31877; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535802 27535802]; doi: [https://dx.doi.org/10.1038/srep31877 10.1038/srep31877]; GPMDB: [http://gpmdb.org/data/keyword/27535802 6]. | ||
#Zhang P, Karani R, Turner RL, Dufresne C, Ferri S, Van Eyk JE, Semba RD, (2016) "The proteome of normal human retrobulbar optic nerve and sclera." <i>Proteomics</i> <b>16</b>(19):2592–2596; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27538499 27538499]; doi: [https://dx.doi.org/10.1002/pmic.201600229 10.1002/pmic.201600229]; GPMDB: [http://gpmdb.org/data/keyword/27538499 60]. | #Zhang P, Karani R, Turner RL, Dufresne C, Ferri S, Van Eyk JE, Semba RD, (2016) "The proteome of normal human retrobulbar optic nerve and sclera." <i>Proteomics</i> <b>16</b>(19):2592–2596; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27538499 27538499]; doi: [https://dx.doi.org/10.1002/pmic.201600229 10.1002/pmic.201600229]; GPMDB: [http://gpmdb.org/data/keyword/27538499 60]. | ||
- | #Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP, (2016) "Integration of omic networks in a developmental atlas of maize." <i>Science</i> <b>353</b>(6301):814–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27540173 27540173]; doi: [https://dx.doi.org/10.1126/science.aag1125 10.1126/science.aag1125]; GPMDB: [http://gpmdb.org/data/keyword/27540173 | + | #Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP, (2016) "Integration of omic networks in a developmental atlas of maize." <i>Science</i> <b>353</b>(6301):814–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27540173 27540173]; doi: [https://dx.doi.org/10.1126/science.aag1125 10.1126/science.aag1125]; GPMDB: [http://gpmdb.org/data/keyword/27540173 9793]. |
+ | #Xie Y, Wang J, Zhang Y, Liu X, Wang X, Liu K, Huang X, Wang Y, (2016) "Quantitative profiling of spreading-coupled protein tyrosine phosphorylation in migratory cells." <i>Sci Rep</i> <b>6</b>:31811; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554326 27554326]; doi: [https://dx.doi.org/10.1038/srep31811 10.1038/srep31811]; GPMDB: [http://gpmdb.org/data/keyword/27554326 6]. | ||
#He PH, Dong WX, Chu XL, Feng MG, Ying SH, (2016) "The cellular proteome is affected by a gelsolin (BbGEL1) during morphological transitions in aerobic surface versus liquid growth in the entomopathogenic fungus Beauveria bassiana." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554994 27554994]; doi: [https://dx.doi.org/10.1111/1462-2920.13500 10.1111/1462-2920.13500]; GPMDB: [http://gpmdb.org/data/keyword/27554994 34]. | #He PH, Dong WX, Chu XL, Feng MG, Ying SH, (2016) "The cellular proteome is affected by a gelsolin (BbGEL1) during morphological transitions in aerobic surface versus liquid growth in the entomopathogenic fungus Beauveria bassiana." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27554994 27554994]; doi: [https://dx.doi.org/10.1111/1462-2920.13500 10.1111/1462-2920.13500]; GPMDB: [http://gpmdb.org/data/keyword/27554994 34]. | ||
#Viktorovskaya OV, Greco TM, Cristea IM, Thompson SR, (2016) "Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements." <i>PLoS Negl Trop Dis</i> <b>10</b>(8):e0004921; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27556644 27556644]; doi: [https://dx.doi.org/10.1371/journal.pntd.0004921 10.1371/journal.pntd.0004921]; GPMDB: [http://gpmdb.org/data/keyword/27556644 7]. | #Viktorovskaya OV, Greco TM, Cristea IM, Thompson SR, (2016) "Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements." <i>PLoS Negl Trop Dis</i> <b>10</b>(8):e0004921; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27556644 27556644]; doi: [https://dx.doi.org/10.1371/journal.pntd.0004921 10.1371/journal.pntd.0004921]; GPMDB: [http://gpmdb.org/data/keyword/27556644 7]. | ||
