Michael MacCoss
maccoss@uw.eduUniversity of Washington,
Computational Biology
Developmental Biology, Stem Cells & Aging
Genetics, Genomics & Evolution
Development and application of proteomics technologies
Faculty Contact Information
Lab Information
Accepting Students For:
Publications
The following publications were retrieved from PubMed:
Vincow ES, Thomas RE, Merrihew G, Shulman NJ, Bammler TK, MacDonald JW, MacCoss MJ, Pallanck LJ.
Autophagy. 2019 Mar 13;
Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.
Amodei D, Egertson J, MacLean BX, Johnson R, Merrihew GE, Keller A, Marsh D, Vitek O, Mallick P, MacCoss MJ.
J Am Soc Mass Spectrom. 2019 Jan 22;
Chalkley RJ, MacCoss MJ, Jaffe JD, Röst HL.
Mol Cell Proteomics. 2019 Jan; 1(18)1-2
Campbell MD, Duan J, Samuelson AT, Gaffrey MJ, Merrihew GE, Egertson JD, Wang L, Bammler TK, Moore RJ, White CC, Kavanagh TJ, Voss JG, Szeto HH, Rabinovitch PS, MacCoss MJ, Qian WJ, Marcinek DJ.
Free Radic Biol Med. 2018 Dec 28; (134)268-281
Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis.
Krahmer J, Goralogia GS, Kubota A, Zardilis A, Johnson RS, Song YH, MacCoss MJ, Le Bihan T, Halliday KJ, Imaizumi T, Millar AJ.
FEBS Lett. 2019 Feb; 3(593)319-338
Searle BC, Pino LK, Egertson JD, Ting YS, Lawrence RT, MacLean BX, Villén J, MacCoss MJ.
Nat Commun. 2018 Dec 3; 1(9)5128
Kim YJ, Sweet SM, Egertson JD, Sedgewick AJ, Woo S, Liao WL, Merrihew GE, Searle BC, Vaske C, Heaton R, MacCoss MJ, Hembrough T.
J Proteome Res. 2018 Nov 27;
DeBlasio SL, Xu Y, Johnson RS, Rebelo AR, MacCoss MJ, Gray SM, Heck M.
Viruses. 2018 Oct 26; 11(10)
Pino LK, Searle BC, Huang EL, Noble WS, Hoofnagle AN, MacCoss MJ.
Anal Chem. 2018 Nov 6; 21(90)13112-13117
Thomas RE, Vincow ES, Merrihew GE, MacCoss MJ, Davis MY, Pallanck LJ.
PLoS Genet. 2018 Sep; 9(14)e1007694
Kruse A, Ramsey JS, Johnson R, Hall DG, MacCoss MJ, Heck M.
J Proteome Res. 2018 Sep 7; 9(17)2995-3011
MacLean BX, Pratt BS, Egertson JD, MacCoss MJ, Smith RD, Baker ES.
J Am Soc Mass Spectrom. 2018 Nov; 11(29)2182-2188
Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems.
Claw KG, George RD, MacCoss MJ, Swanson WJ.
BMC Genomics. 2018 Jun 22; 1(19)488
Novel phosphorylation states of the yeast spindle pole body.
Fong KK, Zelter A, Graczyk B, Hoyt JM, Riffle M, Johnson R, MacCoss MJ, Davis TN.
Biol Open. 2018 Oct 8; 10(7)
Litichevskiy L, Peckner R, Abelin JG, Asiedu JK, Creech AL, Davis JF, Davison D, Dunning CM, Egertson JD, Egri S, Gould J, Ko T, Johnson SA, Lahr DL, Lam D, Liu Z, Lyons NJ, Lu X, MacLean BX, Mungenast AE, Officer A, Natoli TE, Papanastasiou M, Patel J, Sharma V, Toder C, Tubelli AA, Young JZ, Carr SA, Golub TR, Subramanian A, MacCoss MJ, Tsai LH, Jaffe JD.
Cell Syst. 2018 Apr 25; 4(6)424-443.e7
Tseng BS, Reichhardt C, Merrihew GE, Araujo-Hernandez SA, Harrison JJ, MacCoss MJ, Parsek MR.
MBio. 2018 Apr 10; 2(9)
Peckner R, Myers SA, Jacome ASV, Egertson JD, Abelin JG, MacCoss MJ, Carr SA, Jaffe JD.
Nat Methods. 2018 May; 5(15)371-378
Xu Y, Ju HJ, DeBlasio S, Carino EJ, Johnson R, MacCoss MJ, Heck M, Miller WA, Gray SM.
