Svinkina T, Gu H, Silva JC, Mertins P, Qiao J, Fereshetian S, Jaffe JD, Kuhn E, Udeshi ND, Carr SA (2015) Deep, quantitative coverage of the lysine acetylome using novel anti-acetyl-lysine antibodies and an optimized proteomic workflow. Mol Cell Proteomics, in press.
http://www.mcponline.org/content/early/2015/05/07/mcp.O114.047555.full.pdf
Stokes M, Farnsworth CL, Gu H, Jia X, Worsfold CR, Yang V, Ren JM, Lee KA, Silva JC (2015) Complementary PTM profiling of drug response in human gastric carcinoma by immunoaffinity and IMAC methods with total proteome analysis, Proteomes 3(3) 160-183.
www.mdpi.com/2227-7382/3/3/160
Verma R, Su S, McCrann DJ, Green JM, Leu K, Young PR, Schatz PJ, Silva JC, Stokes MP, Wojchowski DM (2014) RHEX, a novel regulator of human erythroid progenitor cell expansion and erythroblast development. J Exp Med, 211(9), 1715-1722.
http://www.ncbi.nlm.nih.gov/pubmed/25092874
Paardekooper Overman J, Yi JS, Bonetti M, Soulsby M, Preisinger C, Stokes MP, Hui L, Silva JC, Overvoorde J, Giansanti P, Heck AJ, Kontaridis MI, den Hertog J, Bennett AM (2014) PZR coordinates Shp2 Noonan and LEOPARD syndrome signaling in zebrafish and mice. Mol Cell Biol, 34(15), 2874-2889.
http://www.ncbi.nlm.nih.gov/pubmed/24865967
Guo A, Gu H, Zhou J, Mulhern D, Wang Y, Lee KA, Yang V, Aguiar M, Kornhauser J, Jia X, Ren J, Beausoleil SA, Silva JC, Vemulapalli V, Bedford MT, Comb MJ (2014) Immunoaffinity enrichment and mass spectrometry analysis of protein methylation. Mol Cell Proteomics, 13(1), 372-378.
http://www.ncbi.nlm.nih.gov/pubmed/24129315
Soderblom EJ, Gu H, Silva J, Thompson JW, Xia W, Spector N, Moseley MA (2014) Quantitative phosphoproteomic phenotyping of acquired resistance to HER2 kinase inhibitors in breast cancer using multimodal phosphopeptide enrichments. In 62nd Annual American Society for Mass Spectrometry, Baltimore, MD.
http://media.cellsignal.com/www/pdfs/proteomics/case-studies-publications/asms-2014-moseley.pdf
Farnsworth CL, Gu H, Jia X, Ren JM, Lee KA, Silva JC (2014) Demonstration of orthogonal complementary enrichment methods for enhanced phosphopeptide profiling of drug-treated gastric carcinoma cells. In 62nd Annual American Society for Mass Spectrometry, Baltimore, MD.
http://media.cellsignal.com/www/pdfs/proteomics/case-studies-publications/asms-2014-farnsworth.pdf
Silva JC, Guo A, Couvillon A, Najjar R, Mulhern D, Lee K, Ren JM, Jia X, Gu H (2014) An improved immunoaffinity reagent for quantitative profiling of lysine acetylation. In 62nd Annual American Society for Mass Spectrometry, Baltimore, MD.
http://media.cellsignal.com/www/pdfs/proteomics/case-studies-publications/asms-2014-silva.pdf
Gu H, Soderblom EJ, Thompson JW, Xia W, Lee KA, Ren JM, Spector N, Moseley MA, Silva JC (2014) Profiling and cross-talk of tyrosine phosphorylation with lysine acetylation and succinylation in tyrosine kinase inhibitor resistant breast cancer cells. In 62nd Annual American Society for Mass Spectrometry, Baltimore, MD.
http://media.cellsignal.com/www/pdfs/proteomics/case-studies-publications/asms-2014-gu.pdf
Stokes MP, Silva JC, Murphy S, Russell J, Jia X, Ren JM, Lee KA (2014) Automated immunoaffinity-based proteomic methods for the study of post-translational modification. In 62nd Annual American Society for Mass Spectrometry, Baltimore, MD.
