University of Washington, Department of Genome Sciences (2004-Present)

1. 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)

2.  MacCoss,M.J., Matthews,D.E. Quantitative mass spectrometry for proteomics: Teaching a new dog old tricks. Anal. Chem. 77, 294A-302A (2005)

3.  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)

4.   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)

5.  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)

6.  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) (PMCID: PMC2535816)

7.  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)

8.  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)

9.  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)

10.  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)

11.  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)

12.  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)

13. 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) (PMCID: PMC2556510)

14. 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)

15. 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)

16. 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)

17. 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)

18. 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)

19. 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)

20. 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)

21. 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)

22. 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) (PMCID: PMC2665034)

23. 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) (PMCID: PMC2667385)

24. 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) (PMCID: PMC2486302)

25. Eng,J.K., Fischer,B., Grossmann,J., MacCoss,M.J., A fast SEQUEST cross correlation algorithm, J. Proteome Res., 7,4598-4602 (2008)

26. 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) (PMCID: PMC2556273)

27. 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)

28. 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) (PMCID: PMC2765113)

29. Major M.B., Roberts B.S., Berndt J.D., Marine S., Anastas J., Chung N., Ferrer M., Yi X., Stoick-Cooper C.L., von Haller P.D., Kategaya L., Chien A., Angers S., MacCoss M., Cleary M.A., Arthur W.T., Moon R.T., New regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening, Sci Signal., 1, ra12 (2008)

30. 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)

31. 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) (PMCID: PMC2671646)

32. 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) (PMCID: PMC2675977)

33. 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) (PMCID: PMC2743471)

34. 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) (PMCID: PMC2734151)

35. 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)

36. 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) (PMCID: PMC2763509)

37. 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) (PMCID: PMC2810160)

38. Aagaard,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., 27, 193-203 (2010) (PMCID: PMC2877556)

39. Hsieh,E.J., Hoopmann,M.R., MacLean,B., MacCoss,M.J., Comparison of database search strategies for high precursor accuracy MS/MS data, J. Proteome Res., 9, 1138-1143 (2010) (PMCID: PMC2818881)

40. Bern,M., Finney,G., Hoopmann,M.R., Merrihew,G., Toth,M.J., MacCoss, M.J., Deconvolution of mixture spectra from ion-trap data-independent acquisition tandem mass spectrometry, Anal. Chem, 82, 833-841 (2010) (PMCID: PMC2813958)

41. MacLean,B., Tomazela,D.M., Shulman,N., Chambers,M., Finney,G.L., Frewen.B., Kern,R., Tabb,D.L., Liebler,D.C., MacCoss, M.J., Skyline: An open source document editor for creating and analyzing targeted proteomics experiments, Bioinformatics, 26, 966-968 (2010) (PMCID: PMC2844992)

42. Tomazela,D.M., Patterson,B.W., Hanson,E., Spence,K.L., Kanion,T.B., Salinger,D.H., Vicini,P., Barret,H., Heins,H.B., Cole,F.S., Hamvas,A., MacCoss,M.J., Measurement of human surfactant protein-B turnover in vivo from tracheal aspirates using targeted proteomics, Anal. Chem., 82, 2561-2567 (2010) (PMCID: PMC2843406)

43. Canterbury,J.D., GladdenJ., Buck,L., Olund,R., MacCoss,M.J., A high voltage asymmetric waveform generator for FAIMS, J. Am. Soc. Mass Spectrom., 21, 1118-1121 (2010) (PMCID: PMC2900502)

44. Kim,J.H., Stevens,R.C., MacCoss,M.J., Goodlett,D.R., Scherl,A., Richter,R.J., Suzuki,S.M., Furlong,C.E., Identification and characterization of biomarkers of organophosphorus exposures in humans, Adv. Exp. Med. Biol. 660, 61-71 (2010) (PMCID:PMC2878371)

45. Zelter,A., Hoopmann,M.R., Vernon,R., Baker,D., MacCoss,M.J., Davis,T.N., Isotope signatures allow identification of chemically crosslinked peptides by mass spectrometry: A novel method to determine interresidue distances in protein structures through crosslinking, J. Proteome Res. 9, 3583-3583 (2010) (PMCID: PMC2917471)

46. Cooper,S.J., Finney,G.L., Brown,S.L., Nelson,S.K., Hesselberth,J., MacCoss,M., Fields, S., High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection, Genome Res., 20,1288-1296 (2010) (PMCID: PMC2928507)

47. Rosenfield,R.J., Bonaventura,J., MacCoss,M.J., Arvai,A.S., Yates,J.R. III, Tainer,J.A., Getzoff,E.D., Inducible nitric oxide synthase mechanism and allostery modulated by N-NO-pterin and S-NO-Cys, J. Biol. Chem., 285, 31581-31589 (2010) (PMCID: PMC2951232)

48. Chakrabarti,L., Jackson,S.M., Eng,J., Martinez,R.A., Sopher,B.L., Merrihew,G., MacCoss,M.J., Pallanck,L., Goodlett,D.R., La Spada,A.R., Mitochondrial dysfunction in NnaD mutant flies and Purkinje cell degeneration (pcd) mice reveals a role for Nna proteins in neuronal bioenergetics, Neuron, 66, 835-847 (2010)

49. Li,Q., MacCoss,M.J., Stephens,M., A nested mixture model for protein identification using mass spectrometry, Annals of Applied Statistics, 4(2) 962-987 (2010)

50. Kelley,J.L., Aagaard,J.E., MacCoss,M.J., Swanson,W.J., Functional diversification and evolution of antifreeze proteins in the Antarctic fish Lycodichthys dearborni, J. Mol. Evol., 71, 111-118 (2010)

51. Sharma,V., Eng,J.K., Feldman,S., von Haller,P.D., MacCoss,M.J., Noble,W.S. Precursor charge state prediction for electron transfer dissociation tandem mass spectra. J. Proteome Res., 9, 5346-5357 (2010) (PMCID: PMC2966942)