J Virol. 2018 Jun 1; 11(92)
Helgeson LA, Zelter A, Riffle M, MacCoss MJ, Asbury CL, Davis TN.
Proc Natl Acad Sci U S A. 2018 Mar 13; 11(115)2740-2745
Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.
Sharma V, Eckels J, Schilling B, Ludwig C, Jaffe JD, MacCoss MJ, MacLean B.
Mol Cell Proteomics. 2018 Jun; 6(17)1239-1244
How many human proteoforms are there?
Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B.
Nat Chem Biol. 2018 Feb 14; 3(14)206-214
Luan Q, Zelter A, MacCoss MJ, Davis TN, Nolen BJ.
Proc Natl Acad Sci U S A. 2018 Feb 13; 7(115)E1409-E1418
Henderson CM, Shulman NJ, MacLean B, MacCoss MJ, Hoofnagle AN.
Clin Chem. 2018 Feb; 2(64)408-410
DnaJ Homolog Subfamily B Member 9 Is a Putative Autoantigen in Fibrillary GN.
Andeen NK, Yang HY, Dai DF, MacCoss MJ, Smith KD.
J Am Soc Nephrol. 2018 Jan; 1(29)231-239
Basisty NB, Liu Y, Reynolds J, Karunadharma PP, Dai DF, Fredrickson J, Beyer RP, MacCoss MJ, Rabinovitch PS.
J Gerontol A Biol Sci Med Sci. 2018 Apr 17; 5(73)561-570
Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R.
Nat Methods. 2017 Sep; 9(14)921-927
DeBlasio SL, Bereman MS, Mahoney J, Thannhauser TW, Gray SM, MacCoss MJ, Cilia Heck M.
J Biomol Tech. 2017 Sep; 3(28)111-121
Ting YS, Egertson JD, Bollinger JG, Searle BC, Payne SH, Noble WS, MacCoss MJ.
Nat Methods. 2017 Sep; 9(14)903-908
A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brain.
Goulding SP, Szumlinski KK, Contet C, MacCoss MJ, Wu CC.
J Proteomics. 2017 Aug 23; (166)127-137
The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics.
Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ.
Mass Spectrom Rev. 2017 Jul 9;
Sakano H, Zorio DAR, Wang X, Ting YS, Noble WS, MacCoss MJ, Rubel EW, Wang Y.
J Comp Neurol. 2017 Oct 15; 15(525)3341-3359
Kruse A, Fattah-Hosseini S, Saha S, Johnson R, Warwick E, Sturgeon K, Mueller L, MacCoss MJ, Shatters RG Jr, Cilia Heck M.
PLoS One. 2017; 6(12)e0179531
Kubota A, Ito S, Shim JS, Johnson RS, Song YH, Breton G, Goralogia GS, Kwon MS, Laboy Cintrón D, Koyama T, Ohme-Takagi M, Pruneda-Paz JL, Kay SA, MacCoss MJ, Imaizumi T.
PLoS Genet. 2017 Jun; 6(13)e1006856
Zimmerman SG, Merrihew GE, MacCoss MJ, Berg CA.
Genetics. 2017 Jun; 2(206)973-984
Automated Trapping Column Exchanger for High-Throughput Nanoflow Liquid Chromatography.
Spencer SE, Corso TN, Bollinger JG, Henderson CM, Hoofnagle AN, MacCoss MJ.
Anal Chem. 2017 Feb 21; 4(89)2383-2389
The Ndc80 complex bridges two Dam1 complex rings.
Kim JO, Zelter A, Umbreit NT, Bollozos A, Riffle M, Johnson R, MacCoss MJ, Asbury CL, Davis TN.
Elife. 2017 Feb 13; (6)
Henderson CM, Bollinger JG, Becker JO, Wallace JM, Laha TJ, MacCoss MJ, Hoofnagle AN.
Proteomics Clin Appl. 2017 Jul; 7-8(11)
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.
Elife. 2016 Nov 2; (5)
Model System-Guided Protein Interaction Mapping for Virus Isolated from Phloem Tissue.
DeBlasio SL, Johnson RS, MacCoss MJ, Gray SM, Cilia M.
J Proteome Res. 2016 Dec 2; 12(15)4601-4611
Bereman MS, Beri J, Sharma V, Nathe C, Eckels J, MacLean B, MacCoss MJ.
J Proteome Res. 2016 Dec 2; 12(15)4763-4769
The M, MacCoss MJ, Noble WS, Käll L.
J Am Soc Mass Spectrom. 2016 Nov; 11(27)1719-1727
Armbruster CR, Wolter DJ, Mishra M, Hayden HS, Radey MC, Merrihew G, MacCoss MJ, Burns J, Wozniak DJ, Parsek MR, Hoffman LR.
