Publications
Rhee HW, Zou P, et al. (2013) "Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging." Science 339(6125):1328-31. Abstract.
Rensvold J.W., S.E. Ong, et al. (2013) "Complementary RNA and Protein Profiling Identifies Iron as a Key Regulator of Mitochondrial Biogenesis." Cell Rep pii: S2211-1247(12)00456-1. doi: 10.1016/j.celrep.2012.11.029. [Epub ahead of print]. Abstract.
Gillette M.A. and S.A. Carr. (2013) "Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry." Nat Methods 10(1): 28-34. Abstract.
Guthals A., K.R. Clauser, et al. (2012) "Shotgun protein sequencing with meta-contig assembly." Mol Cell Proteomics 11(10): 1084-1096. Abstract.
Chalkley R.J. and K.R. Clauser. (2012) "Modification site localization scoring: strategies and performance." Mol Cell Proteomics 11(5): 3-14. Abstract.
Udeshi N.D., T. Svinkina, et al. (2012) "Refined Preparation and Use of Anti-K-{epsilon}-GG Antibody Enables Routine Quantification of 10,000s of Ubiquitination Sites in Single Proteomics Experiments." Mol Cell Proteomics. Epub ahead of print. Abstract.
Mani D.R., S.E. Abbatiello, et al. (2012) "Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics." BMC Bioinformatics. 13 Suppl 16:S9. PMCID: PMC3489552. Abstract.
Lee M.N., M. Roy, et al. (2012) "Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach." Nat Immunol. doi:10.1038/ni.2509; published online 23 December 2012. Abstract.
Wen Q., B. Goldenson, et al. (2012) "Identification of Regulators of Polyploidization Presents Therapeutic Targets for Treatment of AMKL." Cell (2012) 150 (3): 575–589. Abstract.
Greulich H., B. Kaplan, et all. (2012) "Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2." Proc Natl Acad Sci. 109(36): 14476-14481. Abstract.
Udeshi N.D., D.R. Mani, et al. (2012) "Methods for Quantification of in vivo Changes in Protein Ubiquitination following Proteasome and Deubiquitinase Inhibition." Mol Cell Proteomics 11(5):148-159. Abstract.
Peach S.E., E.L. Rudomin, et al. (2012) "Quantitative Assessment of Chromatin Immunoprecipitation Grade Antibodies Directed against Histone Modifications Reveals Patterns of Co-occurring Marks on Histone Protein Molecules." Mol Cell Proteomics 11(5):128-137. Abstract.
Luo T., K. Masson, et al. (2012) "STK33 small-molecule kinase inhibitors do not kill KRAS-dependent cancer cells." Proc Natl Acad Sci 71(17):5818-26. Abstract.
Kuhn E., J.R. Whiteaker, et al. (2012) Inter-laboratory Evaluation of Automated, Multiplexed Peptide Immunoaffinity Enrichment Coupled to Multiple Reaction Monitoring Mass Spectrometry for Quantifying Proteins in Plasma. Mol Cell Proteomics 11(6):M111.013854. Abstract.
Naba A., K.R. Clauser, et al. (2011) "The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices." Mol Cell Proteomics 11(4): M111.014647. PMCID: PMC3322572. Abstract.
Mertins P., N.D. Udeshi, et al. (2011) "iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics." Mol Cell Proteomics 11(6):M111.014423. Abstract.
Frühwirth R., Mani D.R., and S. Pyne. (2011) "Clustering with position-specific constraints on variance: Applying redescending M-estimators to label-free LC-MS data analysis." BMC Bioinformatics 12: 358. Abstract
Tucker E.J., S.G. Hershman, et al. (2011) "Mutations in MTFMT Underlie a Human Disorder of Formylation Causing Impaired Mitochondrial Translation." Cell Metab 14(3): 428-434. Abstract
Burgener A., S. Rahman, et al. (2011) "A comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers." J Proteome Res. Under revision.