52. Serang,O., MacCoss,M.J., Noble,W.S., Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data, J Proteome Res., 9, 5346-5357 (2010) (PMCID: PMC2948606)

53. Ranjitkar,P., Press, M.O., Yi,X., Baker,R., MacCoss,M.J., Biggins,S., An E3 ubiquitin ligase prevents ectopic localization of the centromeric histone H3 variant via the centromere targeting domain,  Mol Cell, 40, 455-464 (2010) (PMCID: PMC2995698)

54. MacLean,B., Tomazela,D.M., Abbatiello,S.E., Zhang,S., Whiteaker,J.R., Paulovich,A.G., Carr,S.A., MacCoss,M.J., Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry, Anal. Chem., 82, 10116-10124 (2010) (PMCID: PMC3005404)

55. The modENCODE Consortium, Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project, Science, 330, 1775-1787 (2010)

56. Friedman,D.B., Andacht,T.M., Bunger,M.K., Hawke,D.H., Krijgsveld,J., Lane,W.S., Lilley,K.S., MacCoss,M.J., Moritz,R.L., Settlage,R.E., Sherman,N.E., Weintraub,S.T., Witkowska,H.E., Yates,N.A., Turck,C.W., The ABRF Proteomics Research Group Studies: Educational exercises for qualitative and quantitative proteomics analysis, Proteomics, 11, 1371-1381 (2011)

57. Falick,A.M., Lane,W.S., Lilley,K.S., MacCoss,M.J., Phinney,B.S., Sherman,N.E., Weintraub,S.T., Witkowska,H.E., Yates,N.A.,  J. Biomol. Tech. 22, 21-26 (2011)

58. Gilligan,D.M., Finney,G.L., Rynes,E., MacCoss,M.J., Lambert,A.J., Peters,L.L., Robledo,R.F., Wooden,J.M., Comparative proteomics reveals deficiency of NHE-1 (Slc9a1) in RBCs from the beta-adducin knockout mouse model of hemolytic anemia, Blood Cells Mol. Dis., 47, 85-94 (2011)

59. Bereman,M.S., Egertson,J.D., MacCoss,M.J., Comparison between procedures using SDS for shotgun proteomic analysis of complex samples, Proteomics, 11, 2931-2935 (2011)

60. Dean,M.D., Findlay,G.D., Hoopmann,M.R., Wu,C.C., MacCoss,M.J., Swanson,W.J., Nachman,M.W. Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling, BMC Genomics, 12, 306 (2011) (PMCID: PMC3144466)

61. Wooden,J.M., Finney,G.L., Rynes,E., MacCoss,M.J., Lambert,A.L., Robledo,R.F., Peters,L.L., Gilligan,D.M., Comparative proteomics reveals deficiency of SLC9A1 (sodium/hydrogen exchanger NHE1) in beta-adducin null red cells, Br J Haematol, 154, 492-501 (2011)

62. Marsillach,J., Richter,R.J., Kim,J.H., Stevens,R.C., MacCoss,M.J., Tomazela,D., Suzuki,S.M., Schopfer,L.M., Lockridge,O., Furlong,C.E., Biomarkers of organophosphorus (OP) exposures in humans, Neurotoxicology, 32, 656-660 (2011)

63. Pierce,S.B., Spurrell,C.H., Mandell,J.B., Lee,M.K., Zeligson,S., Bereman,M.S., Stray,S.M., Fokstuen,S., MacCoss,M.J., Levy-Lahad,E., King,M.C., Motulsky,A.G.,Garrod’s fourth inborn error of metabolism solved by the identification of mutations causing pentosuria, Proc Natl Acad Sci, 108, 18313-18317 (2011)

64. Dai,D.F., Hsieh,E.J., Liu,Y., Chen,T., Beyer,R.P., Chin,M.T., MacCoss,M.J., Rabinovitch,P.S., Mitochondrial proteome remodeling in pressure-overload induced heart failure: the role of mitochondria in oxidative stress, Cardiovasc Res., In Press(2011)

65. Spivak,M., Tomazela,D., Weston,J., MacCoss,M.J., Noble,W.S., Direct maximization of protein identifications from tandem mass spectra, In Press (2011)

66. Stergachis,A.B., MacLean,B., Lee,K., Stamatoyannopoulos,J.A., MacCoss,M.J. Rapid empirical discovery of optimal peptides for targeted proteomics, Nat Methods, 8, 1041-1043 (2011)

67. Bereman MS, Canterbury JD, Egertson JD, Horner J, Remes PM, Schwartz J, Zabrouskov V, MacCoss MJ. Evaluation of front-end higher energy collision-induced dissociation on a benchtop dual-pressure linear ion trap mass spectrometer for shotgun proteomics, Analytical chemistry 84 (3), 1533-1539 (2012)

68. Michael Bereman, Hillary Heins, Aaron Hamvas, Susan Guttentag, F Sessions Cole, Michael J MacCoss, Determination of Protein Turnover in Human Infants and Alveolar Type 2 Cells, JBT 23 (Suppl), S6 (2012)

69. Trisha Davis, Daniel A Skelly, Gennifer Merrihew, Michael Riffle, Sara J Cooper, Emily Mitchell, Beth Graczyk, Vagisha Sharma, Daniel Jaschob, William S Noble, Stanley Fields, Michael J MacCoss, Eric G Muller, Maitreya Dunham, Joshua M Akey, (P1) Technology Development in a Multidisciplinary Center, JBT 23 (Suppl), S1 (2012)

70. Roza Wojcik, Yihan Li, Michael J MacCoss, Norman J Dovichi, Capillary electrophoresis with Orbitrap-Velos mass spectrometry detection, Talanta 88, 324-329 (2012)