MBio. 2016 May 24; 3(7)
The EARP Complex and Its Interactor EIPR-1 Are Required for Cargo Sorting to Dense-Core Vesicles.
Topalidou I, Cattin-Ortolá J, Pappas AL, Cooper K, Merrihew GE, MacCoss MJ, Ailion M.
PLoS Genet. 2016 May; 5(12)e1006074
Basisty N, Dai DF, Gagnidze A, Gitari L, Fredrickson J, Maina Y, Beyer RP, Emond MJ, Hsieh EJ, MacCoss MJ, Martin GM, Rabinovitch PS.
Aging Cell. 2016 Aug; 4(15)634-45
Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A.
J Struct Biol. 2016 Jun; 3(194)303-10
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.
Methods Mol Biol. 2016; (1410)223-36
Bollinger JG, Stergachis AB, Johnson RS, Egertson JD, MacCoss MJ.
Methods Mol Biol. 2016; (1410)207-21
Ramsey JS, Johnson RS, Hoki JS, Kruse A, Mahoney J, Hilf ME, Hunter WB, Hall DG, Schroeder FC, MacCoss MJ, Cilia M.
PLoS One. 2015; 11(10)e0140826
Zelter A, Bonomi M, Kim Jo, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN.
Nat Commun. 2015 Nov 12; (6)8673
Kawahara R, Bollinger JG, Rivera C, Ribeiro AC, Brandão TB, Paes Leme AF, MacCoss MJ.
Proteomics. 2016 Jan; 1(16)159-73
Age modifies respiratory complex I and protein homeostasis in a muscle type-specific manner.
Kruse SE, Karunadharma PP, Basisty N, Johnson R, Beyer RP, MacCoss MJ, Rabinovitch PS, Marcinek DJ.
Aging Cell. 2016 Feb; 1(15)89-99
Kudalkar EM, Scarborough EA, Umbreit NT, Zelter A, Gestaut DR, Riffle M, Johnson RS, MacCoss MJ, Asbury CL, Davis TN.
Proc Natl Acad Sci U S A. 2015 Oct 13; 41(112)E5583-9
Schilling B, MacLean B, Held JM, Sahu AK, Rardin MJ, Sorensen DJ, Peters T, Wolfe AJ, Hunter CL, MacCoss MJ, Gibson BW.
Anal Chem. 2015 Oct 20; 20(87)10222-9
Ting YS, Egertson JD, Payne SH, Kim S, MacLean B, Käll L, Aebersold R, Smith RD, Noble WS, MacCoss MJ.
Mol Cell Proteomics. 2015 Sep; 9(14)2301-7
Riffle M, Merrihew GE, Jaschob D, Sharma V, Davis TN, Noble WS, MacCoss MJ.
J Am Soc Mass Spectrom. 2015 Nov; 11(26)1827-36
A deeper look into Comet--implementation and features.
Eng JK, Hoopmann MR, Jahan TA, Egertson JD, Noble WS, MacCoss MJ.
J Am Soc Mass Spectrom. 2015 Nov; 11(26)1865-74
Searle BC, Egertson JD, Bollinger JG, Stergachis AB, MacCoss MJ.
Mol Cell Proteomics. 2015 Sep; 9(14)2331-40
Multiplexed peptide analysis using data-independent acquisition and Skyline.
Egertson JD, MacLean B, Johnson R, Xuan Y, MacCoss MJ.
Nat Protoc. 2015 Jun; 6(10)887-903
Rardin MJ, Schilling B, Cheng LY, MacLean BX, Sorensen DJ, Sahu AK, MacCoss MJ, Vitek O, Gibson BW.
Mol Cell Proteomics. 2015 Sep; 9(14)2405-19
Karunadharma PP, Basisty N, Chiao YA, Dai DF, Drake R, Levy N, Koh WJ, Emond MJ, Kruse S, Marcinek D, Maccoss MJ, Rabinovitch PS.
FASEB J. 2015 Aug; 8(29)3582-92
Kojak: efficient analysis of chemically cross-linked protein complexes.
Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL.
J Proteome Res. 2015 May 1; 5(14)2190-8
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.
Aging Cell. 2015 Aug; 4(14)547-57
DeBlasio SL, Johnson R, Sweeney MM, Karasev A, Gray SM, MacCoss MJ, Cilia M.
Proteomics. 2015 Jun; 12(15)2098-112
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.
Mol Cell Proteomics. 2015 Sep; 9(14)2357-74
DeBlasio SL, Johnson R, Mahoney J, Karasev A, Gray SM, MacCoss MJ, Cilia M.
