PTMScan^® Proteomic Services: Case Study and Publications

• Thompson SM, Jondal DE, Butters KA, et al. Heat stress induced, ligand-independent MET and EGFR signalling in hepatocellular carcinoma. Int J Hyperthermia. 2017;:1-12.
• Lumpkin RJ, Gu H, Zhu Y, et al. Site-specific identification and quantitation of endogenous SUMO modifications under native conditions. Nat Commun. 2017;8(1):1171.
• Stokes MP, Zhu Y, Farnsworth CL. (2017) Mass spectrometry-based proteomic analysis of the DNA damage response. Front Biosci (Landmark Ed). 23:597-613.
• Hershberger KA, Abraham DM, Martin AS, et al. (2017) Sirtuin 5 is required for mouse survival in response to cardiac pressure overload. J Biol Chem. [Epub ahead of print]
• Gu H, Ren J, Jia X, Stokes MP (2017) Identification of Post-Translational Modifications from Serum/Plasma by Immunoaffinity Enrichment and LC-MS/MS Analysis Without Depletion of Abundant Proteins. Methods Mol. Biol. 1619, 119–125.
• Brockmann M, Blomen VA, Nieuwenhuis J, et al. (2017) Genetic wiring maps of single-cell protein states reveal an off-switch for GPCR signalling. Nature. 2017;546(7657):307-311.
• Dogan T, Gnad F, Chan J, et al. (2017) Role of the E3 ubiquitin ligase RNF157 as a novel downstream effector linking PI3K and MAPK signaling to the cell cycle. J Biol Chem. [Epub ahead of print]
• Potu H, Peterson LF, Kandarpa M, et al. (2017) Usp9x regulates Ets-1 ubiquitination and stability to control NRAS expression and tumorigenicity in melanoma. Nat Commun. 2017;8:14449.
• Lee H, Min K, Yi JS, et al. (2017) A Phosphoproteomic Screen Identifies a Guanine Nucleotide Exchange Factor for Rab3A Protein as a Mitogen-activated Protein (MAP) Kinase Phosphatase-5-regulated MAP Kinase Target in Interleukin 6 (IL-6) Secretion and Myogenesis. J Biol Chem. 2017;292(9):3581-3590.
• Possemato AP, Paulo JA, Mulhern D, Guo A, Gygi SP, Beausoleil SA (2017) Multiplexed Phosphoproteomic Profiling Using Titanium Dioxide and Immunoaffinity Enrichments Reveals Complementary Phosphorylation Events J Proteome Res. [Epub ahead of print].

2017 AACR Poster Presentations

• Targeting critical signaling nodes using multiplexed antibody based phosphopeptide enrichment with iMRM validation 2.2 MB. Charles L Farnsworth, Yiying Zhu, Xiaoying Jia, Kimberly A Lee, Matthew P Stokes

Phosphotyrosine Case Study  2.8 MB Quantitative PhosphoScan^® proteomic analysis of Non-small cell lung cancer cells (H3255) treated with Iressa EGFR inhibitor.

Application Note: Targeted Phosphoproteomics Analysis of Immunoaffinity Enriched Tyrosine Phosphorylation in Mouse Tissue.