71. William Stafford Noble, Michael J MacCoss, Computational and statistical analysis of protein mass spectrometry data, PLoS Comput Biol 8 (1), e1002296 2012

72. Hoopmann MR, MacCoss MJ, Moritz RL., Identification of peptide features in precursor spectra using Hardklör and Krönik, Curr Protoc Bioinformatics, Chapter 13:Unit13.18. (2012)

73. Schilling B, Rardin MJ, MacLean BX, Zawadzka AM, Frewen BE, Cusack MP, Sorensen DJ, Bereman MS, Jing E, Wu CC, Verdin E, Kahn CR, Maccoss MJ, Gibson BW., Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation, Mol Cell Proteomics, 11(5):202-14. (2012)

74. Bereman MS, Tomazela DM, Heins HS, Simonato M, Cogo PE, Hamvas A, Patterson BW, Cole FS, MacCoss MJ, A method to determine the kinetics of multiple proteins in human infants with respiratory distress syndrome, Anal Bioanal Chem. 403(8):2397-402 (2012)

75. Michelle Cilia, Michael Bereman, Tara Fish, Michael J MacCoss, Stewart Gray, Homopteran vector biomarkers for efficient circulative plant virus transmission are conserved in multiple aphid species and the whitefly Bemisia tabaci, Journal of Integrative Agriculture, 11 (2), 249-262 (2012)

76. Escher C, Reiter L, MacLean B, Ossola R, Herzog F, Chilton J, MacCoss MJ, Rinner O., Using iRT, a normalized retention time for more targeted measurement of peptides, Proteomics, 12(8):1111-21 (2012)

77. Bereman MS, MacLean B, Tomazela DM, Liebler DC, MacCoss MJ., The development of selected reaction monitoring methods for targeted proteomics via empirical refinement, Proteomics. 12(8):1134-41. (2012)

78. Sherrod SD, Myers MV, Li M, Myers JS, Carpenter KL, Maclean B, Maccoss MJ, Liebler DC, Ham AJ, Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides, Proteome Res. 1;11(6):3467-79 (2012)

79. BJ Diament, MJ MacCoss, WS Noble, On the feasibility and utility of exploiting real time database search to improve adaptive peak selection, arXiv preprint arXiv:1207.5848 (2012) 

80. Marina Spivak, Michael S Bereman, Michael J MacCoss, William Stafford Noble, Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments, Journal of Proteome Research 11 (9), 4499-4508 (2012)

81. Sharma V, Eng JK, Maccoss MJ, Riffle M., A mass spectrometry proteomics data management platform, Mol Cell Proteomics. 11(9):824-31 (2012)

82. Shane Neph, Jeff Vierstra, Andrew B Stergachis, Alex P Reynolds, Eric Haugen, Benjamin Vernot, Robert E Thurman, Sam John, Richard Sandstrom, Audra K Johnson, Matthew T Maurano, Richard Humbert, Eric Rynes, Hao Wang, Shinny Vong, Kristen Lee, Daniel Bates, Morgan Diegel, Vaughn Roach, Douglas Dunn, Jun Neri, Anthony Schafer, R Scott Hansen, Tanya Kutyavin, Erika Giste, Molly Weaver, Theresa Canfield, Peter Sabo, Miaohua Zhang, Gayathri Balasundaram, Rachel Byron, Michael J MacCoss, Joshua M Akey, MA Bender, Mark Groudine, Rajinder Kaul, John A Stamatoyannopoulos, An expansive human regulatory lexicon encoded in transcription factor footprints, Nature 489 (7414), 83-90 (2012)

83. Hsieh EJ, Shulman NJ, Dai DF, Vincow ES, Karunadharma PP, Pallanck L, Rabinovitch PS, MacCoss MJ, Topograph, a software platform for precursor enrichment corrected global protein turnover measurements, Mol Cell Proteomics, (11):1468- 74 (2012)

84. Egertson JD, Eng JK, Bereman MS, Hsieh EJ, Merrihew GE, MacCoss MJ, De novo correction of mass measurement error in low resolution tandem MS spectra for shotgun proteomics, Am Soc Mass Spectrometry 23(12):2075-82 (2012)

85. Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak MY, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P., A cross-platform toolkit for mass spectrometry and proteomics, Nat Biotechnol. 30(10):918-20 (2012)

86. Cilia M, Peter KA, Bereman MS, Howe K, Fish T, Smith D, Gildow F, MacCoss MJ, Thannhauser TW, Gray SM, Discovery and targeted LC-MS/MS of purified polerovirus reveals differences in the virus-host interactome associated with altered aphid transmission, PLoS One ;7(10):e48177 (2012)

87. McIlwain S, Mathews M, Bereman MS, Rubel EW, MacCoss MJ, Noble WS, Estimating relative abundances of proteins from shotgun proteomics data, BMC Bioinformatics,  19;13:308 (2012)

88. Marsillach J, Hsieh EJ, Richter RJ, MacCoss MJ, Furlong CE, Proteomic analysis of adducted butyrylcholinesterase for biomonitoring organophosphorus exposures, Chem Biol Interact,  25;203(1):85-90 (2013)

89. Hsieh EJ, Bereman MS, Durand S, Valaskovic GA, MacCoss MJ, Effects of column and gradient lengths on peak capacity and peptide identification in nanoflow LC-MS/MS of complex proteomic samples, Am Soc Mass Spectrometry 24(1):148-53 (2013)

90. Bereman MS, Hsieh EJ, Corso TN, Van Pelt CK, Maccoss MJ, Development and characterization of a novel plug and play liquid chromatography-mass spectrometry (LC-MS) source that automates connections between the capillary trap, column, and emitter, Mol Cell Proteomics, 12(6):1701-8 (2013)