Mol Plant Microbe Interact. 2015 Apr; 4(28)467-81
Song YH, Estrada DA, Johnson RS, Kim SK, Lee SY, MacCoss MJ, Imaizumi T.
Proc Natl Acad Sci U S A. 2014 Dec 9; 49(111)17672-7
Marsillach J, Suzuki SM, Richter RJ, McDonald MG, Rademacher PM, MacCoss MJ, Hsieh EJ, Rettie AE, Furlong CE.
PLoS One. 2014; 10(9)e110054
Substrate trapping proteomics reveals targets of the βTrCP2/FBXW11 ubiquitin ligase.
Kim TY, Siesser PF, Rossman KL, Goldfarb D, Mackinnon K, Yan F, Yi X, MacCoss MJ, Moon RT, Der CJ, Major MB.
Mol Cell Biol. 2015 Jan; 1(35)167-81
Canterbury JD, Merrihew GE, MacCoss MJ, Goodlett DR, Shaffer SA.
J Am Soc Mass Spectrom. 2014 Dec; 12(25)2048-59
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.
Genetics. 2014 Dec; 4(198)1483-93
Crux: rapid open source protein tandem mass spectrometry analysis.
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.
J Proteome Res. 2014 Oct 3; 10(13)4488-91
Panorama: a targeted proteomics knowledge base.
Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B.
J Proteome Res. 2014 Sep 5; 9(13)4205-10
Hyaluronan enhances wound repair and increases collagen III in aged dermal wounds.
Damodarasamy M, Johnson RS, Bentov I, MacCoss MJ, Vernon RB, Reed MJ.
Wound Repair Regen. 2014 Jul-Aug; 4(22)521-6
Evidence for lysine acetylation in the coat protein of a polerovirus.
Cilia M, Johnson R, Sweeney M, DeBlasio SL, Bruce JE, MacCoss MJ, Gray SM.
J Gen Virol. 2014 Oct; Pt 10(95)2321-7
A framework for installable external tools in Skyline.
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.
Bioinformatics. 2014 Sep 1; 17(30)2521-3
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.
Aging Cell. 2014 Jun; 3(13)529-39
Pinheiro P, Bereman MS, Burd J, Pals M, Armstrong S, Howe KJ, Thannhauser TW, MacCoss MJ, Gray SM, Cilia M.
J Proteome Res. 2014 Apr 4; 4(13)2094-108
Implementation of statistical process control for proteomic experiments via LC MS/MS.
Bereman MS, Johnson R, Bollinger J, Boss Y, Shulman N, MacLean B, Hoofnagle AN, MacCoss MJ.
J Am Soc Mass Spectrom. 2014 Apr; 4(25)581-7
Aagaard JE, George RD, Fishman L, Maccoss MJ, Swanson WJ.
PLoS Genet. 2013; 12(9)e1003965
Accounting for population variation in targeted proteomics.
Fujimoto GM, Monroe ME, Rodriguez L, Wu C, MacLean B, Smith RD, MacCoss MJ, Payne SH.
J Proteome Res. 2014 Jan 3; 1(13)321-3
Tamborindeguy C, Bereman MS, DeBlasio S, Igwe D, Smith DM, White F, MacCoss MJ, Gray SM, Cilia M.
PLoS One. 2013; 8(8)e71620
Dai DF, Hsieh EJ, Chen T, Menendez LG, Basisty NB, Tsai L, Beyer RP, Crispin DA, Shulman NJ, Szeto HH, Tian R, MacCoss MJ, Rabinovitch PS.
Circ Heart Fail. 2013 Sep 1; 5(6)1067-76
Molecular mechanisms underlying genotype-dependent responses to dietary restriction.
Schleit J, Johnson SC, Bennett CF, Simko M, Trongtham N, Castanza A, Hsieh EJ, Moller RM, Wasko BM, Delaney JR, Sutphin GL, Carr D, Murakami CJ, Tocchi A, Xian B, Chen W, Yu T, Goswami S, Higgins S, Holmberg M, Jeong KS, Kim JR, Klum S, Liao E, Lin MS, Lo W, Miller H, Olsen B, Peng ZJ, Pollard T, Pradeep P, Pruett D, Rai D, Ros V, Singh M, Spector BL, Vander Wende H, An EH, Fletcher M, Jelic M, Rabinovitch PS, MacCoss MJ, Han JD, Kennedy BK, Kaeberlein M.
Aging Cell. 2013 Dec; 6(12)1050-61
Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer.