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#Jiang Y, Lee J, Lee JH, Lee JW, Kim JH, Choi WH, Yoo YD, Cha-Molstad H, Kim BY, Kwon YT, Noh SA, Kim KP, Lee MJ, (2016) "The arginylation branch of the N-end rule pathway positively regulates cellular autophagic flux and clearance of proteotoxic proteins." <i>Autophagy</i> <b></b>:1–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27560450 27560450]; doi: [https://dx.doi.org/10.1080/15548627.2016.1222991 10.1080/15548627.2016.1222991]; GPMDB: [http://gpmdb.org/data/keyword/27560450 2]. | #Jiang Y, Lee J, Lee JH, Lee JW, Kim JH, Choi WH, Yoo YD, Cha-Molstad H, Kim BY, Kwon YT, Noh SA, Kim KP, Lee MJ, (2016) "The arginylation branch of the N-end rule pathway positively regulates cellular autophagic flux and clearance of proteotoxic proteins." <i>Autophagy</i> <b></b>:1–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27560450 27560450]; doi: [https://dx.doi.org/10.1080/15548627.2016.1222991 10.1080/15548627.2016.1222991]; GPMDB: [http://gpmdb.org/data/keyword/27560450 2]. | ||
#Ross SH, Rollings C, Anderson KE, Hawkins PT, Stephens LR, Cantrell DA, (2016) "Phosphoproteomic Analyses of Interleukin 2 Signaling Reveal Integrated JAK Kinase-Dependent and -Independent Networks in CD8(+) T Cells." <i>Immunity</i> <b>45</b>(3):685–700; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27566939 27566939]; doi: [https://dx.doi.org/10.1016/j.immuni.2016.07.022 10.1016/j.immuni.2016.07.022]; GPMDB: [http://gpmdb.org/data/keyword/27566939 208]. | #Ross SH, Rollings C, Anderson KE, Hawkins PT, Stephens LR, Cantrell DA, (2016) "Phosphoproteomic Analyses of Interleukin 2 Signaling Reveal Integrated JAK Kinase-Dependent and -Independent Networks in CD8(+) T Cells." <i>Immunity</i> <b>45</b>(3):685–700; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27566939 27566939]; doi: [https://dx.doi.org/10.1016/j.immuni.2016.07.022 10.1016/j.immuni.2016.07.022]; GPMDB: [http://gpmdb.org/data/keyword/27566939 208]. | ||
- | #Larsen SC, Sylvestersen KB, Mund A, Lyon D, Mullari M, Madsen MV, Daniel JA, Jensen LJ, Nielsen ML, (2016) "Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells." <i>Sci Signal</i> <b>9</b>(443):rs9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27577262 27577262]; doi: [https://dx.doi.org/10.1126/scisignal.aaf7329 10.1126/scisignal.aaf7329]; GPMDB: [http://gpmdb.org/data/keyword/27577262 | + | #Larsen SC, Sylvestersen KB, Mund A, Lyon D, Mullari M, Madsen MV, Daniel JA, Jensen LJ, Nielsen ML, (2016) "Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells." <i>Sci Signal</i> <b>9</b>(443):rs9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27577262 27577262]; doi: [https://dx.doi.org/10.1126/scisignal.aaf7329 10.1126/scisignal.aaf7329]; GPMDB: [http://gpmdb.org/data/keyword/27577262 10]. |
#Delaveau T, Davoine D, Jolly A, Vallot A, Rouvière JO, Gerber A, Brochet S, Plessis M, Roquigny R, Merhej J, Leger T, Garcia C, Lelandais G, Laine E, Palancade B, Devaux F, Garcia M, (2016) "Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae." <i>Nucleic Acids Res</i> <b>44</b>(18):8826–8841; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27580715 27580715]; doi: [https://dx.doi.org/10.1093/nar/gkw732 10.1093/nar/gkw732]; GPMDB: [http://gpmdb.org/data/keyword/27580715 19]. | #Delaveau T, Davoine D, Jolly A, Vallot A, Rouvière JO, Gerber A, Brochet S, Plessis M, Roquigny R, Merhej J, Leger T, Garcia C, Lelandais G, Laine E, Palancade B, Devaux F, Garcia M, (2016) "Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae." <i>Nucleic Acids Res</i> <b>44</b>(18):8826–8841; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27580715 27580715]; doi: [https://dx.doi.org/10.1093/nar/gkw732 10.1093/nar/gkw732]; GPMDB: [http://gpmdb.org/data/keyword/27580715 19]. | ||