http://media.cellsignal.com/www/pdfs/proteomics/case-studies-publications/asms-2014-stokes.pdf
Stokes MP, Silva JC, Jia X, Lee KA, Polakiewicz RD, Comb MJ (2013) Quantitative profiling of DNA damage and apoptotic pathways in UV damaged cells using PTMScan Direct. Int J Mol Sci, 14(1), 286–307.
http://www.mdpi.com/1422-0067/14/1/286
Gnad F, Young A, Zhou W, Lyle K, Ong CC, Stokes MP, Silva JC, Belvin M, Friedman LS, Koeppen H, Minden A, Hoeflich K (2013) Systems-wide analysis of K-Ras, Cdc42 and PAK4 signaling by quantitative phosphoproteomics. Mol Cell Proteomics 12(8) 2070-80.
http://www.ncbi.nlm.nih.gov/pubmed/23608596
Hirschey, MD (2013) Sirtuins. Methods in Molecular Biology. Li Y, Silva JC, Skinner ME, Lombard DB, Mass Spectrometry-Based Detection of Protein Acetylation. Chapter 6, 1077: 81 - 104.
http://www.ncbi.nlm.nih.gov/pubmed/24014401
Gu H, Stokes MP, Guo A, Lee KA, Ren JM, Jia X, Suri V, Silva JC (2013) Quantitative profiling of the acetylome in mouse tissue using lysine acetylation reagents in immunoaffinity LC-MS/MS. In 61st Annual American Society for Mass Spectrometry, Minneapolis, MN.
http://media.cellsignal.com/www/pdfs/services/publications-asms13-hgu.pdf
Silva JC, Tugendreich S, Gu H, Farnsworth CL, Lee KA, Jia X, Ren JM, Stokes MP (2013) Network and pathway analysis of post-translationally modified peptides identified by immunoaffinity-based proteomics. In 61st Annual American Society for Mass Spectrometry, Minneapolis, MN.
http://media.cellsignal.com/www/pdfs/services/publications-asms13-jsilva.pdf
Stokes MP, Ren JM, Lee KA, Jia X, Silva JC (2013) Quantitative profiling of signaling pathways using immunoaffinity purification and LC-MS/MS. In 61st Annual American Society for Mass Spectrometry, Minneapolis, MN.
http://media.cellsignal.com/www/pdfs/services/publications-asms13-mstokes.pdf
Giansanti P, Stokes MP, Silva JC, Scholten A, Heck AJ (2013) Interrogating cAMP-dependent kinase signaling in Jurkat T-Cells by a protein kinase A targeted immune-precipitation phosphoproteomics approach. Mol Cell Proteomics, 12(11) 3350-9.
http://www.ncbi.nlm.nih.gov/pubmed/23882029
Mielcarek M, Seredenina T, Stokes MP, Osborne GF, Landles C, Inuabasi L, Franklin SA, Silva JC, LuthiCarter R, Beaumont V, Bates GP (2013) HDAC4 does not act as a protein deacetylase in the postnatal murine brain in vivo. PLoS One, 8(11) e80849.
http://www.ncbi.nlm.nih.gov/pubmed/24278330
Buckley SM, ArandaOrgilles B, Strikoudis A, Apostolou E, Loizou E, MoranCrusio K, Farnsworth CL, Koller AA, Dasgupta R, Silva JC, Stadtfeld M, Hochedlinger K, Chen EI, Aifantis I (2012) Regulation of pluripotency and cellular reprogramming by the ubiquitin-proteasome system. Cell Stem Cell 11(6), 783–98.
http://www.ncbi.nlm.nih.gov/pubmed/23103054
Stokes MP, Farnsworth CL, Moritz A, Silva JC, Jia X, Lee KA, Guo A, Polakiewicz RD, Comb MJ (2012) PTMScan direct: identification and quantification of peptides from critical signaling proteins by immunoaffinity enrichment coupled with LC-MS/MS. Mol Cell Proteomics 11(5), 187–201.