Conlon KP, Basrur V, Rolland D, Wolfe T, Nesvizhskii AI, MacCoss MJ, Lim MS, Elenitoba-Johnson KS.
Mol Cell Proteomics. 2013 Oct; 10(12)2714-23
Bateman NW, Goulding SP, Shulman NJ, Gadok AK, Szumlinski KK, MacCoss MJ, Wu CC.
Mol Cell Proteomics. 2014 Jan; 1(13)329-38
Multiplexed MS/MS for improved data-independent acquisition.
Egertson JD, Kuehn A, Merrihew GE, Bateman NW, MacLean BX, Ting YS, Canterbury JD, Marsh DM, Kellmann M, Zabrouskov V, Wu CC, MacCoss MJ.
Nat Methods. 2013 Aug; 8(10)744-6
Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast.
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.
Genome Res. 2013 Sep; 9(23)1496-504
Glukhova VA, Tomazela DM, Findlay GD, Monnat RJ Jr, MacCoss MJ.
J Proteome Res. 2013 Jul 5; 7(12)3246-54
Label-free differential analysis of murine postsynaptic densities.
Goulding SP, Maccoss MJ, Wu CC.
Methods Mol Biol. 2013; (1002)295-309
Palmer MR, McDowall MH, Stewart L, Ouaddi A, MacCoss MJ, Swanson WJ.
Mol Reprod Dev. 2013 Jun; 6(80)460-5
The PINK1-Parkin pathway promotes both mitophagy and selective respiratory chain turnover in vivo.
Vincow ES, Merrihew G, Thomas RE, Shulman NJ, Beyer RP, MacCoss MJ, Pallanck LJ.
Proc Natl Acad Sci U S A. 2013 Apr 16; 16(110)6400-5
Bereman MS, Hsieh EJ, Corso TN, Van Pelt CK, Maccoss MJ.
Mol Cell Proteomics. 2013 Jun; 6(12)1701-8
Hsieh EJ, Bereman MS, Durand S, Valaskovic GA, MacCoss MJ.
J Am Soc Mass Spectrom. 2013 Jan; 1(24)148-53
Estimating relative abundances of proteins from shotgun proteomics data.
McIlwain S, Mathews M, Bereman MS, Rubel EW, MacCoss MJ, Noble WS.
BMC Bioinformatics. 2012 Nov 19; (13)308
Proteomic analysis of adducted butyrylcholinesterase for biomonitoring organophosphorus exposures.
Marsillach J, Hsieh EJ, Richter RJ, MacCoss MJ, Furlong CE.
Chem Biol Interact. 2013 Mar 25; 1(203)85-90
Cilia M, Peter KA, Bereman MS, Howe K, Fish T, Smith D, Gildow F, MacCoss MJ, Thannhauser TW, Gray SM.
PLoS One. 2012; 10(7)e48177
Egertson JD, Eng JK, Bereman MS, Hsieh EJ, Merrihew GE, MacCoss MJ.
J Am Soc Mass Spectrom. 2012 Dec; 12(23)2075-82
An expansive human regulatory lexicon encoded in transcription factor footprints.
Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA.
Nature. 2012 Sep 6; 7414(489)83-90
Spivak M, Bereman MS, Maccoss MJ, Noble WS.
J Proteome Res. 2012 Sep 7; 9(11)4499-508
Hsieh EJ, Shulman NJ, Dai DF, Vincow ES, Karunadharma PP, Pallanck L, Rabinovitch PS, MacCoss MJ.
Mol Cell Proteomics. 2012 Nov; 11(11)1468-74
A mass spectrometry proteomics data management platform.
Sharma V, Eng JK, Maccoss MJ, Riffle M.
Mol Cell Proteomics. 2012 Sep; 9(11)824-31
Bereman MS, MacLean B, Tomazela DM, Liebler DC, MacCoss MJ.
Proteomics. 2012 Apr; 8(12)1134-41
Using iRT, a normalized retention time for more targeted measurement of peptides.
Escher C, Reiter L, MacLean B, Ossola R, Herzog F, Chilton J, MacCoss MJ, Rinner O.
Proteomics. 2012 Apr; 8(12)1111-21
Sherrod SD, Myers MV, Li M, Myers JS, Carpenter KL, Maclean B, Maccoss MJ, Liebler DC, Ham AJ.
J Proteome Res. 2012 Jun 1; 6(11)3467-79
Bereman MS, Tomazela DM, Heins HS, Simonato M, Cogo PE, Hamvas A, Patterson BW, Cole FS, MacCoss MJ.
Anal Bioanal Chem. 2012 Jun; 8(403)2397-402
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.
