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
   
4. Developing computational tools for the automated conversion of mass spectrometry data into biologically meaningful results

   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)  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., Totowa, NJ; 2006).

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., Totowa, NJ; 2006).

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)

• A simple way to plumb a traditional binary HPLC system for nanoflow chromatography. Download PDF
• Simple and robust nanospray stages for Thermo Fisher Ion Max Source. Go to UW Proteomics Resource website

• RelEx (Relative Expression) is a program for quantitative proteomics available through a software transfer agreement from The Scripps Research Institute, La Jolla, CA.  Contact Mike MacCoss with questions, feature requests, and bugs.
• MakeMS2 is a windows based program to produce compact and easily parsed text based datafile formats from Xcaliber RAW files using the XDK libraries.  These datafile formats are well documented in:
•  McDonald,W.H. et al. 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)
• These file formats offer advantages over XML based formats for high-throughput data because they consume only a tiny fraction of the disk space.
• An indexer is also available upon request to speed the retrieval of data from these file.
• Contact Mike MacCoss to request source code for MakeMS2.
• Charge Czar is a program that uses a support vector machine to assign a charge state to low resolution tandem mass spectra of peptides. Contact Aaron Klammer for details.
• BiblioSpec is a suite of software tools for creating and searching MS/MS peptide spectrum libraries. The software is particularly useful for those performing repeated proteomics profiling experiments on the same organism. After the identity of a peptide spectrum has been determined, this information can be used to speed and improve all future analyses.
• Hardklör is a computer program for the analysis of high resolution mass spectrometry data.  Hardklör will return monoisotopic m/z and charge states for single or overlapping peptide/protein isotope distributions.
• Percolator is a semi-supervised machine learning approach for improving the analysis of tandem mass spectrometry data of peptides.   Percolator uses a machine learning technique call a support vector machine to dynamically discriminate between correct and decoy spectrum identifications obtained by database searching.  By using our approach, we are able to identify approximately 50% more peptides from a given µLC-MS/MS dataset.
  
• CRAWDAD is a software suite for label-free relative quantitation of high- and low-resolution LC-MS data. Replicate runs are aligned in the retention time dimension prior to feature detection using dynamic time warping. Features of differential intensity are detected using statistical tests, and annotated using MS/MS peptide identifcations.
  
• MScout is a software tool for assessing LC-MS data quality.
  
• P3 Predictor is a simple windows program to aide in establishing SRM transitions for targeted proteomics.
  
• IDCalc is an implementation of the method reported by Kubinyi, Analytica Chimica Acta, 247 (1991) 107-119 for the prediction of isotope distributions.
  


• MacCoss Lab Users can read detailed information about all of our available software and standard protocols. (You will be prompted for a password)
  

Useful Tools for Proteomics

FASTA Database Download