UW Genome Sciences

Research:

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:

Searle BC, Lawrence RT, MacCoss MJ, Villén J. Thesaurus: quantifying phosphopeptide positional isomers. Nat Methods. 2019 Aug;16(8):703-706. doi: 10.1038/s41592-019-0498-4. Epub 2019 Jul 29. PubMed PMID: 31363206.

Amodei D, Egertson J, MacLean BX, Johnson R, Merrihew GE, Keller A, Marsh D, Vitek O, Mallick P, MacCoss MJ. Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows. J Am Soc Mass Spectrom. 2019 Apr;30(4):669-684. doi: 10.1007/s13361-018-2122-8. Epub 2019 Jan 22. PubMed PMID: 30671891; PubMed Central PMCID: PMC6445824.

Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL. Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis. Mol Cell Proteomics. 2019 Jan;18(1):1-2. doi: 10.1074/mcp.E118.001286. PubMed PMID: 30602589; PubMed Central PMCID: PMC6317474.

Searle BC, Pino LK, Egertson JD, Ting YS, Lawrence RT, MacLean BX, Villén J, MacCoss MJ. Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry. Nat Commun. 2018 Dec 3;9(1):5128. doi: 10.1038/s41467-018-07454-w. PubMed PMID: 30510204; PubMed Central PMCID: PMC6277451.

Pino LK, Searle BC, Huang EL, Noble WS, Hoofnagle AN, MacCoss MJ. Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories. Anal Chem. 2018 Nov 6;90(21):13112-13117. doi: 10.1021/acs.analchem.8b04581. Epub 2018 Oct 23. PubMed PMID: 30350613.

MacLean BX, Pratt BS, Egertson JD, MacCoss MJ, Smith RD, Baker ES. Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions. J Am Soc Mass Spectrom. 2018 Nov;29(11):2182-2188. doi: 10.1007/s13361-018-2028-5. Epub 2018 Jul 25. PubMed PMID: 30047074; PubMed Central PMCID: PMC6191345.