91. Maia M Chan, Jason M Wooden, Mark Tsang, Diana M Gilligan, Dinesh K Hirenallur-S, Greg L Finney, Eric Rynes, Michael MacCoss, Julita A Ramirez, Heon Park, Brian M Iritani, Hematopoietic protein-1 regulates the actin membrane skeleton and membrane stability in murine erythrocytes, PloS one 8 (2), e54902 (2013)

92. Vincow ES, Merrihew G, Thomas RE, Shulman NJ, Beyer RP, MacCoss MJ, Pallanck LJ, The PINK1-Parkin pathway promotes both mitophagy and selective respiratory chain turnover in vivo, Proc Natl Acad Sci U S A.  16;110(16):6400-5 (2013)

93. Michael S Bereman, Edward J Hsieh, Thomas N Corso, Colleen K Van Pelt, Michael J MacCoss, Development and characterization of a novel plug and play LC-MS source which automates connections between the capillary trap, column, and emitter, Molecular & Cellular Proteomics, mcp. O112. 024893 (2013)

94. Palmer MR, McDowall MH, Stewart L, Ouaddi A, MacCoss MJ, Swanson WJ, Mass spectrometry and next-generation sequencing reveal an abundant and rapidly evolving abalone sperm protein, Mol Reprod Dev. 80(6):460-5 (2013)

95. Scott P Goulding, Michael J MacCoss, Christine C Wu, Label-Free Differential Analysis of Murine Postsynaptic Densities, Proteomics for Biomarker Discovery, 295-309 (2013)

96. K Chen, J Egertson, M MacCoss, Targeted data independent acquisition for mass spectroscopy proteomics, PloS one8 (2), e54902 (2013)

97. SE Kruse, P Karunadharma, M MacCoss, P Rabinovitch, Divergent Effects of Age on Mitochondrial Function in Fast Twitch and Slow Twitch Skeletal Muscle, Free Radical Biology and Medicine, S116 (2013)

98. M Roudier, L True, M MacCoss, M Bereman, Determination of the Intra-individual Variability of Protein Expression in Benign/Cancerous Prostate Tissue via LC-MS–Efforts Towards Molecular Classification, Journal of Biomolecular Techniques: 24 (Suppl), S61 (2013)

99. MS Bereman, EJ Hsieh, TN Corso, CK Van Pelt, MJ MacCoss, Development and characterization of a novel plug and play liquid chromatography-mass spectrometry (LC-MS) source that automates connections between the capillary trap, column, and emitter, Molecular & Cellular Proteomics 12 (6), 1701-1708 (2013)

100. AK D’Souza, Birgit Schilling, Julian Chytrowski, BX MacLean, Daniel Broudy, Nicholas J Shulman, Michael J MacCoss, Bradford W Gibson, MS1Probe–Implementation of a Statistical Tool for MS1-based Quantitation in Skyline for High Throughput Quantitative Analysis, Proceedings of the 61st Annual ASMS Conference, Minneapolis, MN. (2013) 

101. Abbatiello SE, Mani DR, Schilling B, Maclean B, Zimmerman LJ, Feng X, Cusack MP, Sedransk N, Hall SC, Addona T, Allen S, Dodder NG, Ghosh M, Held JM, Hedrick V, Inerowicz HD, Jackson A, Keshishian H, Kim JW, Lyssand JS, Riley CP, Rudnick P, Sadowski P, Shaddox K, Smith D, Tomazela D, Wahlander A, Waldemarson S, Whitwell CA, You J, Zhang S, Kinsinger CR, Mesri M, Rodriguez H, Borchers CH, Buck C, Fisher SJ, Gibson BW, Liebler D, Maccoss M, Neubert TA, Paulovich A, Regnier F, Skates SJ, Tempst P, Wang M, Carr SA, Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS), Mol Cell Proteomics, 12(9):2623-39 (2013) 

102. D Igwe, S Ngatat, M Cilia, MS Bereman, MJ MacCoss, SM Gray, R Hanna, L Kumar, Characterization of protein biomarkers linked to transmission competent and transmission refractive aphid and whitefly populations in Nigeria, Journal of Proteome Research 12 (7), 3246-3254 (2013)

103. VA Glukhova, DM Tomazela, GD Findlay, RJ Monnat Jr, MJ MacCoss, Rapid assessment of RNAi-mediated protein depletion by selected reaction monitoring mass spectrometry, Journal of proteome research 12 (7), 3246-3254 (2013)

104. Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, Johansson M, Jaschob D, Graczyk B, Shulman NJ, Wakefield J, Cooper SJ, Fields S, Noble WS, Muller EG, Davis TN, Dunham MJ, Maccoss MJ, Akey JM, Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast,  Genome Res. 23(9):1496-504 (2013)

105. Sunghee Woo, Seong Won Cha, Gennifer Merrihew, Yupeng He, Natalie Castellana, Clark Guest, Michael MacCoss,Vineet Bafna, Proteogenomic database construction driven from large scale RNA-seq data, Journal of Proteome Research 13 (1), 21-28 (2013)

106. Egertson JD, Kuehn A, Merrihew GE, Bateman NW, MacLean BX, Ting YS, Canterbury JD, Marsh DM, Kellmann M, Zabrouskov V, Wu CC, MacCoss MJ, Multiplexed MS/MS for improved data-independent acquisition, Nat Methods. 10(8):744-6 (2013)

107. Jarrett D Egertson, Andreas Kuehn, Gennifer E Merrihew, Nicholas W Bateman, Brendan X MacLean, Ying S Ting, Jesse D Canterbury, Donald M Marsh, Markus Kellmann, Vlad Zabrouskov, Christine C Wu, Michael J MacCoss, HHS Public Access, Nat Methods 10 (8), 744-746 (2013)

108. Cecilia Tamborindeguy, Michael S Bereman, Stacy DeBlasio, David Igwe, Dawn M Smith, Frank White, Michael J MacCoss, Stewart M Gray, Michelle Cilia, Genomic and proteomic analysis of Schizaphis graminum reveals cyclophilin proteins are involved in the transmission of cereal yellow dwarf virus, PloS one 8 (8), e71620, (2013)