• Corbet C, Pinto A, Martherus R, et al. (2016) Acidosis Drives the Reprogramming of Fatty Acid Metabolism in Cancer Cells through Changes in Mitochondrial and Histone Acetylation. Cell Metab. 2016;24(2):311-23.
• Standish AJ, Teh MY, Tran EN, Doyle MT, Baker PJ, Morona R (2016) Unprecedented Abundance of Protein Tyrosine Phosphorylation Modulates Shigella flexneri Virulence J Mol Biol. 428(20):4197-4208.
• Auburger G, Gispert S, Brehm N (2016) Methyl-Arginine Profile of Brain from Aged PINK1-KO+A53T-SNCA Mice Suggests Altered Mitochondrial Biogenesis Parkinsons Dis. 2016 2016: 4686185.
• Gnad F, Doll S, Song K, Stokes MP, Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M (2016) Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms. Proteomics [Epub ahead of print].
• Gnad F, Wallin J, Edgar K, Doll S, Arnott D, Robillard L, Kirkpatrick DS, Stokes MP, Vijapurkar U, Hatzivassiliou G, Friedman LS, Belvin M (2016) Quantitative phosphoproteomic analysis of the PI3K-regulated signaling network. Proteomics [Epub ahead of print].
• Gu H, Ren JM, Jia X, Levy T, Rikova K, Yang V, Lee KA, Stokes MP, Silva JC (2016) Quantitative Profiling of Post-translational Modifications by Immunoaffinity Enrichment and LC-MS/MS in Cancer Serum without Immunodepletion. Mol. Cell Proteomics 15(2), 692–702.
• Stokes M., et al. Antibody-Based Proteomic Analysis of Apoptosis Signaling. In: Perpetua M. (Ed.) Apoptosis Methods in Toxicology. New York, NY: Humana Press; 2016: 163-178.
• Gu H, Stokes MP, Silva JC. Proteomic Analysis of Post-Translational Modifications in Neurobiology. In: Grant J, Hong L (Eds.) Analysis of Post-Translation Modifications and Proteolysis in Neuroscience. Vol. 114. New York, NY: Humana Press; 2016: TBD.
• Ivanova E, Carpino N (2016) Negative regulation of TCR signaling by ubiquitination of Zap-70 Lys-217. Mol. Immunol. 73, 19–28.

2016 ASMS Poster Presentations

• Global, Site Specific Identification and Quantification of Endogenous SUMO Modifications under Native Conditions 1.3 MB. Hongbo Gu, Xiaoying Jia, Jian Min Ren, Elizabeth Komoves, Matthew P. Stokes
• Sequential Immunoaffinity Purification of Post-Translationally Modified Peptides for Improved Enrichment Specificity 1.5 MB. Matthew P. Stokes, Charles L. Farnsworth, Hongbo Gu, Xiaoying Jia, Kimberly A. Lee, Jian Min Ren, Vicky Yang
• Quantitative Profiling of Prokaryotic Post Translational Modifications 1.6 MB. Charles L. Farnsworth, Xiaoying Jia, Jian Min Ren, Kimberly Lee, Jake Namaroff, Matthew P. Stokes

• Patterson HC, Gerbeth C, Thiru P, Vögtle NF, Knoll M, Shahsafaei A, Samocha KE, Huang CX, Harden MM, Song R, Chen C, Kao J, Shi J, Salmon W, Shaul YD, Stokes MP, Silva JC, Bell GW, MacArthur DG, Ruland J, Meisinger C, Lodish HF (2015) A respiratory chain controlled signal transduction cascade in the mitochondrial intermembrane space mediates hydrogen peroxide signaling. Proc. Natl. Acad. Sci. U.S.A. 112(42), E5679–88.
• Ryder DJ, Judge SM, Beharry AW, Farnsworth CL, Silva JC, Judge AR (2015) Identification of the Acetylation and Ubiquitin-Modified Proteome during the Progression of Skeletal Muscle Atrophy. PLoS ONE 10(8), e0136247.
• Bouchut A, Chawla AR, Jeffers V, Hudmon A, Sullivan WJ (2015) Proteome-Wide Lysine Acetylation in Cortical Astrocytes and Alterations That Occur during Infection with Brain Parasite Toxoplasma gondii. PLoS ONE 10(3), e0117966.
• Palacios-Moreno J, Foltz L, Guo A, Stokes MP, Kuehn ED, George L, Comb M, Grimes ML (2015) Neuroblastoma tyrosine kinase signaling networks involve FYN and LYN in endosomes and lipid rafts. PLoS Comput. Biol. 11(4), e1004130.
• 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 [Epub ahead of print].
• Stokes M, Farnsworth C, Gu H, Jia X, Worsfold C, Yang V, Ren J, Lee K, Silva J (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.