#Lee H, Chae S, Park J, Bae J, Go EB, Kim SJ, Kim H, Hwang D, Lee SW, Lee SY, (2016) "Comprehensive proteome profiling of platelet identified a protein profile predictive of responses to an antiplatelet agent sarpogrelate." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27601597 27601597]; doi: [https://dx.doi.org/10.1074/mcp.M116.059154 10.1074/mcp.M116.059154]; GPMDB: [http://gpmdb.org/data/keyword/27601597 96]. | #Lee H, Chae S, Park J, Bae J, Go EB, Kim SJ, Kim H, Hwang D, Lee SW, Lee SY, (2016) "Comprehensive proteome profiling of platelet identified a protein profile predictive of responses to an antiplatelet agent sarpogrelate." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27601597 27601597]; doi: [https://dx.doi.org/10.1074/mcp.M116.059154 10.1074/mcp.M116.059154]; GPMDB: [http://gpmdb.org/data/keyword/27601597 96]. | ||
#Treitz C, Enjalbert B, Portais JC, Letisse F, Tholey A, (2016) "Differential quantitative proteome analysis of Escherichia coli grown on acetate versus glucose." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27604403 27604403]; doi: [https://dx.doi.org/10.1002/pmic.201600303 10.1002/pmic.201600303]; GPMDB: [http://gpmdb.org/data/keyword/27604403 42]. | #Treitz C, Enjalbert B, Portais JC, Letisse F, Tholey A, (2016) "Differential quantitative proteome analysis of Escherichia coli grown on acetate versus glucose." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27604403 27604403]; doi: [https://dx.doi.org/10.1002/pmic.201600303 10.1002/pmic.201600303]; GPMDB: [http://gpmdb.org/data/keyword/27604403 42]. | ||
+ | #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]. | ||
#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]. | ||
+ | #Worah K, Mathan TS, Vu Manh TP, Keerthikumar S, Schreibelt G, Tel J, Duiveman-de Boer T, Sköld AE, van Spriel AB, de Vries IJ, Huynen MA, Wessels HJ, Gloerich J, Dalod M, Lasonder E, Figdor CG, Buschow SI, (2016) "Proteomics of Human Dendritic Cell Subsets Reveals Subset-Specific Surface Markers and Differential Inflammasome Function." <i>Cell Rep</i> <b>16</b>(11):2953–66; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27626665 27626665]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.08.023 10.1016/j.celrep.2016.08.023]; GPMDB: [http://gpmdb.org/data/keyword/27626665 719]. | ||
#Bennike TB, Ellingsen T, Glerup H, Bonderup OK, Carlsen TG, Meyer MK, Bøgsted M, Christiansen G, Birkelund S, Andersen V, Stensballe A, (2016) "Proteome Analysis of Rheumatoid Arthritis Gut Mucosa." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27627584 27627584]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00598 10.1021/acs.jproteome.6b00598]; GPMDB: [http://gpmdb.org/data/keyword/27627584 33]. | #Bennike TB, Ellingsen T, Glerup H, Bonderup OK, Carlsen TG, Meyer MK, Bøgsted M, Christiansen G, Birkelund S, Andersen V, Stensballe A, (2016) "Proteome Analysis of Rheumatoid Arthritis Gut Mucosa." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27627584 27627584]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00598 10.1021/acs.jproteome.6b00598]; GPMDB: [http://gpmdb.org/data/keyword/27627584 33]. | ||
+ | #Altmann C, Hardt S, Fischer C, Heidler J, Lim HY, Häussler A, Albuquerque B, Zimmer B, Möser C, Behrends C, Koentgen F, Wittig I, Schmidt MH, Clement AM, Deller T, Tegeder I, (2016) "Progranulin overexpression in sensory neurons attenuates neuropathic pain in mice: Role of autophagy." <i>Neurobiol Dis</i> <b>96</b>:294–311; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27629805 27629805]; doi: [https://dx.doi.org/10.1016/j.nbd.2016.09.010 10.1016/j.nbd.2016.09.010]; GPMDB: [http://gpmdb.org/data/keyword/27629805 5]. | ||
