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
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| Who
are we? Michael MacCoss, Assistant Professor
Jesse Canterbury, Research Scientist Greg Finney, Graduate Student Barbara Frewen, Programmer Veronika Glukhova, Graduate Student Mike Hoopmann, Graduate Student Edward Hsieh, Post-Doc Gennifer Merrihew, Research Scientist Jea Park, Undergraduate Student Daniela Tomazela, Post-Doc Jason Wooden, Post-Doc |
Where
are we? University of Washington
Department of Genome Sciences Foege Building S113 1705 N.E. Pacific St Seattle, WA 98195 Click here for map Telephone Numbers: Lab: (206) 616-9023 Mike's Office: (206) 616-7451 |
Mass Spectrometry Instrumentation: |
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| LTQ Linear Ion-Trap Mass Spectrometers (ThermoElectron) Two LTQ mass spectrometers operate in the lab 24 hours a day, 7 days a week producing data for our proteomics experiments. |
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| TSQ Quantum Ultra AM Triple Quadrupole Mass Spectrometer (ThermoElectron) |
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| LTQ-FT Ultra Hybrid Linear Ion Trap FTICR Mass Spectrometer (ThermoElectron) |
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| Mariner Electrospray-Time of Flight Mass Spectrometer (ABI) | ![]() |
Selected Publications: Complete Publication List from PubMed
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.
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. 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. 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. 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) Supplementary
Data 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, In
Press, (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.
Prot. Res., In Press (2008) 42. Merrihew,G.E.,
Davis,C., Ewing,B.,
Williams,G., Käll,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, Submitted (2008) Supplementary
Data 43. 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, In Press
(2008) 44. 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, Submitted (2008) 45. 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, Submitted
(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, Submitted (2008) Reviews 1. MacCoss,M.J.,
Yates,J.R., III Proteomics: analytical tools and techniques. Curr.
Opin.
Clin. Nutr. Metab Care 4,
369-375 (2001). 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.
Computational analysis of shotgun proteomics data. Curr.
Opin. Chem. Biol., 9, 88-94 (2005) Book
Chapters 1.
MacCoss,M.J. &
Wu,C.C. Computational analysis of
quantitative proteomics data using stable isotope labeling. In: Quantitative Proteomics by Mass Spectrometry.
ed. Sechi,S. (Humana Press Inc., 2.
Wu,C.C. & MacCoss,M.J. Quantitative proteomic
analysis of mammalian organisms using metabolically labeled tissues.
In: Quantitative Proteomics by Mass Spectrometry.
ed. Sechi,S. (Humana Press, Inc., 3.
Frewen, B. & MacCoss,M.J. Using BiblioSpec for creating and searching peptide spectrum
libraries. In: Current Protocols in
Bioinformatics. ed. Yates,J.R. III (Humana Press, Inc., Totowa, NJ;
2007) |
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Useful Info for Mass Spectrometry Based Proteomics:
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Software for the Analysis of Mass Spectrometry Data:
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Classes
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Links: Useful Tools for
Proteomics PepProbe
Web Based Database Search - Powerful protein database
search engine from the Yates Lab
that can use XCorr, normalized XCorrs, hypergeometric probabilities, a
central limiting theorem intensity model, and many many more for
identification of tandem mass spectra. Input is an MS2 file that can be
produced from the MakeMS2 program listed
above.
Database and De Novo search Tools - Pavel Pevzner's Computational Mass Spectrometry group. Peptide Mass Calculator - Simple script for calculating the MW and amino acid composition of a protein or peptide. Protein Digestion Calculator - Simple program for calculating the peptides expected from a specific enzyme digest. Protein Prospector - Web Based Protein Mass Spectrometry Tools as UCSF Proteomics Tool Kit at ISB - Scripts for predicting peptide fragment ion spectra, tryptic peptides, etc... FASTA Database
Download NCBI Reference
Sequences
- Download
NCBI Nonredundant Databases - Download NCBI Organism Specific Annotations - Download WormBase C. elegans Release Freezes - Download Saccharomyces Genome Database - Download IPI (International Protein Index)- Download Mass Spectrometry Links Research Groups Yates' Lab - The Scripps
Research Laboratory, Department of Cell Biology
Miscellaneous Wu Lab - University of Colorado, Health Sciences Center Matthews' Group - University of Vermont, Departments of Medicine and Chemistry Protein Mass Spectrometry Resource - Brian Chait's Lab at Rockefeller University University of Washington Proteomics Resource National Center for Research Resources'
Yeast Resource Center
IonSource.Com - An excellent resource for mass spectrometry based information ABRF Delta Mass - A database of protein post-translational modifications The Whys and Wherefores of Quadrupole Ion Trap Mass Spectrometry - Tutorial by Karen Jonscher and John R. Yates, III American Society for Mass Spectrometry ISOGEOCHEM Web Page Mass Spectrometry Resource from Wiley Journal of the American Society of Mass Spectrometry A History of Mass Spectrometry |
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| Lab
Photos Click here to see photos of the lab Lab Alumni Former Graduate Students Aaron Klammer, Ph.D. (2004 - 2008) -- Pacific Biosciences, Menlo Park, CA Former Post-Docs Josh McElwee, Ph.D. (2006 - 2007) -- Rosetta / Merck, Seattle, WA Xianhua Yi, Ph.D. (2004 - 2007) -- Momenta Pharmaceuticals, Boston, MA Former Staff Jessica Novak (2006 - 2008) -- Institute for Systems Biology, Seattle, WA Former Undergraduate Students Angie Sibounheuang (2005-2006) |
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