2015 ASMS Poster Presentations

• Broad Spectrum Lysine Acylation Profiling to Investigate Regulation of SIRT5 using Four Different Acyl-Lysine PTM Antibodies 11.7 MB. Hongbo Gu, Rami Najjar, Justin Mason, Jian Min Ren, Matthew Hirschey, Jeffrey Silva. In 63rd Annual American Society for Mass Spectrometry, ASMS (2015), St. Louis, MO.
• Total Protein Profiling Employing a Novel Protein Fraction Method Combined with Tandem Mass Tag Labeling 5.5 MB. Charles L. Farnsworth, Matthew P. Stokes, Hongbo Gu, Xiaoying Jia, Jian Min Ren, Kimberly A. Lee, Sadaf Hoda, Bryan Spencer2, Ezra S. Abrams, T. Christian Boles, Jeffrey C. Silva. In 63rd Annual American Society for Mass Spectrometry, ASMS (2015), St. Louis, MO.
• PTM- and protein-level proteome profiling of drug response in human gastric carcinoma cells using antibody and metal affinity phosphopeptide enrichment. 8.1 MB. Matthew P. Stokes, Charles L. Farnsworth, Hongbo Gu, Jian Min Ren, Vicky Yang, Camilla R. Worsfold, Kimberly A. Lee, Jeffrey C. Silva. In 63rd Annual American Society for Mass Spectrometry, ASMS (2015), St. Louis, MO.