#Musunuri S, Khoonsari PE, Mikus M, Wetterhall M, Häggmark-Mänberg A, Lannfelt L, Erlandsson A, Bergquist J, Ingelsson M, Shevchenko G, Nilsson P, Kultima K, (2016) "Increased Levels of Extracellular Microvesicle Markers and Decreased Levels of Endocytic/Exocytic Proteins in the Alzheimer's Disease Brain." <i>J Alzheimers Dis</i> <b>54</b>(4):1671–1686; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27636840 27636840]; doi: [https://dx.doi.org/10.3233/JAD-160271 10.3233/JAD-160271]; GPMDB: [http://gpmdb.org/data/keyword/27636840 107]. | #Musunuri S, Khoonsari PE, Mikus M, Wetterhall M, Häggmark-Mänberg A, Lannfelt L, Erlandsson A, Bergquist J, Ingelsson M, Shevchenko G, Nilsson P, Kultima K, (2016) "Increased Levels of Extracellular Microvesicle Markers and Decreased Levels of Endocytic/Exocytic Proteins in the Alzheimer's Disease Brain." <i>J Alzheimers Dis</i> <b>54</b>(4):1671–1686; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27636840 27636840]; doi: [https://dx.doi.org/10.3233/JAD-160271 10.3233/JAD-160271]; GPMDB: [http://gpmdb.org/data/keyword/27636840 107]. | ||
+ | #Eyckerman S, Impens F, Van Quickelberghe E, Samyn N, Vandemoortele G, De Sutter D, Tavernier J, Gevaert K, (2016) "Intelligent Mixing of Proteomes for Elimination of False Positives in Affinity Purification-Mass Spectrometry." <i>J Proteome Res</i> <b>15</b>(10):3929–3937; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27640904 27640904]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00517 10.1021/acs.jproteome.6b00517]; GPMDB: [http://gpmdb.org/data/keyword/27640904 29]. | ||
+ | #Jean Beltran PM, Mathias RA, Cristea IM, (2016) "A Portrait of the Human Organelle Proteome In Space and Time during Cytomegalovirus Infection." <i>Cell Syst</i> <b>3</b>(4):361–373.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27641956 27641956]; doi: [https://dx.doi.org/10.1016/j.cels.2016.08.012 10.1016/j.cels.2016.08.012]; GPMDB: [http://gpmdb.org/data/keyword/27641956 45]. | ||
#Athanason MG, Stevens SM Jr, Burkhardt BR, (2016) "Hepatic SILAC proteomic data from PANDER transgenic model." <i>Data Brief</i> <b>9</b>:159–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27642623 27642623]; doi: [https://dx.doi.org/10.1016/j.dib.2016.08.017 10.1016/j.dib.2016.08.017]; GPMDB: [http://gpmdb.org/data/keyword/27642623 18]. | #Athanason MG, Stevens SM Jr, Burkhardt BR, (2016) "Hepatic SILAC proteomic data from PANDER transgenic model." <i>Data Brief</i> <b>9</b>:159–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27642623 27642623]; doi: [https://dx.doi.org/10.1016/j.dib.2016.08.017 10.1016/j.dib.2016.08.017]; GPMDB: [http://gpmdb.org/data/keyword/27642623 18]. | ||
#Kubicek-Sutherland JZ, Lofton H, Vestergaard M, Hjort K, Ingmer H, Andersson DI, (2016) "Antimicrobial peptide exposure selects for Staphylococcus aureus resistance to human defence peptides." <i>J Antimicrob Chemother</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27650186 27650186]; doi: [https://dx.doi.org/10.1093/jac/dkw381 10.1093/jac/dkw381]; GPMDB: [http://gpmdb.org/data/keyword/27650186 42]. | #Kubicek-Sutherland JZ, Lofton H, Vestergaard M, Hjort K, Ingmer H, Andersson DI, (2016) "Antimicrobial peptide exposure selects for Staphylococcus aureus resistance to human defence peptides." <i>J Antimicrob Chemother</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27650186 27650186]; doi: [https://dx.doi.org/10.1093/jac/dkw381 10.1093/jac/dkw381]; GPMDB: [http://gpmdb.org/data/keyword/27650186 42]. | ||