Mol Cell Proteomics. 2012 May; 5(11)202-14
Identification of peptide features in precursor spectra using Hardklör and Krönik.
Hoopmann MR, MacCoss MJ, Moritz RL.
Curr Protoc Bioinformatics. 2012 Mar; (Chapter 13)Unit13.18
Computational and statistical analysis of protein mass spectrometry data.
Noble WS, MacCoss MJ.
PLoS Comput Biol. 2012 Jan; 1(8)e1002296
Capillary electrophoresis with Orbitrap-Velos mass spectrometry detection.
Wojcik R, Li Y, Maccoss MJ, Dovichi NJ.
Talanta. 2012 Jan 15; (88)324-9
Bereman MS, Canterbury JD, Egertson JD, Horner J, Remes PM, Schwartz J, Zabrouskov V, MacCoss MJ.
Anal Chem. 2012 Feb 7; 3(84)1533-9
Rapid empirical discovery of optimal peptides for targeted proteomics.
Stergachis AB, MacLean B, Lee K, Stamatoyannopoulos JA, MacCoss MJ.
Nat Methods. 2011 Nov 6; 12(8)1041-3
Direct maximization of protein identifications from tandem mass spectra.
Spivak M, Weston J, Tomazela D, MacCoss MJ, Noble WS.
Mol Cell Proteomics. 2012 Feb; 2(11)M111.012161
Pierce SB, Spurrell CH, Mandell JB, Lee MK, Zeligson S, Bereman MS, Stray SM, Fokstuen S, MacCoss MJ, Levy-Lahad E, King MC, Motulsky AG.
Proc Natl Acad Sci U S A. 2011 Nov 8; 45(108)18313-7
Dai DF, Hsieh EJ, Liu Y, Chen T, Beyer RP, Chin MT, MacCoss MJ, Rabinovitch PS.
Cardiovasc Res. 2012 Jan 1; 1(93)79-88
Biomarkers of organophosphorus (OP) exposures in humans.
Marsillach J, Richter RJ, Kim JH, Stevens RC, MacCoss MJ, Tomazela D, Suzuki SM, Schopfer LM, Lockridge O, Furlong CE.
Neurotoxicology. 2011 Oct; 5(32)656-60
Wooden JM, Finney GL, Rynes E, Maccoss MJ, Lambert AJ, Robledo RF, Peters LL, Gilligan DM.
Br J Haematol. 2011 Aug; 4(154)492-501
Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling.
Dean MD, Findlay GD, Hoopmann MR, Wu CC, MacCoss MJ, Swanson WJ, Nachman MW.
BMC Genomics. 2011 Jun 10; (12)306
Comparison between procedures using SDS for shotgun proteomic analyses of complex samples.
Bereman MS, Egertson JD, MacCoss MJ.
Proteomics. 2011 Jul; 14(11)2931-5
Gilligan DM, Finney GL, Rynes E, Maccoss MJ, Lambert AJ, Peters LL, Robledo RF, Wooden JM.
Blood Cells Mol Dis. 2011 Aug 15; 2(47)85-94
ABRF-PRG07: advanced quantitative proteomics study.
Falick AM, Lane WS, Lilley KS, MacCoss MJ, Phinney BS, Sherman NE, Weintraub ST, Witkowska HE, Yates NA.
J Biomol Tech. 2011 Apr; 1(22)21-6
Friedman DB, Andacht TM, Bunger MK, Chien AS, Hawke DH, Krijgsveld J, Lane WS, Lilley KS, MacCoss MJ, Moritz RL, Settlage RE, Sherman NE, Weintraub ST, Witkowska HE, Yates NA, Turck CW.
Proteomics. 2011 Apr; 8(11)1371-81
Maclean B, Tomazela DM, Abbatiello SE, Zhang S, Whiteaker JR, Paulovich AG, Carr SA, Maccoss MJ.
Anal Chem. 2010 Dec 15; 24(82)10116-24
Ranjitkar P, Press MO, Yi X, Baker R, MacCoss MJ, Biggins S.
Mol Cell. 2010 Nov 12; 3(40)455-64
Precursor charge state prediction for electron transfer dissociation tandem mass spectra.
Sharma V, Eng JK, Feldman S, von Haller PD, MacCoss MJ, Noble WS.
J Proteome Res. 2010 Oct 1; 10(9)5438-44
Serang O, MacCoss MJ, Noble WS.
J Proteome Res. 2010 Oct 1; 10(9)5346-57
Kelley JL, Aagaard JE, MacCoss MJ, Swanson WJ.