• Theurillat JP, Udeshi ND, Errington WJ, Svinkina T, Baca SC, Pop M, Wild PJ, Blattner M, Groner AC, Rubin MA, Moch H, Privé GG, Carr SA, Garraway LA (2014) Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer. Science 346(6205), 85–9.
• Gispert S, Brehm N, Weil J, Seidel K, Rüb U, Kern B, Walter M, Roeper J, Auburger G (2014) Potentiation of neurotoxicity in double mutant mice with Pink1 ablation and A53T-SNCA overexpression. Hum. Mol. Genet. [Epub ahead of print].
• Xu G, Deglincerti A, Paige JS, Jaffrey SR (2014) Profiling lysine ubiquitination by selective enrichment of ubiquitin remnant-containing peptides. Methods Mol. Biol. 1174, 57–71.
• Thompson JW, Nagel J, Hoving S, Gerrits B, Bauer A, Thomas JR, Kirschner MW, Schirle M, Luchansky SJ (2014) Quantitative diGly Proteomics Coupled with Inducible RNAi Reveals Ubiquitin-Mediated Proteolysis of DDIT4 by the E3 Ligase HUWE1. J. Biol. Chem. [Epub ahead of print].
• Tammsalu T, Matic I, Jaffray EG, Ibrahim AF, Tatham MH, Hay RT (2014) Proteome-wide identification of SUMO2 modification sites. Sci Signal 7(323), rs2.
• Tong Z, Kim MS, Pandey A, Espenshade PJ (2014) Identification of Candidate Substrates for the Golgi Tul1 E3 Ligase Using Quantitative diGly Proteomics in Yeast. Mol. Cell Proteomics [Epub ahead of print].
• Anania VG, Pham VC, Huang X, Masselot A, Lill JR, Kirkpatrick DS (2014) Peptide level immunoaffinity enrichment enhances ubiquitination site identification on individual proteins. Mol. Cell Proteomics 13(1), 145–56.
• Renaudin X, Guervilly JH, Aoufouchi S, Rosselli F (2014) Proteomic analysis reveals a FANCA-modulated neddylation pathway involved in CXCR5 membrane targeting and cell mobility. J. Cell. Sci. 127(Pt 16), 3546–54.
• Iesmantavicius V, Weinert BT, Choudhary C (2014) Convergence of Ubiquitylation and Phosphorylation Signaling in Rapamycin-treated Yeast Cells. Mol. Cell Proteomics 13(8), 1979–92.
• Sylvestersen KB, Horn H, Jungmichel S, Jensen LJ, Nielsen ML (2014) Proteomic analysis of arginine methylation sites in human cells reveals dynamic regulation during transcriptional arrest. Mol. Cell Proteomics 13(8), 2072–88.
• 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. [Epub ahead of print].
• 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), 2874–89.
• Yoshida T, Zhang G, Smith MA, Lopez AS, Bai Y, Li J, Fang B, Koomen J, Rawal B, Fisher KJ, Chen AY, Kitano M, Morita Y, Yamaguchi H, Shibata K, Okabe T, Okamoto I, Nakagawa K, Haura EB (2014) Tyrosine Phosphoproteomics Identifies Both Codrivers and Cotargeting Strategies for T790M-Related EGFR-TKI Resistance in Non-Small Cell Lung Cancer. Clin. Cancer Res. [Epub ahead of print].
• Gerarduzzi C, He Q, Antoniou J, Di Battista JA (2014) Prostaglandin E2 -Dependent Blockade of Actomyosin and Stress Fiber Formation Is Mediated Through S1379 Phosphorylation of ROCK2. J. Cell. Biochem. [Epub ahead of print].
• 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), 372–87.
• Krönke J, Udeshi ND, Narla A, Grauman P, Hurst SN, McConkey M, Svinkina T, Heckl D, Comer E, Li X, Ciarlo C, Hartman E, Munshi N, Schenone M, Schreiber SL, Carr SA, Ebert BL (2014) Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science 343(6168), 301–5.
• Handschick K, Beuerlein K, Jurida L, Bartkuhn M, Müller H, Soelch J, Weber A, Dittrich-Breiholz O, Schneider H, Scharfe M, Jarek M, Stellzig J, Schmitz ML, Kracht M (2013) Cyclin-Dependent Kinase 6 Is a Chromatin-Bound Cofactor for NF-κB-Dependent Gene Expression. Mol. Cell [Epub ahead of print].
• Erik J. Soderblom, Hongbo Gu, Jeffrey Sliva, J. Will Thompson, Wenle Xia, Neil Spector, M. Arthur Moseley, 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, ASMS (2014), Baltimore, MD.
• Charles L. Farnsworth, Hongbo Gu, Xiaoying Jia, Jian Min Ren, Kimberly Lee, Jeffrey C. Silva, Demonstration of Orthogonal Complementary Enrichment Methods for Enhanced Phosphopeptide Profiling of Drug-Treated Gastric Carcinoma Cells. In 62nd Annual American Society for Mass Spectrometry, ASMS (2014), Baltimore, MD.
• Jeffrey C. Silva, Ailan Guo, Anthony Couvillon, Rami Najjar, Daniel Mulhern, Kimberly A. Lee, Jian-min Ren, Xiaoying Jia, Hongbo Gu, An Improved Immunoaffinity Reagent for Quantitative Profiling of Lysine Acetylation. In 62nd Annual American Society for Mass Spectrometry, ASMS (2014), Baltimore, MD.
• Hongbo Gu, Erik J. Soderblom, J. Will Thompson, Wenle Xia, Kimberly A. Lee, Jian-min Ren, Neil Spector, M. Arthur Moseley, Jeffrey C. Silva 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, ASMS (2014), Baltimore, MD.
• Matthew P. Stokes, Jeffrey C. Silva, Steven Murphy, Jason Russell, Xiaoying Jia, Jian Min Ren, Kimberly Lee Automated Immunoaffinity-based Proteomic Methods for the Study of Post-translational Modification. In 62nd Annual American Society for Mass Spectrometry, ASMS (2014), Baltimore, MD.