#Goldman AR, Bitler BG, Schug Z, Conejo-Garcia JR, Zhang R, Speicher DW, (2016) "The Primary Effect on the Proteome of ARID1A-Mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post-Transcriptional Level." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27654507 27654507]; doi: [https://dx.doi.org/10.1074/mcp.M116.062539 10.1074/mcp.M116.062539]; GPMDB: [http://gpmdb.org/data/keyword/27654507 12]. | #Goldman AR, Bitler BG, Schug Z, Conejo-Garcia JR, Zhang R, Speicher DW, (2016) "The Primary Effect on the Proteome of ARID1A-Mutated Ovarian Clear Cell Carcinoma is Downregulation of the Mevalonate Pathway at the Post-Transcriptional Level." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27654507 27654507]; doi: [https://dx.doi.org/10.1074/mcp.M116.062539 10.1074/mcp.M116.062539]; GPMDB: [http://gpmdb.org/data/keyword/27654507 12]. | ||
#Radzikowski JL, Vedelaar S, Siegel D, Ortega ÁD, Schmidt A, Heinemann M, (2016) "Bacterial persistence is an active σS stress response to metabolic flux limitation." <i>Mol Syst Biol</i> <b>12</b>(9):882; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27655400 27655400]; GPMDB: [http://gpmdb.org/data/keyword/27655400 30]. | #Radzikowski JL, Vedelaar S, Siegel D, Ortega ÁD, Schmidt A, Heinemann M, (2016) "Bacterial persistence is an active σS stress response to metabolic flux limitation." <i>Mol Syst Biol</i> <b>12</b>(9):882; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27655400 27655400]; GPMDB: [http://gpmdb.org/data/keyword/27655400 30]. | ||
+ | #Rose CM, Isasa M, Ordureau A, Prado MA, Beausoleil SA, Jedrychowski MP, Finley DJ, Harper JW, Gygi SP, (2016) "Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes." <i>Cell Syst</i> <b>3</b>(4):395–403.e4; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27667366 27667366]; doi: [https://dx.doi.org/10.1016/j.cels.2016.08.009 10.1016/j.cels.2016.08.009]; GPMDB: [http://gpmdb.org/data/keyword/27667366 26]. | ||
+ | #Abad MA, Zou J, Medina-Pritchard B, Nigg EA, Rappsilber J, Santamaria A, Jeyaprakash AA, (2016) "Ska3 Ensures Timely Mitotic Progression by Interacting Directly With Microtubules and Ska1 Microtubule Binding Domain." <i>Sci Rep</i> <b>6</b>:34042; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27667719 27667719]; doi: [https://dx.doi.org/10.1038/srep34042 10.1038/srep34042]; GPMDB: [http://gpmdb.org/data/keyword/27667719 10]. | ||
+ | #Dörfel MJ, Fang H, Crain J, Klingener M, Weiser J, Lyon GJ, (2016) "Proteomic and genomic characterization of a yeast model for Ogden syndrome." <i>Yeast</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27668839 27668839]; doi: [https://dx.doi.org/10.1002/yea.3211 10.1002/yea.3211]; GPMDB: [http://gpmdb.org/data/keyword/27668839 1]. | ||
#Lee A, Miller D, Henry R, Paruchuri VD, O'Meally RN, Boronina T, Cole RN, Zachara NE, (2016) "Combined Antibody/Lectin Enrichment Identifies Extensive Changes in the O-GlcNAc Sub-proteome upon Oxidative Stress." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27669760 27669760]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00369 10.1021/acs.jproteome.6b00369]; GPMDB: [http://gpmdb.org/data/keyword/27669760 14]. | #Lee A, Miller D, Henry R, Paruchuri VD, O'Meally RN, Boronina T, Cole RN, Zachara NE, (2016) "Combined Antibody/Lectin Enrichment Identifies Extensive Changes in the O-GlcNAc Sub-proteome upon Oxidative Stress." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27669760 27669760]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00369 10.1021/acs.jproteome.6b00369]; GPMDB: [http://gpmdb.org/data/keyword/27669760 14]. | ||
#Lyon SM, Mayampurath A, Rogers MR, Wolfgeher DJ, Fisher SM, Volchenboum SL, He TC, Reid RR, (2016) "A method for whole protein isolation from human cranial bone." <i>Anal Biochem</i> <b>515</b>:33–39; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27677936 27677936]; doi: [https://dx.doi.org/10.1016/j.ab.2016.09.021 10.1016/j.ab.2016.09.021]; GPMDB: [http://gpmdb.org/data/keyword/27677936 10]. | #Lyon SM, Mayampurath A, Rogers MR, Wolfgeher DJ, Fisher SM, Volchenboum SL, He TC, Reid RR, (2016) "A method for whole protein isolation from human cranial bone." <i>Anal Biochem</i> <b>515</b>:33–39; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27677936 27677936]; doi: [https://dx.doi.org/10.1016/j.ab.2016.09.021 10.1016/j.ab.2016.09.021]; GPMDB: [http://gpmdb.org/data/keyword/27677936 10]. | ||