109. Daniel A Skelly, Gennifer E Merrihew, Michael Riffle, Caitlin F Connelly, Emily O Kerr, Marnie Johansson, Daniel Jaschob, Beth Graczyk, Nicholas J Shulman, Jon Wakefield, Sara J Cooper, Stanley Fields, William S Noble, Eric GD Muller, Trisha N Davis, Maitreya J Dunham, Michael J MacCoss, Joshua M Akey, Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast, Genome Research 23 (9), 1496-1504 (2013)

110. Conlon KP, Basrur V, Rolland D, Wolfe T, Nesvizhskii AI, MacCoss MJ, Lim MS, Elenitoba-Johnson KS, Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer, Mol Cell Proteomics. 12(10):2714-23 (2013)

111. Dao-Fu Dai, Edward J Hsieh, Tony Chen, Lorena G Menendez, Nathan B Basisty, Lauren Tsai, Richard P Beyer, David A Crispin, Nicholas J Shulman, Hazel H Szeto, Rong Tian, Michael J MacCoss, Peter S Rabinovitch, Global proteomics and pathway analysis of pressure-overload–induced heart failure and its attenuation by mitochondrial-targeted peptides, Molecular & Cellular Proteomics 12 (10), 2714-2723 (2013)

112. Ying Ann Chiao, Dao-Fu Dai, Pabalu Karunadharma, Nathan Basisty, Haiwei Gu, Simon C Johnson, Danijel Djukovic, Daniel Raftery, Michael MacCoss, Peter S Rabinovitch, Subacute Treatment With Rapamycin Reverses Cardiac Aging by Proteome Remodeling and Improved Mitochondrial Energy Metabolism, Circulation 128 (22 Supplement), A17128 (2013)

113. Jennifer Schleit, Simon C Johnson, Christopher F Bennett, Marissa Simko, Natalie Trongtham, Anthony Castanza, Edward J Hsieh, Richard M Moller, Brian M Wasko, Joe R Delaney, George L Sutphin, Daniel Carr, Christopher J Murakami, Autumn Tocchi, Bo Xian, Weiyang Chen, Tao Yu, Sarani Goswami, Sean Higgins, Mollie Holmberg, Ki‐Soo Jeong, Jin R Kim, Shannon Klum, Eric Liao, Michael S Lin, Winston Lo, Hillary Miller, Brady Olsen, Zhao J Peng, Tom Pollard, Prarthana Pradeep, Dillon Pruett, Dilreet Rai, Vanessa Ros, Minnie Singh, Benjamin L Spector, Helen Vander Wende, Elroy H An, Marissa Fletcher, Monika Jelic, Peter S Rabinovitch, Michael J MacCoss, Jing‐Dong J Han, Brian K Kennedy, Matt Kaeberlein, Molecular mechanisms underlying genotype‐dependent responses to dietary restriction, Aging cell 12 (6), 1050-1061 (2013)

114. Conlon KP, Basrur V, Rolland D, Wolfe T, Nesvizhskii AI, MacCoss MJ, Lim MS, Elenitoba-Johnson KS, Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer, Mol Cell Proteomics. 12(10):2714-23 (2013)

115. Fujimoto GM, Monroe ME, Rodriguez L, Wu C, MacLean B, Smith RD, MacCoss MJ, Payne SH, Accounting for population variation in targeted proteomics, Proteome Res. 13(1):321-3 (2013) 

116. Aagaard JE, George RD, Fishman L, Maccoss MJ, Swanson WJ, Selection on plant male function genes identifies candidates for reproductive isolation of yellow monkeyflowers, PLoS Genet. 9(12):e1003965 (2013)

117. Nicholas W Bateman, Scott P Goulding, Nicholas J Shulman, Avinash K Gadok, Karen K Szumlinski, Michael J MacCoss, Christine C Wu, Maximizing peptide identification events in proteomic workflows using data-dependent acquisition (DDA), Molecular & Cellular Proteomics 13 (1), 329-338 (2013) 

118. Bereman MS, Johnson R, Bollinger J, Boss Y, Shulman N, MacLean B, Hoofnagle AN, MacCoss MJ, Implementation of statistical process control for proteomic experiments via LC MS/MS, Am Soc Mass Spectrom. 25(4):581-7 (2014)

119. Pinheiro P, Bereman MS, Burd J, Pals M, Armstrong S, Howe KJ, Thannhauser TW, MacCoss MJ, Gray SM, Cilia M, Evidence of the biochemical basis of host virulence in the greenbug aphid, Schizaphis graminum (Homoptera: Aphididae), Proteome Res.  4;13(4):2094-108 (2014)

120. Dai DF, Karunadharma PP, Chiao YA, Basisty N, Crispin D, Hsieh EJ, Chen T, Gu H, Djukovic D, Raftery D, Beyer RP, MacCoss MJ, Rabinovitch PS, Altered proteome turnover and remodeling by short-term caloric restriction or rapamycin rejuvenate the aging heart, Aging Cell. 13(3):529-39 (2014)

121. Reiko Kiyonami, Bhavin Patel, Michael Senko, Vlad Zabrouskov, Jarrett Egertson, Sonia Ting, Michael MacCoss, John Rogers, Andreas FR HühmerLarge scale targeted protein quantification using WiSIM-DIA workflow on a Orbitrap fusion tribrid mass spectrometer, ASMS, (2014)

122. Bateman NW, Goulding SP, Shulman NJ, Gadok AK, Szumlinski KK, MacCoss MJ, Wu CC, Maximizing peptide identification events in proteomic workflows using data-dependent acquisition (DDA), Mol Cell Proteomics. 13(1):329-38 (2014) 