Zhao L., J.R. Whiteaker, et al. (2011) "Quantification of proteins using Peptide immunoaffinity enrichment coupled with mass spectrometry." J Vis Exp 53: pii: 2812. Abstract
Yu M., K.A. Romer, et al. (2011) "Exoplasmic cysteine Cys384 of the HDL receptor SR-BI is critical for its sensitivity to a small-molecule inhibitor and normal lipid transport activity." Proc Natl Acad Sci USA 108(30): 12243-12248. Abstract
Kuai L., S.E. Ong, et al. (2011) "AAK1 Identified as an Inhibitor of Neuregulin-1/ErbB4-Dependent Neurotrophic Factor Signaling Using Integrative Chemical Genomics and Proteomics." Chem Biol 18(7): 891-906. Abstract
Addona T.A., X. Shi, et al. (2011) "A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease." Nature Biotechnol. 29(7): 635-643. Abstract
Raj L., T. Ide, et al. (2011) "Selective killing of cancer cells by a small molecule targeting the stress response to ROS." Nature 475(7355): 231-234. Abstract
Gerszten R.E., A. Asnani, et al. (2011) "Status and Prospects for Discovery and Verification of New Biomarkers of Cardiovascular Disease by Proteomics." Circ Res 209(4): 463-474. Abstract
Rhee E.P., S. Cheng, et al. (2011) "Lipid Profiling Identifies a Triacylglycerol Signature of Insulin Resistance and Improves Diabetes Prediction in Humans." J Clin Investigation 121(4): 1402-1411. Abstract
Wang T.J., M.G. Larson, et al. (2011) "Metabolite Profiles and the Risk of Developing Diabetes." Nat Med 17(4): 448-453. Abstract
Whiteaker J.R., L. Zhao, et al. (2011) "Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry." Mol Cell Proteomics 10(4): M110.005645. Abstract
Lewis, G. D., L. Farrell, et al. (2010) "Metabolic signatures of exercise in human plasma." Sci Transl Med 2:33ra37. Abstract
Boulbes, D., C. H. Chen, et al. (2010) "Rictor phosphorylation on the Thr-1135 site does not require mammalian target of rapamycin complex 2." Mol Cancer Res 8:896-906. Abstract
Bradner, J. E., R. Mak, et al. (2010) "Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease." Proc Natl Acad Sci U S A 107:12617-22. Abstract
van Vugt, M. A., A. K. Gardino, et al. (2010) "A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint." PLoS Biol 8:e1000287. Abstract
Tabb, D. L., L. Vega-Montoto, et al. (2010) "Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry." J Proteome Res 9:761-76. Abstract
Rodriguez, H., Z. Tezak, et al. (2010) "Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA interagency oncology task force on molecular diagnostics." Clin Chem 56:237-43. Abstract
Regnier, F. E., S. J. Skates, et al. (2010) "Protein-based multiplex assays: mock presubmissions to the US Food and Drug Administration." Clin Chem 56:165-71. Abstract
Paulovich, A. G., D. Billheimer, et al. (2010) "A CPTAC Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance." Mol Cell Proteomics 9:242-54. Abstract
Hortin, G. L., S. A. Carr, et al. (2010) "Introduction: Advances in protein analysis for the clinical laboratory." Clin Chem 56:149-51. Abstract
Gerszten, R. E., S. A. Carr, et al. (2010) "Integration of proteomic-based tools for improved biomarkers of myocardial injury." Clin Chem 56:194-201. Abstract
Abbatiello, S. E., D. R. Mani, et al. (2010) "Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry." Clin Chem 56:291-305. Abstract
Rudnick, P. A., K. R. Clauser, et al. (2010) "Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses." Mol Cell Proteomics 9:225-41. Abstract
Berven, F. S., R. Ahmad, et al. (2010) "Optimizing performance of glycopeptide capture for plasma proteomics." J Proteome Res 9:1706-15. Abstract
Hahn, C. K., J. E. Berchuck, et al. (2009) "Proteomic and genetic approaches identify Syk as an AML target." Cancer Cell 16:281-94. Abstract
Keshishian, H., T. Addona, et al. (2009) "Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution." Mol Cell Proteomics 8:2339-49. Abstract