http://www.ncbi.nlm.nih.gov/pubmed/22322096
Stokes MP, Silva JC, Farnsworth CL, Jia X, Lee KA, Polakiewicz RD, Comb MJ (2012) PTMScan Direct: Quantitative, Multiplexed Monitoring of Signaling Pathways. In 11th Annual World Congress, HUPO, #106, Boston, MA.
http://media.cellsignal.com/www/pdfs/services/publications-hupo-mstokes.pdf
Gu H, Guo A, Zhou J, Mulhern D, Wang Y, Lee KA, Yang V, Aguiar M, Kornhauser J, Jia X, Ren JM, Beausoleil S, Silva JC (2012) MethylScan: affinity enrichment and mass spectrometry analysis of protein methylation. In 11th Annual World Congress, HUPO, #503, Boston, MA.
http://media.cellsignal.com/www/pdfs/services/publications-hupo-hgu.pdf
Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR (2011) Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels. J Biol Chem 286(48) 41530-8.
http://www.ncbi.nlm.nih.gov/pubmed/21987572
Brave SR, Ratcliffe K, Wilson Z, James NH, Ashton S, Wainwright A, Kendrew J, Dudley P, Broadbent N, Sproat G, Taylor S, Barnes C, Silva JC, Farnsworth CL, Hennequin L, Ogilvie DJ, Jurgensmeier JM, Shibuya M, Wedge SR, Barry ST (2011) Assessing the activity of cediranib, a VEGFR-2/3 tyrosine kinase inhibitor, against VEGFR-1 and members of the structurally related PDGFR family. Mol Cancer Ther 10(5), 861-73.
http://www.ncbi.nlm.nih.gov/pubmed/21441409
Bonnette PC, Robinson BS, Silva JC, Stokes MP, Brosius AD, Baumann A, Buckbinder L (2010) Phosphoproteomic characterization of PYK2 signaling pathways involved in osteogenesis. J Proteomics 73(7), 1306-20.
http://www.ncbi.nlm.nih.gov/pubmed/20116462" target="_blank
Carretero J, Shimamura T, Rikova K, Jackson AL, Wilkerson MD, Borgman CL, Buttarazzi MS, Sanofsky BA, McNamara KL, Brandstetter KA, Walton ZE, Gu TL, Silva JC, Crosby K, Shapiro GI, Maira SM, Ji H, Castrillon DH, Kim CF, Garcia-Echeverria C, Bardeesy N, Sharpless NE, Hayes ND, Kim WY, Engelman JA, Wong KK (2010) Integrative genomic and proteomic analysis identify targets for Lkb1-deficient metastatic lung tumors. Cancer Cell 17(6) 547-59.
http://www.ncbi.nlm.nih.gov/pubmed/20541700
Schwer B, Eckersdorff M, Li Y, Silva JC, Fermin D, Kurtev MV, Giallourakis C, Comb MJ, Alt FW, Lombard DB (2009) Calorie restriction alters mitochondrial protein acetylation. Aging Cell 8(5), 604-606.
http://www.ncbi.nlm.nih.gov/pubmed/19594485
Stokes MP, Rush J, MacNeill J, Ren JM, Sprott K, Nardone J, Yang V, Beausoleil SA, Gygi SP, Livingstone M, Zhang H, Polakiewicz RD, Comb MJ (2008) Profiling of UV-induced ATM/ATR signaling pathways. Proc Natl Acad Sci USA, 104(50), 19855-19860.
http://www.ncbi.nlm.nih.gov/pubmed/18077418/
Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, MacNeill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ (2007) Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell, 131(6), 1190-1203.
http://www.ncbi.nlm.nih.gov/pubmed/18083107/
Goss VL, Lee KA, Moritz A, Nardone J, Spek EJ, MacNeill J, Rush J, Comb MJ, Polakiewicz RD (2006) A common phosphotyrosine signature for the Bcr-Abl kinase. Blood, 107(12), 4888-4897.
http://www.ncbi.nlm.nih.gov/pubmed/16497976/
Rush J, Moritz A, Lee KA, Guo A, Goss VL, Spek EJ, Zhang H, Zha XM, Polakiewicz RD, Comb MJ (2005) Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat Biotechnol, 23(1), 94-101.
http://www.ncbi.nlm.nih.gov/pubmed/15592455/
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