PTMScan^® Case Studies & Publications

2013

• Stokes M.P., Silva J.C., Jia X., Lee K.A., Polakiewicz R.D., Comb M.J. Quantitative Profiling of DNA Damage and Apoptotic Pathways in UV Damaged Cells Using PTMScan Direct. International Journal of Molecular Sciences (2013), 14(1), 286–307.
• Xue B, Jeffers V, Sullivan WJ, Uversky VN (2013) Protein intrinsic disorder in the acetylome of intracellular and extracellular Toxoplasma gondii. Mol Biosyst 9(4), 645–57.
• 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 [Epub ahead of print].

2012

• Wang IT, Allen M, Goffin D, Zhu X, Fairless AH, Brodkin ES, Siegel SJ, Marsh ED, Blendy JA, Zhou Z (2012) Loss of CDKL5 disrupts kinome profile and event-related potentials leading to autistic-like phenotypes in mice. Proc. Natl. Acad. Sci. U.S.A. 109(52), 21516–21.
• Buckley SM, Aranda-Orgilles B, Strikoudis A, Apostolou E, Loizou E, Moran-Crusio 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.
• Mathew R, Seiler MP, Scanlon ST, Mao AP, Constantinides MG, Bertozzi-Villa C, Singer JD, Bendelac A (2012) BTB-ZF factors recruit the E3 ligase cullin 3 to regulate lymphoid effector programs. Nature 491(7425), 618–21.
• 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.
• Jeffers V, Sullivan WJ (2012) Lysine Acetylation Is Widespread on Proteins of Diverse Function and Localization in the Protozoan Parasite Toxoplasma gondii. Eukaryotic Cell 11(6), 735–42.
• PTMScan^® Direct: Quantitative, Multiplexed Monitoring of Signaling Pathways  0.9 MB. Matthew P. Stokes, Jeffrey C. Silva, Charles L. Farnsworth, Xiaoying Jia, Kimberly A. Lee, Roberto D. Polakiewicz, Michael J. Comb. In 11th Annual World Congress, HUPO (2012), #106, Boston, MA.
• MethylScan^®: Affinity Enrichment and Mass Spectrometry Analysis of Protein Methylation  0.4 MB. Hongbo Gu, Ailan Guo, Jing Zhou, Daniel Mulhern, Yi Wang, Kimberly Lee, Vicky Yang, Mike Aguiar, Jon Kornhauser, Xiaoying Jia, Jian-Min Ren, Sean Beausoleil, Jeffrey Silva. In 11th Annual World Congress, HUPO (2012), #503, Boston, MA.

2011

• Gu TL, Deng X, Huang F, Tucker M, Crosby K, Rimkunas V, Wang Y, Deng G, Zhu L, Tan Z, Hu Y, Wu C, Nardone J, MacNeill J, Ren J, Reeves C, Innocenti G, Norris B, Yuan J, Yu J, Haack H, Shen B, Peng C, Li H, Zhou X, Liu X, Rush J, Comb MJ (2011) Survey of tyrosine kinase signaling reveals ROS kinase fusions in human cholangiocarcinoma. PLoS ONE 6(1), e15640.
• Pighi C, Gu TL, Dalai I, Barbi S, Parolini C, Bertolaso A, Pedron S, Parisi A, Ren J, Cecconi D, Chilosi M, Menestrina F, Zamò A (2011) Phospho-proteomic analysis of mantle cell lymphoma cells suggests a pro-survival role of B-cell receptor signaling. Cell Oncol (Dordr) 34(2), 141–53.
• 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, Jürgensmeier 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.
• Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ (2011) Global Identification of Modular Cullin-RING Ligase Substrates. Cell 147(2), 459–74.
• 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.
• Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP (2011) Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol. Cell 44(2), 325–40.

