Peer Reviewed Publications:
1. Griffin,P.R., MacCoss,M.J., Eng,J.K., Blevins,R.A., Aaronson,J.S., Yates,J.R., III Direct database searching with MALDI-PSD spectra of peptides. Rapid Commun. Mass Spectrom. 9, 1546-1551 (1995).
2. MacCoss,M.J., Fukagawa,N.K., Matthews,D.E. Measurement of homocysteine concentrations and stable isotope tracer enrichments in human plasma. Anal. Chem. 71, 4527-4533 (1999).
3. Toth,M.J., Poehlman,E.T., Matthews,D.E., Tchernof,A., MacCoss,M.J. Effects of estradiol and progesterone on body composition, protein synthesis, and lipoprotein lipase in rats. Am. J. Physiol Endocrinol. Metab 280, E496-E501 (2001).
4. MacCoss,M.J., Fukagawa,N.K., Matthews,D.E. Measurement of intracellular sulfur amino acid metabolism in humans. Am. J. Physiol Endocrinol. Metab 280, E947-E955 (2001).
5. Toth,M.J., MacCoss,M.J., Poehlman,E.T., Matthews,D.E. Recovery of (13)CO(2) from infused [1-(13)C]leucine and [1,2-(13)C(2)]leucine in healthy humans. Am. J. Physiol Endocrinol. Metab 281, E233-E241 (2001).
6. MacCoss,M.J., Toth,M.J., Matthews,D.E. Evaluation and optimization of ion-current ratio measurements by selected-ion-monitoring mass spectrometry. Anal. Chem. 73, 2976-2984 (2001).
7. MacCoss,M.J., McDonald,W.H., Saraf,A., Sadygov,R., Clark,J.M., Tasto,J.J., Gould,K.L., Wolters,D., Washburn,M., Weiss,A., Clark,J.I., Yates,J.R., III Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci. U. S. A 99, 7900-7905 (2002).
8. Anderson,L.B., Maderia,M., Ouellette,A.J., Putnam-Evans,C., Higgins,L., Krick,T., MacCoss,M.J., Lim,H., Yates,J.R., III, Barry,B.A. Posttranslational modifications in the CP43 subunit of photosystem II. Proc. Natl. Acad. Sci. U. S. A 99, 14676-14681 (2002).
9. MacCoss,M.J., Wu,C.C., Yates,J.R., III Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal. Chem. 74, 5593-5599 (2002).
10. Sadygov,R.G., Eng,J., Durr,E., Saraf,A., McDonald,H., MacCoss,M.J., Yates,J.R., III Code developments to improve the efficiency of automated MS/MS spectra interpretation. J. Proteome. Res. 1, 211-215 (2002).
11. Wu,C.C., MacCoss,M.J., Howell,K.E., Yates,J.R, III. A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol. 21, 532-538 (2003).
12. Tabb,D.L., MacCoss,M.J., Wu,C.C., Anderson,S.D., Yates,J.R., III Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal. Chem. 75, 2470-2477 (2003).
13. MacCoss,M.J., Wu,C.C., Liu,H., Sadygov,R., Yates,J.R., III A correlation algorithm for the automated analysis of quantitative ‘shotgun’ proteomics data. Anal. Chem. 75, 6912-6921 (2003).
14. Wu,C.C., MacCoss,M.J., Mardones,G. Finnigan,C., Mogelsvang,S. Yates, JR III, Howell,KE. Organellar proteomics reveals golgi arginine dimethylation. Mol. Biol. Cell., 15, 2907-2919 (2004)
15. Anderson,L.B., Ouellette,A.J.A., Eaton-Rye,J., Maderia,M., MacCoss,M.J., Yates,J.R. III, Barry,B.A. Evidence for a post-translational modification in the CP47 subunit of Photosystem II. J. Am. Chem. Soc., 126, 8399-8405 (2004).
16. Wu,C.C., MacCoss,M.J., Howell,K.E., Matthews, D.E., Yates,J.R. III Metabolic labeling of mammalian organisms for quantitative proteomics analysis. Anal. Chem., 76, 4951-4959 (2004).