• Udeshi ND, Mertins P, Svinkina T, Carr SA (2013) Large-scale identification of ubiquitination sites by mass spectrometry. Nat Protoc 8(10), 1950–60.
• Rardin MJ, He W, Nishida Y, Newman JC, Carrico C, Danielson SR, Guo A, Gut P, Sahu AK, Li B, Uppala R, Fitch M, Riiff T, Zhu L, Zhou J, Mulhern D, Stevens RD, Ilkayeva OR, Newgard CB, Jacobson MP, Hellerstein M, Goetzman ES, Gibson BW, Verdin E (2013) SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks. Cell Metab. 18(6), 920–33.
• 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.
• Pullikuth AK, Ozdemir A, Cardenas D, Bailey E, Sherman NE, Pfister KK, Catling AD (2013) Epidermal growth factor stimulates extracellular-signal regulated kinase phosphorylation of a novel site on cytoplasmic Dynein intermediate chain 2. Int J Mol Sci 14(2), 3595–620.
• 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].
• Kirkpatrick DS, Bustos DJ, Dogan T, Chan J, Phu L, Young A, Friedman LS, Belvin M, Song Q, Bakalarski CE, Hoeflich KP (2013) Phosphoproteomic characterization of DNA damage response in melanoma cells following MEK/PI3K dual inhibition. Proc. Natl. Acad. Sci. U.S.A. 110(48), 19426–31.
• Marusina K (2013) Metabolomics Advances Reshape Dx Arena. Genetic Engineering & Biotechnology News 33(9), 16, 18–19.
• Carrano AC, Bennett EJ (2013) Using the ubiquitin modified proteome to monitor protein homeostasis function. Mol. Cell Proteomics [Epub ahead of print].
• Nalepa G, Barnholtz-Sloan J, Enzor R, Dey D, He Y, Gehlhausen JR, Lehmann AS, Park SJ, Yang Y, Yang X, Chen S, Guan X, Chen Y, Renbarger J, Yang FC, Parada LF, Clapp W (2013) The tumor suppressor CDKN3 controls mitosis. J. Cell Biol. 201(7), 997–1012.
• Hirschey, M. D. (2013) Sirtuins. Methods in Molecular Biology. 1077, 338.
• Quantitative Profiling of the Acetylome in Mouse Tissue using Lysine Acetylation Reagents in Immunoaffinity LC-MS/MS  0.9 MB. Hongbo Gu, Matthew P. Stokes, Ailan Guo, Kimberly Lee, Jian Min Ren, Xiaoying Jia, Vipin Suri, Jeffrey Silva. In 61st Annual American Society for Mass Spectrometry, ASMS (2013), Minneapolis, MN.
• Network and Pathway Analysis of Post-translationally Modified Peptides Identified by Immunoaffinity-based Proteomics  3.5 MB. Jeffrey C. Silva, Stuart Tugendreich, Hongbo Gu, Charles L. Farnsworth, Kimberly A. Lee, Xiaoying Jia, Jian Min Ren, Matthew P. Stokes. In 61st Annual American Society for Mass Spectrometry, ASMS (2013), Minneapolis, MN.
• Quantitative profiling of signaling pathways using immunoaffinity purification and LC-MS/MS  4.2 MB. Matthew P. Stokes, Jian Min Ren, Kimberly A. Lee, Xiaoying Jia, Jeffrey C. Silva. In 61st Annual American Society for Mass Spectrometry, ASMS (2013), Minneapolis, MN.
• 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 [Epub ahead of print].
• Anania VG, Pham VC, Huang X, Masselot A, Lill JR, Kirkpatrick DS (2013) Peptide level immunoaffinity enrichment enhances ubiquitination site identification on individual proteins. Mol. Cell Proteomics [Epub ahead of print].
• Mielcarek M, Seredenina T, Stokes MP, Osborne GF, Landles C, Inuabasi L, Franklin SA, Silva JC, Luthi-Carter 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.

• Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA (2012) Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol. Cell Proteomics 11(5), 148–59.
• 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.
• Pham VC, Pitti R, Anania VG, Bakalarski CE, Bustos D, Jhunjhunwala S, Phung QT, Yu K, Forrest WF, Kirkpatrick DS, Ashkenazi A, Lill JR (2012) Complementary proteomic tools for the dissection of apoptotic proteolysis events. J. Proteome Res. 11(5), 2947–54.
• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.