123. J Marsillach, EJ Hsieh, RJ Richter, MJ Maccoss, AN Hoofnagle, CE Furlong, Use of dried blood spots and mass spectrometry for biomonitoring organophosphorus exposures, Neurotoxicology and Teratology, 92 (2014)

124. Ying Ann Chiao, Nathan Basisty, Ying Sonia Ting, Hazel H Szeto, Michael J MacCoss, Peter S Rabinovitch, Short Term Treatment with Mitochondrial Protective Peptide Reverses Cardiac Aging in Mice, Free Radical Biology and Medicine, S31 (2014)

125. Broudy D, Killeen T, Choi M, Shulman N, Mani DR, Abbatiello SE, Mani D, Ahmad R, Sahu AK, Schilling B, Tamura K, Boss Y, Sharma V, Gibson BW, Carr SA, Vitek O, MacCoss MJ, MacLean B, A framework for installable external tools in Skyline, Bioinformatics. 1;30(17):2521-3 (2014)

126. Mamatha Damodarasamy, Richard S Johnson, Itay Bentov, Michael J MacCoss, Robert B Vernon, May J Reed, Hyaluronan enhances wound repair and increases collagen III in aged dermal wounds, Wound Repair Regen, 22(4):521-6  (2014)

127. Michael MacCoss, Jarrett Egertson, Sonia Ting, Richard Johnson, Han-Yin Yang, Nick Shulman, Brendan MacLean, Improving the Robustness and Reproducibility of Mass Spectrometry Based Proteomics, Molecular & Cellular Proteomics 13 (8), S11-S11 (2014)

128. Vagisha Sharma, Josh Eckels, Greg K Taylor, Nicholas J Shulman, Andrew B Stergachis, Shannon A Joyner, Ping Yan, Jeffrey R Whiteaker, Goran N Halusa, Birgit Schilling, Bradford W Gibson, Christopher M Colangelo, Amanda G Paulovich, Steven A Carr, Jacob D Jaffe, Michael J MacCoss, Brendan MacLean, Panorama: a targeted proteomics knowledge base, Proteome Res. 5;13(9):4205-10 (2014)

129. Mark B Gerstein, Joel Rozowsky, Koon-Kiu Yan, Daifeng Wang, Chao Cheng, James B Brown, Carrie A Davis, LaDeana Hillier, Cristina Sisu, Jingyi Jessica Li, Baikang Pei, Arif O Harmanci, Michael O Duff, Sarah Djebali, Roger P Alexander, Burak H Alver, Raymond Auerbach, Kimberly Bell, Peter J Bickel, Max E Boeck, Nathan P Boley, Benjamin W Booth, Lucy Cherbas, Peter Cherbas, Chao Di, Alex Dobin, Jorg Drenkow, Brent Ewing, Gang Fang, Megan Fastuca, Elise A Feingold, Adam Frankish, Guanjun Gao, Peter J Good, Roderic Guigó, Ann Hammonds, Jen Harrow, Roger A Hoskins, Cédric Howald, Long Hu, Haiyan Huang, Tim JP Hubbard, Chau Huynh, Sonali Jha, Dionna Kasper, Masaomi Kato, Thomas C Kaufman, Robert R Kitchen, Erik Ladewig, Julien Lagarde, Eric Lai, Jing Leng, Zhi Lu, Michael MacCoss, Gemma May, Rebecca McWhirter, Gennifer Merrihew, David M Miller, Ali Mortazavi, Rabi Murad, Brian Oliver, Sara Olson, Peter J Park, Michael J Pazin, Norbert Perrimon, Dmitri Pervouchine, Valerie Reinke, Alexandre Reymond, Garrett Robinson, Anastasia Samsonova, Gary I Saunders, Felix Schlesinger, Anurag Sethi, Frank J Slack, William C Spencer, Marcus H Stoiber, Pnina Strasbourger, Andrea Tanzer, Owen A Thompson, Kenneth H Wan, Guilin Wang, Huaien Wang, Kathie L Watkins, Jiayu Wen, Kejia Wen, Chenghai Xue, Li Yang, Kevin Yip, Chris Zaleski, Yan Zhang, Henry Zheng, Steven E Brenner, Brenton R Graveley, Susan E Celniker, Thomas R Gingeras, Robert Waterston, Comparative analysis of the transcriptome across distant species, Nature512 (7515), 445-448 (2014)

130. Cilia M, Johnson R, Sweeney M, DeBlasio SL, Bruce JE, MacCoss MJ, Gray SM, Evidence for lysine acetylation in the coat protein of a polerovirus, Gen Virol. 95(Pt 10):2321-7 (2014)

131. McIlwain S, Tamura K, Kertesz-Farkas A, Grant CE, Diament B, Frewen B, Howbert JJ, Hoopmann MR, Käll L, Eng JK, MacCoss MJ, Noble WS, Crux: rapid open source protein tandem mass spectrometry analysis, Proteome Res. 3;13(10):4488-91 (2014)

132. Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR, Yates JR 3rd, MacCoss MJ, Moritz RL, Asbury CL, Davis TN. Kinetochore biorientation in Saccharomyces cerevisiae requires a tightly folded conformation of the Ndc80 complex, Genetics, 198(4):1483-93 (2014)

133. Judit Marsillach, Stephanie M Suzuki, Rebecca J Richter, Matthew G McDonald, Peter M Rademacher, Michael J MacCoss, Edward J Hsieh, Allan E Rettie, Clement E Furlong, Human valacyclovir hydrolase/biphenyl hydrolase-like protein is a highly efficient homocysteine thiolactonase, PloS one 9 (10), e110054 (2014)

134. Canterbury JD, Merrihew GE, MacCoss MJ, Goodlett DR, Shaffer SA, Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics, PMID: 25261218 (2014)