17. McDonald,W.H., Tabb,D.L., Sadygov,R.G., MacCoss,M.J., Venable,J., Graumann,J., Johnson,J.R., Cociorva,D., Yates,J.R. III MS1, MS2, and SQT-three unified, compact and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun. Mass Spectrom., 18, 2162-2168 (2004)
18. Hisert,K.B., MacCoss,M., Shiloh,M., Darwin,H., Murray,D., Jones,R. Ehrt,S., Gandotra,S., Holden,D.W. Nathan,C. Regulation of bacterial cyclic-diGMP by an EAL domain protein controls host-pathogen interactions Mol. Microbiol. 56, 1234-1245 (2005)
19. MacCoss,M.J., Matthews,D.E. Quantitative mass spectrometry for proteomics: Teaching a new dog old tricks. Anal. Chem. 77, 294A-302A (2005)
20. Hoffman,L. D’Argenio,D., MacCoss,M.J., Zhang,Z., Jones,R.A., Miller,S.I. Aminoglycoside antibiotics induce bacterial biofilm formation. Nature, 436, 1171-1175 (2005)
21. MacCoss,M.J., Wu,C.C., Matthews,D.E., Yates,J.R. III, Measurement of isotopic enrichment of stable isotope labeled proteins using high resolution mass spectra of peptides. Anal. Chem. 77, 7646-7653 (2005)
22.Klammer,A.A., Wu,C.C., MacCoss,M.J., Noble,W.S. Peptide charge state determination for low-resolution tandem mass spectra. Proc. IEEE Comput. Syst. Bioinform. Conf., 4, 175-185 (2005)
23. Blackler,A.R., Klammer,A.A., MacCoss,M.J., Wu,C.C., Quantitative comparison of proteomics data quality between a 2D and 3D quadrupole ion trap. Anal. Chem., 78, 1337-1344 (2006)
24.Klammer,A.A., MacCoss,M.J. Effects of modified digestion schemes on the identification of proteins from complex mixtures. J. Proteome Res., 5, 695-700 (2006)
25.Angers,S., Thorpe,C.J., Biechele,T.L., Goldenberg,S.J., Zheng,N., MacCoss,M.J., Moon,R.T. The KLHL12-cullin3 ubiquitin ligase negatively regulates the Wnt/β-catenin pathway by targeting Dishevelled for degradation. Nat Cell Biol., 8, 348-357 (2006)
26.Frewen,B., Merrihew,G, Wu,C.C., Noble,W.S., MacCoss,M.J. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal. Chem., 78, 5678-5684 (2006)
27.Angers,S., Li,T., Yi,X., MacCoss,M.J., Moon,R.T., Zheng,N., Molecular architecture and assembly of the DDB1-Cul4A ubiquitin ligase machinery. Nature, 443, 590-593 (2006)
28.Aagaard,J.E., Yi,X., MacCoss,M.J., Swanson,W.J., Rapidly evolving Zona Pellucida domain proteins are a major component of vitelline envelope of abalone eggs. Proc. Natl. Acad. Sci. U. S. A., 103, 17302-17307 (2006)
29.Wegner,D.J., Hertzberg,T., Heins,H.B., Elmberger,G., MacCoss,M.J., Carlson,C., Trusgnich,M.A., Hallberg,B., Nogee,L.M., Cole, F.S., Hamvas, A., A novel 3000 basepair deletion in SFTPB causing SP-B deficiency. Acta Paediatrica, 96, 516-520 (2007)
30.Eakin,C.M., MacCoss,M.J., Finney,G.L., Klevit,R.E., ERα as a putative substrate for the BRCA1 ubiquitin ligase, Proc. Natl. Acad. Sci. U. S. A., 104, 5794-5799 (2007)
31.Hoopmann,M.R., Finney,G.L., MacCoss,M.J., High speed data reduction, feature selection, and MS/MS spectrum quality assessment of shotgun proteomics datasets using high resolution mass spectrometry, Anal. Chem., 79, 5630-5632 (2007)
32.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)
33.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)
34.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)
35.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)
36.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)
37.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)
38.Käll,L., Storey,J.D., MacCoss,M.J., Noble,W.S., Posterior error probabilities and false discovery rates: Two sides of the same coin, J. Proteome Res., 7, 40-44 (2008)
39.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. 80, 961-971 (2008)
40.Klammer,A.A, Reynolds,S.M., Bilmes,J.A., MacCoss,M.J., Noble,W.S., Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification, Bioinformatics, 24, i348-i356 (2008)
41.Park,C.Y., Klammer,A.A., Käll,L., MacCoss,M.J., Noble,W.S., Rapid and accurate peptide identification from tandem mass spectra, J. Proteome Res., 7, 3022-3027 (2008)
42.Findlay,G.D., Yi,X., MacCoss,M.J., Swanson,W.J., Isotopic labeling and comparative proteomics identify seminal fluid proteins transferred during Drosphila mating, PLOS Biology, 6, 1417-1426 (2008)
43.Eng,J.K., Fischer,B., Grossmann,J., MacCoss,M.J., A fast SEQUEST cross correlation algorithm, J. Proteome Res., 7,4598-4602 (2008)
44.Merrihew,G.E., Davis,C., Ewing,B., Williams,G., Kall,L., Frewen,B.E., Noble,W.S., Green,P., Thomas,J.H., MacCoss,M.J., Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations, Genome Res., 18:1660-1669 (2008)
