The focus of our research is in the development of stable isotope and mass spectrometry based approaches to improve our understanding of biology on a molecular, cellular, and whole organism level. Presently, individuals in the laboratory are working on technology for 1) automating biochemical sample preparation methods for the analysis of protein mixtures; 2) developing in vivo stable isotope methods for studying protein metabolism; 3) increasing the dynamic range of liquid chromatography-mass spectrometry for the analysis of peptides; and 4) developing computational tools for the automated conversion of mass spectrometry data into biologically meaningful results. These technologies are presently being demonstrated in the model organisms C. elegans and S. cerevisiae. Although our current research interests are presently in model systems, our long-term goal is have technologies robust enough to handle the automated high-throughput characterization of human clinical samples.

Selected Publications:

Major,M.B., Camp,N.D., Berndt,J.D., Yi,X., Goldenberg,S.J., Hubbert,C., Biechele,T.L., Gingras,A.-C., Zheng,N., MacCoss,M.J., Angers,S., Moon,R.T., Wilms tumor suppressor WTX negatively regulates Wnt/β-Catenin signaling, Science, 316, 1043-1046 (2007)

Mayor,T., Graumann,J., MacCoss,M.J., Deshaies,R.J., Profiling ubiquitylated proteins using quantitative mass spectrometry to unveil 26S proteasome substrates and the Rpn10 proteasomal receptor pathway flux. Mol. Cell. Proteomics, 6, 1885-1895 (2007)

Clark,N.L., Findlay,G.D., Yi,X., MacCoss,M.J., Swanson,W.J., Selection and duplication of sperm lysin in an allopatric abalone population, Mol. Biol. Evol., 24, 2081-2090 (2007)

Käll,L., Canterbury,J.D., Weston,J., Noble,W.S., MacCoss,M.J., A semi-supervised machine learning technique for peptide identification from shotgun proteomics datasets, Nat. Methods, 4, 923-925 (2007)

Klammer,A.A., Yi,X., MacCoss,M.J., Noble,W.S., Peptide retention time prediction yields improved tandem mass spectrum identification for diverse chromatography conditions, Anal. Chem., 79, 6111-6118 (2007)

Käll,L., Storey,J.D., MacCoss,M.J., Noble,W.S., Assigning significance to peptides identified by tandem mass spectrometry using decoy databases, J. Proteome Res., 7, 29-34 (2008)

Finney,G.L., Blackler,A.R., Hoopmann,M.R., Canterbury,J.D., Wu,C.C., MacCoss,M.J., Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high resolution µLC-MS data, Anal. Chem. In Press (2008)

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