Burkard, M. E., J. Maciejowski, et al. (2009) "Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells." PLoS Biol 7:e1000111. Abstract
Anderson, N. L., N. G. Anderson, et al. (2009) "A human proteome detection and quantitation project." Mol Cell Proteomics 8:883-6. Abstract
Ong, S. E., M. Schenone, et al. (2009) "Identifying the proteins to which small-molecule probes and drugs bind in cells." Proc Natl Acad Sci U S A 106:4617-22. Abstract
Rudomin, E. L., S. A. Carr, et al. (2009) "Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx)." J Proteome Res 8:3154-60. Abstract
Kuhn, E., T. Addona, et al. (2009) "Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry." Clin Chem 55:1108-17. Abstract
Addona, T. A., S. E. Abbatiello, et al. (2009) "Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma." Nat Biotechnol 27:633-41. Abstract
Du, J., P. Bernasconi, et al. (2009) "Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy." Nat Biotechnol 27:77-83. Abstract
Fusaro, V. A., D. R. Mani, et al. (2009) "Prediction of high-responding peptides for targeted protein assays by mass spectrometry." Nat Biotechnol 27:190-8. Abstract
Markljung, E., L. Jiang, et al. (2009) "ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth." PLoS Biol 7:e1000256. Abstract
Margolin, A. A., S. E. Ong, et al. (2009) "Empirical Bayes analysis of quantitative proteomics experiments." PLoS One 4:e7454. Abstract
Lewis, G. D., R. Wei, et al. (2008) "Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury." J Clin Invest 118:3503-12. Abstract
Jaffe, J. D., H. Keshishian, et al. (2008) "Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification." Mol Cell Proteomics 7:1952-62. Abstract PDF
Carr, S. A. and L. Anderson (2008) "Protein quantitation through targeted mass spectrometry: the way out of biomarker purgatory?" Clin Chem 54:1749-52. Abstract
Pagliarini, D. J., S. E. Calvo, et al. (2008) "A mitochondrial protein compendium elucidates complex I disease biology." Cell 134:112-23. Abstract
Shaham, O., R. Wei, et al. (2008) "Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity." Mol Syst Biol 4:214. Abstract
Lowery, D. M., K. R. Clauser, et al. (2007) "Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate." Embo J 26:2262-73. Abstract
Sancak, Y., C. C. Thoreen, et al. (2007) "PRAS40 is an insulin-regulated inhibitor of the mTORC1 protein kinase." Mol Cell 25:903-15. Abstract
Keshishian, H., T. Addona, et al. (2007) "Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution." Mol Cell Proteomics 6:2212-29. Abstract
Lamb, J., E. D. Crawford, et al. (2006) "The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease." Science 313:1929-35. Abstract
Frias, M. A., C. C. Thoreen, et al. (2006) "mSin1 is necessary for Akt/PKB phosphorylation, and its isoforms define three distinct mTORC2s." Curr Biol 16:1865-70. Abstract
Jaffe, J. D., D. R. Mani, et al. (2006) "PEPPeR, a platform for experimental proteomic pattern recognition." Mol Cell Proteomics 5:1927-41. Abstract
Calvo, S., M. Jain, et al. (2006) "Systematic identification of human mitochondrial disease genes through integrative genomics." Nat Genet 38:576-82. Abstract
Rifai, N., M. A. Gillette, et al. (2006) "Protein biomarker discovery and validation: the long and uncertain path to clinical utility." Nat Biotechnol 24:971-83. Abstract
Gillette, M. A., D. R. Mani, et al. (2005) "Place of pattern in proteomic biomarker discovery." J Proteome Res 4:1143-54. Abstract
Carr, S. A., R. S. Annan, et al. (2005) "Mapping posttranslational modifications of proteins by MS-based selective detection: application to phosphoproteomics." Methods Enzymol 405:82-115. Abstract
Sullivan, B., T. A. Addona, et al. (2004) "Selective detection of glycopeptides on ion trap mass spectrometers." Anal Chem 76:3112-8. Abstract