2010

• Moritz A, Li Y, Guo A, Villén J, Wang Y, MacNeill J, Kornhauser J, Sprott K, Zhou J, Possemato A, Ren JM, Hornbeck P, Cantley LC, Gygi SP, Rush J, Comb MJ (2010) Akt-RSK-S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases. Sci Signal 3(136), ra64. More Information.
• 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.
• 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, García-Echeverría C, Bardeesy N, Sharpless NE, Hayes ND, Kim WY, Engelman JA, Wong KK (2010) Integrative genomic and proteomic analyses identify targets for Lkb1-deficient metastatic lung tumors. Cancer Cell 17(6), 547-59.
• Andersen JN, Sathyanarayanan S, Di Bacco A, Chi A, Zhang T, Chen AH, Dolinski B, Kraus M, Roberts B, Arthur W, Klinghoffer RA, Gargano D, Li L, Feldman I, Lynch B, Rush J, Hendrickson RC, Blume-Jensen P, Paweletz CP (2010) Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors. Sci Transl Med 2(43), 43ra55.
• Knowlton ML, Selfors LM, Wrobel CN, Gu TL, Ballif BA, Gygi SP, Polakiewicz R, Brugge JS (2010) Profiling Y561-dependent and -independent substrates of CSF-1R in epithelial cells. PLoS ONE 5(10), e13587.

2009

• 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), 604–6.

2008

• Guo A, Villén J, Kornhauser J, Lee KA, Stokes MP, Rikova K, Possemato A, Nardone J, Innocenti G, Wetzel R, Wang Y, MacNeill J, Mitchell J, Gygi SP, Rush J, Polakiewicz RD, Comb MJ (2008) Signaling networks assembled by oncogenic EGFR and c-Met. Proc. Natl. Acad. Sci. U.S.A. 105(2), 692–7.
• 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 (2007) Profiling of UV-induced ATM/ATR signaling pathways. Proc. Natl. Acad. Sci. U.S.A. 104(50), 19855–60.

2007

• 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), 1190–203.
• Gu TL, Popova L, Reeves C, Nardone J, Macneill J, Rush J, Nimer SD, Polakiewicz RD (2007) Phosphoproteomic analysis identifies the M0-91 cell line as a cellular model for the study of TEL-TRKC fusion-associated leukemia. Leukemia 21(3), 563–6.
• Gu TL, Mercher T, Tyner JW, Goss VL, Walters DK, Cornejo MG, Reeves C, Popova L, Lee K, Heinrich MC, Rush J, Daibata M, Miyoshi I, Gilliland DG, Druker BJ, Polakiewicz RD (2007) A novel fusion of RBM6 to CSF1R in acute megakaryoblastic leukemia. Blood 110(1), 323–33.

2006

• Mercher T, Wernig G, Moore SA, Levine RL, Gu TL, Frohling S, Cullen D, Polakiewicz RD, Bernard OA, Boggon TJ, Lee BH, Gilliland DG (2006) JAK2T875N is a novel activating mutation that results in myeloproliferative disease with features of megakaryoblastic leukemia in a murine bone marrow transplantation model. Blood 108(8), 2770–9.
• Walters DK, Goss VL, Stoffregen EP, Gu TL, Lee K, Nardone J, McGreevey L, Heinrich MC, Deininger MW, Polakiewicz R, Druker BJ (2006) Phosphoproteomic analysis of AML cell lines identifies leukemic oncogenes. Leuk. Res. 30(9), 1097–104.
• Griswold IJ, MacPartlin M, Bumm T, Goss VL, O'Hare T, Lee KA, Corbin AS, Stoffregen EP, Smith C, Johnson K, Moseson EM, Wood LJ, Polakiewicz RD, Druker BJ, Deininger MW (2006) Kinase domain mutants of Bcr-Abl exhibit altered transformation potency, kinase activity, and substrate utilization, irrespective of sensitivity to imatinib. Mol. Cell. Biol. 26(16), 6082–93.
• Gu TL, Goss VL, Reeves C, Popova L, Nardone J, Macneill J, Walters DK, Wang Y, Rush J, Comb MJ, Druker BJ, Polakiewicz RD (2006) Phosphotyrosine profiling identifies the KG-1 cell line as a model for the study of FGFR1 fusions in acute myeloid leukemia. Blood 108(13), 4202–4.
• 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), 4888–97.

2005

• Zhang Y, Wolf-Yadlin A, Ross PL, Pappin DJ, Rush J, Lauffenburger DA, White FM (2005) Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol. Cell Proteomics 4(9), 1240–50.
• 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.