J Mol Evol. 2010 Aug; 2(71)111-8
Rosenfeld RJ, Bonaventura J, Szymczyna BR, MacCoss MJ, Arvai AS, Yates JR 3rd, Tainer JA, Getzoff ED.
J Biol Chem. 2010 Oct 8; 41(285)31581-9
Chakrabarti L, Zahra R, Jackson SM, Kazemi-Esfarjani P, Sopher BL, Mason AG, Toneff T, Ryu S, Shaffer S, Kansy JW, Eng J, Merrihew G, MacCoss MJ, Murphy A, Goodlett DR, Hook V, Bennett CL, Pallanck LJ, La Spada AR.
Neuron. 2010 Jun 24; 6(66)835-47
Cooper SJ, Finney GL, Brown SL, Nelson SK, Hesselberth J, MacCoss MJ, Fields S.
Genome Res. 2010 Sep; 9(20)1288-96
Zelter A, Hoopmann MR, Vernon R, Baker D, MacCoss MJ, Davis TN.
J Proteome Res. 2010 Jul 2; 7(9)3583-9
A high voltage asymmetric waveform generator for FAIMS.
Canterbury JD, Gladden J, Buck L, Olund R, MacCoss MJ.
J Am Soc Mass Spectrom. 2010 Jul; 7(21)1118-21
Identification and characterization of biomarkers of organophosphorus exposures in humans.
Kim JH, Stevens RC, MacCoss MJ, Goodlett DR, Scherl A, Richter RJ, Suzuki SM, Furlong CE.
Adv Exp Med Biol. 2010; (660)61-71
Tomazela DM, Patterson BW, Hanson E, Spence KL, Kanion TB, Salinger DH, Vicini P, Barret H, Heins HB, Cole FS, Hamvas A, MacCoss MJ.
Anal Chem. 2010 Mar 15; 6(82)2561-7
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.
MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ.
Bioinformatics. 2010 Apr 1; 7(26)966-8
Bern M, Finney G, Hoopmann MR, Merrihew G, Toth MJ, MacCoss MJ.
Anal Chem. 2010 Feb 1; 3(82)833-41
Comparison of database search strategies for high precursor mass accuracy MS/MS data.
Hsieh EJ, Hoopmann MR, MacLean B, MacCoss MJ.
J Proteome Res. 2010 Feb 5; 2(9)1138-43
Aagaard JE, Vacquier VD, MacCoss MJ, Swanson WJ.
Mol Biol Evol. 2010 Jan; 1(27)193-203
Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures.
Second TP, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ, Swaney DL, Russell JD, Coon JJ, Zabrouskov V.
Anal Chem. 2009 Sep 15; 18(81)7757-65
Patiño S, Aagaard JE, MacCoss MJ, Swanson WJ, Hart MW.
Evol Dev. 2009 Jul-Aug; 4(11)376-81
Overexpression of catalase targeted to mitochondria attenuates murine cardiac aging.
Dai DF, Santana LF, Vermulst M, Tomazela DM, Emond MJ, MacCoss MJ, Gollahon K, Martin GM, Loeb LA, Ladiges WC, Rabinovitch PS.
Circulation. 2009 Jun 2; 21(119)2789-97
Dean MD, Clark NL, Findlay GD, Karn RC, Yi X, Swanson WJ, MacCoss MJ, Nachman MW.
Mol Biol Evol. 2009 Aug; 8(26)1733-43
Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila.
Findlay GD, MacCoss MJ, Swanson WJ.
Genome Res. 2009 May; 5(19)886-96
Prakash A, Tomazela DM, Frewen B, Maclean B, Merrihew G, Peterman S, Maccoss MJ.
J Proteome Res. 2009 Jun; 6(8)2733-9
Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures.
Hoopmann MR, Merrihew GE, von Haller PD, MacCoss MJ.
J Proteome Res. 2009 Apr; 4(8)1870-5
High quality catalog of proteotypic peptides from human heart.
Kline KG, Frewen B, Bristow MR, Maccoss MJ, Wu CC.
J Proteome Res. 2008 Nov; 11(7)5055-61
A fast SEQUEST cross correlation algorithm.
Eng JK, Fischer B, Grossmann J, Maccoss MJ.
J Proteome Res. 2008 Oct; 10(7)4598-602
Canterbury JD, Yi X, Hoopmann MR, MacCoss MJ.
Anal Chem. 2008 Sep 15; 18(80)6888-97
Proteomics reveals novel Drosophila seminal fluid proteins transferred at mating.
Findlay GD, Yi X, Maccoss MJ, Swanson WJ.
PLoS Biol. 2008 Jul 29; 7(6)e178
Merrihew GE, Davis C, Ewing B, Williams G, Käll L, Frewen BE, Noble WS, Green P, Thomas JH, MacCoss MJ.