- | #Larkin SE, Johnston HE, Jackson TR, Jamieson DG, Roumeliotis TI, Mockridge CI, Michael A, Manousopoulou A, Papachristou EK, Brown MD, Clarke NW, Pandha H, Aukim-Hastie CL, Cragg MS, Garbis SD, Townsend PA, (2016) "Detection of candidate biomarkers of prostate cancer progression in serum: a depletion-free 3D LC/MS quantitative proteomics pilot study." <i>Br J Cancer</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27685442 27685442]; doi: [https://dx.doi.org/10.1038/bjc.2016.291 10.1038/bjc.2016.291]; GPMDB: [http://gpmdb.org/data/keyword/27685442 | + | #Larkin SE, Johnston HE, Jackson TR, Jamieson DG, Roumeliotis TI, Mockridge CI, Michael A, Manousopoulou A, Papachristou EK, Brown MD, Clarke NW, Pandha H, Aukim-Hastie CL, Cragg MS, Garbis SD, Townsend PA, (2016) "Detection of candidate biomarkers of prostate cancer progression in serum: a depletion-free 3D LC/MS quantitative proteomics pilot study." <i>Br J Cancer</i> <b>115</b>(9):1078–1086; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27685442 27685442]; doi: [https://dx.doi.org/10.1038/bjc.2016.291 10.1038/bjc.2016.291]; GPMDB: [http://gpmdb.org/data/keyword/27685442 8]. |
#Martello R, Leutert M, Jungmichel S, Bilan V, Larsen SC, Young C, Hottiger MO, Nielsen ML, (2016) "Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue." <i>Nat Commun</i> <b>7</b>:12917; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27686526 27686526]; doi: [https://dx.doi.org/10.1038/ncomms12917 10.1038/ncomms12917]; GPMDB: [http://gpmdb.org/data/keyword/27686526 15]. | #Martello R, Leutert M, Jungmichel S, Bilan V, Larsen SC, Young C, Hottiger MO, Nielsen ML, (2016) "Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue." <i>Nat Commun</i> <b>7</b>:12917; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27686526 27686526]; doi: [https://dx.doi.org/10.1038/ncomms12917 10.1038/ncomms12917]; GPMDB: [http://gpmdb.org/data/keyword/27686526 15]. | ||
#Greenwood EJ, Matheson NJ, Wals K, van den Boomen DJ, Antrobus R, Williamson JC, Lehner PJ, (2016) "Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27690223 27690223]; doi: [https://dx.doi.org/10.7554/eLife.18296 10.7554/eLife.18296]; GPMDB: [http://gpmdb.org/data/keyword/27690223 10]. | #Greenwood EJ, Matheson NJ, Wals K, van den Boomen DJ, Antrobus R, Williamson JC, Lehner PJ, (2016) "Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27690223 27690223]; doi: [https://dx.doi.org/10.7554/eLife.18296 10.7554/eLife.18296]; GPMDB: [http://gpmdb.org/data/keyword/27690223 10]. | ||
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#Witzke KE, Rosowski K, Müller C, Ahrens M, Eisenacher M, Megger DA, Knobloch J, Koch AR, Bracht T, Sitek B, (2016) "Quantitative Secretome Analysis of Activated Jurkat Cells using Click Chemistry-Based Enrichment of Secreted Glycoproteins." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27696881 27696881]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00575 10.1021/acs.jproteome.6b00575]; GPMDB: [http://gpmdb.org/data/keyword/27696881 82]. | #Witzke KE, Rosowski K, Müller C, Ahrens M, Eisenacher M, Megger DA, Knobloch J, Koch AR, Bracht T, Sitek B, (2016) "Quantitative Secretome Analysis of Activated Jurkat Cells using Click Chemistry-Based Enrichment of Secreted Glycoproteins." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27696881 27696881]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00575 10.1021/acs.jproteome.6b00575]; GPMDB: [http://gpmdb.org/data/keyword/27696881 82]. | ||