135. Young Hun Song, Daniel A Estrada, Richard S Johnson, Somi K Kim, Sang Yeol Lee, Michael J MacCoss, Takato Imaizumi, Distinct roles of FKF1, GIGANTEA, and ZEITLUPE proteins in the regulation of CONSTANS stability in Arabidopsis photoperiodic flowering, Proceedings of the National Academy of Sciences 111 (49), 17672-17677, (2014)

136. Kim TY, Siesser PF, Rossman KL, Goldfarb D, Mackinnon K, Yan F, Yi X, MacCoss MJ, Moon RT, Der CJ, Major MB, Substrate trapping proteomics reveals targets of the βTrCP2/FBXW11 ubiquitin ligase, Mol Cell Biol. 35(1):167-81 (2015)

137. Marsillach J, Suzuki SM, Richter RJ, McDonald MG, Rademacher PM, MacCoss MJ, Hsieh EJ, Rettie AE, Furlong CE, Human valacyclovir hydrolase/biphenyl hydrolase-like protein is a highly efficient homocysteine thiolactonase, PLoS One.  9(10):e110054 (2015)

138. DeBlasio SL, Johnson R, Mahoney J, Karasev A, Gray SM, MacCoss MJ, Cilia M, Insights into the polerovirus-plant interactome revealed by coimmunoprecipitation and mass spectrometry, Mol Plant Microbe Interact. 28(4):467-81 (2015)

139. Dao-Fu Doi, Han-Yin Yang, Charles Alpers, Michael MacCoss, Kelly Smith, Quantitative Shotgun Proteomics Analysis of Amyloid From Paraffom-Embedded Tissue, Laboratory Investigation 95, 407A-407A (2015)

140. Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA, Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma, Mol Cell Proteomics. 14(9):2357-74 (2015)

141. Michael R Hoopmann, Alex Zelter, Richard S Johnson, Michael Riffle, Michael J MacCoss, Trisha N Davis, Robert L Moritz, Kojak: efficient analysis of chemically cross-linked protein complexes, Journal of proteome research 14 (5), 2190-2198 (2015)

142. Karunadharma PP, Basisty N, Dai DF, Chiao YA, Quarles EK, Hsieh EJ, Crispin D, Bielas JH, Ericson NG, Beyer RP, MacKay VL, MacCoss MJ, Rabinovitch PS, Subacute calorie restriction and rapamycin discordantly alter mouse liver proteome homeostasis and reverse aging effects, Aging Cell. 14(4):547-57 (2015)

143. Karunadharma PP, Basisty N, Chiao YA, Dai DF, Drake R, Levy N, Koh WJ, Emond MJ, Kruse S, Marcinek D, Maccoss MJ, Rabinovitch PS, Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments, FASEB 29(8):3582-92 (2015)

144. Egertson JD, MacLean B, Johnson R, Xuan Y, MacCoss MJ, Multiplexed peptide analysis using data-independent acquisition and Skyline, Nat Protoc. 10(6):887-903 (2015)

145. Rardin MJ, Schilling B, Cheng LY, MacLean BX, Sorensen DJ, Sahu AK, MacCoss MJ, Vitek O, Gibson BW, MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments, Mol Cell Proteomics, 14(9):2405-19 (2015)

146. Searle BC, Egertson JD, Bollinger JG, Stergachis AB, MacCoss MJ, Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments, Molecular & Cellular Proteomics 14 (9), 2331-2340  (2015)

147. Ting YS, Egertson JD, Payne SH, Kim S, MacLean B, Käll L, Aebersold R, Smith RD, Noble WS, MacCoss MJ, Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data, Mol Cell Proteomics. 14(9):2301-7 (2015)

148. Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ, A deeper look into Comet--implementation and features, Am Soc Mass Spectrom, 26(11):1865-74 (2015)

149. Schilling B, MacLean B, Held JM, Sahu AK, Rardin MJ, Sorensen DJ, Peters T, Wolfe AJ, Hunter CL, MacCoss MJ, Gibson BW, Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflow, Anal Chem. 20;87(20):10222-9 (2015)

150. Riffle M, Merrihew GE, Jaschob D, Sharma V, Davis TN, Noble WS, MacCoss MJ, Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development, Am Soc Mass Spectrom. 26(11):1827-36 (2015)

151. Kudalkar EM, Scarborough EA, Umbreit NT, Zelter A, Gestaut DR, Riffle M, Johnson RS, MacCoss MJ, Asbury CL, Davis TN, Regulation of outer kinetochore Ndc80 complex-based microtubule attachments by the central kinetochore Mis12/MIND complex, Proc Natl Acad Sci U S A. 13;112(41):E5583-9 (2015)

152. Zelter A, Bonomi M, Kim Jo, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN, The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling, Nat Commun. 12;6:8673   (2015)

153. John S Ramsey, Richard S Johnson, Jason S Hoki, Angela Kruse, Jaclyn Mahoney, Mark E Hilf, Wayne B Hunter, David G Hall, Frank C Schroeder, Michael J MacCoss, Michelle Cilia, Metabolic Interplay between the Asian citrus psyllid and its Profftella symbiont: An Achilles’ heel of the citrus greening insect vector, PloS one 10 (11), e0140826  (2015)

154. Kruse SE, Karunadharma PP, Basisty N, Johnson R, Beyer RP, MacCoss MJ, Rabinovitch PS, Marcinek DJ, Age modifies respiratory complex I and protein homeostasis in a muscle type-specific manner, Aging Cell 15(1):89-99 (2016) 

155. Kawahara R, Bollinger JG, Rivera C, Ribeiro AC, Brandão TB, Paes Leme AF, MacCoss MJ, A targeted proteomic strategy for the measurement of oral cancer candidate biomarkers in human saliva, Proteomics. 16(1):159-73 (2016)

156. Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Boja E, Carr SA, Chan DW, Chen X, Chen J, Davies SR, Ellis MJ, Fenyö D, Hiltke T, Ketchum KA, Kinsinger C, Kuhn E, Liebler DC, Liu T, Loss M, MacCoss MJ, Qian WJ, Rivers R, Rodland KD, Ruggles KV, Scott MG, Smith RD, Thomas S, Townsend RR, Whiteley G, Wu C, Zhang H, Zhang Z, Rodriguez H, Paulovich AG, Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays, Methods Mol Biol. 1410:223-36 (2016) 

157. Bollinger JG, Stergachis AB, Johnson RS, Egertson JD, MacCoss MJ, Selecting Optimal Peptides for Targeted Proteomic Experiments in Human Plasma Using In Vitro Synthesized Proteins as Analytical Standards, Methods Mol Biol. 1410:207-21  (2016)

158. The M, MacCoss MJ, Noble WS, Käll L, Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0,  Am Soc Mass Spectrom. 27(11):1719-1727 (2016)

159. Chiao YA, Kolwicz SC, Basisty N, Gagnidze A, Zhang J, Gu H, Djukovic D, Beyer RP, Raftery D, MacCoss M, Tian R, Rabinovitch PS, Rapamycin transiently induces mitochondrial remodeling to reprogram energy metabolism in old hearts, Aging (Albany NY). 8(2):314-27 (2016) 

160. Basisty N, Dai DF, Gagnidze A, Gitari L, Fredrickson J, Maina Y, Beyer RP, Emond MJ, Hsieh EJ, MacCoss MJ, Martin GM, Rabinovitch PS, Mitochondrial-targeted catalase is good for the old mouse proteome, but not for the young: 'reverse' antagonistic pleiotropy?, Aging Cell. 15(4):634-45  (2016)

161. Topalidou I, Cattin-Ortolá J, Pappas AL, Cooper K, Merrihew GE, MacCoss MJ, Ailion M, The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles, PLoS Genet.  18;12(5):e1006074 (2016)

162. Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A, Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure, Struct Biol. 194(3):303-10 (2016)

163. Armbruster CR, Wolter DJ, Mishra M, Hayden HS, Radey MC, Merrihew G, MacCoss MJ, Burns J, Wozniak DJ, Parsek MR, Hoffman LR, Staphylococcus aureus Protein A Mediates Interspecies Interactions at the Cell Surface of Pseudomonas aeruginosa, MBio,  24;7(3). pii: e00538-16. 

164. Catherine R Armbruster, Daniel J Wolter, Meenu Mishra, Hillary S Hayden, Matthew C Radey, Gennifer Merrihew, Michael J MacCoss, Jane Burns, Daniel J Wozniak, Matthew R Parsek, Lucas R Hoffman, Staphylococcus aureus Protein A Mediates Interspecies Interactions at the Cell Surface of Pseudomonas aeruginosa, mBio 7 (3), e00538-16 (2016)

165. Bereman MS, Beri J, Sharma V, Nathe C, Eckels J, MacLean B, MacCoss MJ, An Automated Pipeline to Monitor System Performance in Liquid Chromatography-Tandem Mass Spectrometry Proteomic Experiments, Proteome Res.(2016) 

166. DeBlasio SL, Johnson RS, MacCoss MJ, Gray SM, Cilia M, Model system-guided protein interaction mapping for virus isolated from phloem tissue, Proteome Res. (2016)

167. Berger S, Procko E, Margineantu D, Lee EF, Shen BW, Zelter A, Silva DA, Chawla K, Herold MJ, Garnier JM, Johnson R, MacCoss MJ, Lessene G, Davis TN, Stayton PS, Stoddard BL, Fairlie WD, Hockenbery DM, Baker D, Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer, Elife  2;5. pii: e20352 (2016)

168. The M, MacCoss MJ, Noble WS, Käll L., Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0. J Am Soc Mass Spectrom. Nov. 27, 2016.

169. Henderson CM, Bollinger JG, Becker JO, Wallace JM, Laha TJ, MacCoss MJ, Hoofnagle AN.,  Quantification by nano liquid chromatography-parallel reaction monitoring-mass spectrometry of human apolipoprotein A-I, apolipoprotein B, and hemoglobin A1c in dried blood spots.  Proteomics Clin Appl. 2017 Jan 23. 

170. Sandra Elizabeth Spencer, Thomas N Corso, James G Bollinger, Clark M Henderson, Andrew N Hoofnagle, Michael J MacCoss, An Automated Trapping Column Exchanger for High Throughput Nanoflow Liquid Chromatography, Analytical Chemistry, 2017. 

171. Clark M Henderson, James G Bollinger, Jessica O Becker, Jennifer M Wallace, Thomas J Laha, Michael J MacCoss,Andrew N Hoofnagle, Quantification by nano liquid chromatography parallel reaction monitoring mass spectrometry of human apolipoprotein A‐I, apolipoprotein B, and hemoglobin A1c in dried blood spots, PROTEOMICS-Clinical Applications (2017)

172. JS Ramsey, JD Chavez, R Johnson, S Hosseinzadeh, JE Mahoney, JP Mohr, F Robison, X Zhong, DG Hall, M MacCoss, J Bruce, M Cilia, Protein interaction networks at the host–microbe interface in Diaphorina citri, the insect vector of the citrus greening pathogen, Open Science (2017)

173. A Kruse, S Saha, R Johnson, S Fattahalhosseini, E Warwick, K Sturgeon, M MacCoss, R Shatters, M Cilia, Comparative proteomics to identify critical proteins for transmission of Candidatus Liberibacter asiacticus by the Asian citrus psyllid, PHYTOPATHOLOGY (2017)

174. Jae ook Kim, Alex Zelter, Neil T Umbreit, Athena Bollozos, Michael Riffle, Richard Johnson, Michael J MacCoss,Charles L Asbury, Trisha N Davis, The Ndc80 complex bridges two Dam1 complex rings, eLife, (2017)

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