45.Canterbury,J.D., Yi,X., Hoopmann,M.R., MacCoss,M.J., Assessing the dynamic range and peak capacity of nanoflow LC-FAIMS-MS on an ion trap mass spectrometer for proteomics applications, Anal. Chem., 80, 6888-6897 (2008)
46.Kline,K.G., Frewen,B.E., Bristow,M.R., MacCoss,M.J., Wu,C.C., High quality catalog of proteotypic peptides from human heart, J. Proteome Res., 7, 5055-5061 (2008)
47.Major,M.B., Roberts,B., Berndt,J.D., Anastas,J., Yi,X., Stoich-Cooper,C., von Haller,P.D., Kategaya,L., Chien,A., Angers,S, Lewis,P., MacCoss,M., Marine,S., Ferrer,M., Cleary,M.A., Arthur,B., Moon,R.T., An integrative molecular screening approach identifies AGGF1 as a transducer of Wnt/β-catenin signal transduction, Sci Signal., 1, ra12 (2008)
48.Dai,D.-F., Vermulst,M., Tomazela,D.M., Emond,M.J., MacCoss,M.J., Gollahon,K., Ladiges,W.C., Rabinovitch,P.S., Overexpression of catalase targeted to mitochondria (MCAT) attenuates cardiac aging, Circulation, 119, 21, 2789-2797 (2009)
49.Hoopmann,M.R., Merrihew,G.E., von Haller,P.D., MacCoss,M.J., Post analysis data acquisition for the interative sampling of proteomics mixtures, J. Proteome Res., 8, 6, 2733-2739 (2009)
50.Findlay,G.D., MacCoss,M.J., Swanson,W.J., Proteomic discovery of rapidly evolving seminal fluid genes in Drosophilia, Genome Res., 19, 5, 886-896 (2009)
51.Prakash,A., Tomazela,D.M., Frewen,B., MacLean,B., Merrihew,G., Peterman,S., MacCoss,M.J., Expediting the development of targeted SRM assays: Using data from shotgun proteomics to automate method development, J. Proteome Res., 8, 6, 2733-2739 (2009)
52.Dean,M.D., Clark,N.L., Findlay,G.D., Karn,R.C., Yi,X., Swanson,W.J., MacCoss,M.J., Nachman,M., Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus), Mol. Biol. Evol., 26, 8, 1733-1743 (2009)
53.James,R.G., Biechele,T.L., Conrad,W.H., Camp,N.D., Fass,D.M., Major,M.B., Sommer,K., Yi,X., Roberts,B.S., Cleary,M.A., Arthur,W.T., MacCoss,M., Rawlings,D.J., Haggarty,S.J., Moon,R.T., Bruton’s tyrosine kinase revealed as a negative regulator of Wnt-beta-catenin signaling, Sci. Signal, 2, 72:ra25 (2009)
54.Patino,S., Aagaard,J.E., MacCoss,M.J., Swanson,W.J., Hart,M.W., Bindin from a sea star, Evol. Dev., 11, 4, 376-381 (2009)
55.Pekar Second,T., Blethrow,J.D., Schwartz,J.C., Merrihew,G.E., MacCoss,M.J., Swaney,D.L., Russell,J.D., Coon,J.J., Zabrouskov,V., A novel dual-pressure linear ion trap mass spectrometer improves the analysis of complex protein mixtures, Anal. Chem., 81, 18, 7757-7765 (2009)
56.Aagard,J.E., Vacquier,V.D., MacCoss,M.J., Swanson,W.J., ZP domain proteins in the abalone egg coat include a paralog of VERL under positive selection that binds lysine and 18-kDa sperm proteins, Mol Biol. Evol., In press, (2009)
57.Hsieh,E.J., Hoopmann,M.R., MacLean,B., MacCoss,M.J., Comparison of database search strategies for high precursor accuracy MS/MS data, Submitted (2009)
Reviews:
1. MacCoss,M.J. Computational analysis of shotgun proteomics data. Curr. Opin. Chem. Biol., 9, 88-94 (2005)
2. Wu,C.C. MacCoss,M.J. Shotgun proteomics: tools for the analysis of complex biological systems. Curr. Opin. Mol. Ther. 4, 242-250 (2002).
3. MacCoss,M.J., Yates,J.R., III Proteomics: analytical tools and techniques. Curr. Opin. Clin. Nutr. Metab Care 4, 369-375 (2001).
Book Chapters:
1. MacCoss,M.J. Computational analysis of shotgun proteomics data. Curr. Opin. Chem. Biol., 9, 88-94 (2005)
2. Wu,C.C. MacCoss,M.J. Shotgun proteomics: tools for the analysis of complex biological systems. Curr. Opin. Mol. Ther. 4, 242-250 (2002).
3. MacCoss,M.J., Yates,J.R., III Proteomics: analytical tools and techniques. Curr. Opin. Clin. Nutr. Metab Care 4, 369-375 (2001).
Recent News & Updates
Sept 24, 2009Skyline v0.5 Released
The latest release of our popular software tool for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM) methods and analyzing the resulting mass spectrometer data. More ...
May 2009Interview by Environmental Health Perspective
Discussion on the use of targeted proteomics for the analysis of environmental toxicants on proteins. More ...
Feb 26, 2009MacCoss honored at UW Early Career Award Recognition
Four Assistant Professors recognized for winning national awards. More ...
Dec 19, 2008Mike MacCoss wins 2007 PECASE Award
The Presidential Early Career Award for Scientists and Engineers is the nation's highest honor for scientists at the onset of their careers.
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