#Baas R, Sijm A, van Teeffelen HA, van Es R, Vos HR, Timmers HT, (2016) "Quantitative Proteomics of the SMAD (Suppressor of Mothers Against Decapentaplegic) Transcription Factor Family Identifies Importin 5 as a Bone Morphogenic Protein Receptor-SMAD specific Importin." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27703004 27703004]; doi: [https://dx.doi.org/10.1074/jbc.M116.748582 10.1074/jbc.M116.748582]; GPMDB: [http://gpmdb.org/data/keyword/27703004 108]. | #Baas R, Sijm A, van Teeffelen HA, van Es R, Vos HR, Timmers HT, (2016) "Quantitative Proteomics of the SMAD (Suppressor of Mothers Against Decapentaplegic) Transcription Factor Family Identifies Importin 5 as a Bone Morphogenic Protein Receptor-SMAD specific Importin." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27703004 27703004]; doi: [https://dx.doi.org/10.1074/jbc.M116.748582 10.1074/jbc.M116.748582]; GPMDB: [http://gpmdb.org/data/keyword/27703004 108]. | ||
- | #Hughes CS, McConechy MK, Cochrane DR, Nazeran T, Karnezis AN, Huntsman DG, Morin GB, (2016) "Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research." <i>Sci Rep</i> <b>6</b>:34949; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27713570 27713570]; doi: [https://dx.doi.org/10.1038/srep34949 10.1038/srep34949]; GPMDB: [http://gpmdb.org/data/keyword/27713570 | + | #Hughes CS, McConechy MK, Cochrane DR, Nazeran T, Karnezis AN, Huntsman DG, Morin GB, (2016) "Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research." <i>Sci Rep</i> <b>6</b>:34949; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27713570 27713570]; doi: [https://dx.doi.org/10.1038/srep34949 10.1038/srep34949]; GPMDB: [http://gpmdb.org/data/keyword/27713570 172]. |
#Sivadasan R, Hornburg D, Drepper C, Frank N, Jablonka S, Hansel A, Lojewski X, Sterneckert J, Hermann A, Shaw PJ, Ince PG, Mann M, Meissner F, Sendtner M, (2016) "C9ORF72 interaction with cofilin modulates actin dynamics in motor neurons." <i>Nat Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27723745 27723745]; doi: [https://dx.doi.org/10.1038/nn.4407 10.1038/nn.4407]; GPMDB: [http://gpmdb.org/data/keyword/27723745 6]. | #Sivadasan R, Hornburg D, Drepper C, Frank N, Jablonka S, Hansel A, Lojewski X, Sterneckert J, Hermann A, Shaw PJ, Ince PG, Mann M, Meissner F, Sendtner M, (2016) "C9ORF72 interaction with cofilin modulates actin dynamics in motor neurons." <i>Nat Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27723745 27723745]; doi: [https://dx.doi.org/10.1038/nn.4407 10.1038/nn.4407]; GPMDB: [http://gpmdb.org/data/keyword/27723745 6]. | ||
#Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE, (2016) "Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27726376 27726376]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00386 10.1021/acs.jproteome.6b00386]; GPMDB: [http://gpmdb.org/data/keyword/27726376 61]. | #Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE, (2016) "Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27726376 27726376]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00386 10.1021/acs.jproteome.6b00386]; GPMDB: [http://gpmdb.org/data/keyword/27726376 61]. | ||
+ | #Al-Daghri NM, Alokail MS, Manousopoulou A, Heinson A, Al-Attas O, Al-Saleh Y, Sabico S, Yakout S, Woelk CH, Chrousos GP, Garbis SD, (2016) "Sex specific vitamin D effects on blood coagulation among overweight adults." <i>Eur J Clin Invest</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27727459 27727459]; doi: [https://dx.doi.org/10.1111/eci.12688 10.1111/eci.12688]; GPMDB: [http://gpmdb.org/data/keyword/27727459 50]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of October 30, 2016.