Genome Res. 2008 Oct; 10(18)1660-9
Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification.
Klammer AA, Reynolds SM, Bilmes JA, MacCoss MJ, Noble WS.
Bioinformatics. 2008 Jul 1; 13(24)i348-56
Rapid and accurate peptide identification from tandem mass spectra.
Park CY, Klammer AA, Käll L, MacCoss MJ, Noble WS.
J Proteome Res. 2008 Jul; 7(7)3022-7
Using BiblioSpec for creating and searching tandem MS peptide libraries.
Frewen B, MacCoss MJ.
Curr Protoc Bioinformatics. 2007 Dec; (Chapter 13)Unit 13.7
Finney GL, Blackler AR, Hoopmann MR, Canterbury JD, Wu CC, MacCoss MJ.
Anal Chem. 2008 Feb 15; 4(80)961-71
Proteomic solutions for analytical challenges associated with alcohol research.
MacCoss MJ, Wu CC.
Alcohol Res Health. 2008; 3(31)251-5
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases.
Käll L, Storey JD, MacCoss MJ, Noble WS.
J Proteome Res. 2008 Jan; 1(7)29-34
Posterior error probabilities and false discovery rates: two sides of the same coin.
Käll L, Storey JD, MacCoss MJ, Noble WS.
J Proteome Res. 2008 Jan; 1(7)40-4
Semi-supervised learning for peptide identification from shotgun proteomics datasets.
Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ.
Nat Methods. 2007 Nov; 11(4)923-5
Mayor T, Graumann J, Bryan J, MacCoss MJ, Deshaies RJ.
Mol Cell Proteomics. 2007 Nov; 11(6)1885-95
Duplication and selection on abalone sperm lysin in an allopatric population.
Clark NL, Findlay GD, Yi X, MacCoss MJ, Swanson WJ.
Mol Biol Evol. 2007 Sep; 9(24)2081-90
Klammer AA, Yi X, MacCoss MJ, Noble WS.
Anal Chem. 2007 Aug 15; 16(79)6111-8
Hoopmann MR, Finney GL, MacCoss MJ.
Anal Chem. 2007 Aug 1; 15(79)5620-32
Wilms tumor suppressor WTX negatively regulates WNT/beta-catenin signaling.
Major MB, Camp ND, Berndt JD, Yi X, Goldenberg SJ, Hubbert C, Biechele TL, Gingras AC, Zheng N, Maccoss MJ, Angers S, Moon RT.
Science. 2007 May 18; 5827(316)1043-6
Quantitative proteomic analysis of mammalian organisms using metabolically labeled tissues.
Wu CC, MacCoss MJ.
Methods Mol Biol. 2007; (359)191-201
Computational analysis of quantitative proteomics data using stable isotope labeling.
MacCoss MJ, Wu CC.
Methods Mol Biol. 2007; (359)177-89
Estrogen receptor alpha is a putative substrate for the BRCA1 ubiquitin ligase.
Eakin CM, Maccoss MJ, Finney GL, Klevit RE.
Proc Natl Acad Sci U S A. 2007 Apr 3; 14(104)5794-9
A major deletion in the surfactant protein-B gene causing lethal respiratory distress.
Wegner DJ, Hertzberg T, Heins HB, Elmberger G, MacCoss MJ, Carlson CS, Nogee LM, Cole FS, Hamvas A.
Acta Paediatr. 2007 Apr; 4(96)516-20
Aagaard JE, Yi X, MacCoss MJ, Swanson WJ.
Proc Natl Acad Sci U S A. 2006 Nov 14; 46(103)17302-7
Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery.
Angers S, Li T, Yi X, MacCoss MJ, Moon RT, Zheng N.
Nature. 2006 Oct 5; 7111(443)590-3
Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries.
Frewen BE, Merrihew GE, Wu CC, Noble WS, MacCoss MJ.
Anal Chem. 2006 Aug 15; 16(78)5678-84
Angers S, Thorpe CJ, Biechele TL, Goldenberg SJ, Zheng N, MacCoss MJ, Moon RT.
Nat Cell Biol. 2006 Apr; 4(8)348-57
Effects of modified digestion schemes on the identification of proteins from complex mixtures.
Klammer AA, MacCoss MJ.
J Proteome Res. 2006 Mar; 3(5)695-700
Quantitative comparison of proteomic data quality between a 2D and 3D quadrupole ion trap.
Blackler AR, Klammer AA, MacCoss MJ, Wu CC.
Anal Chem. 2006 Feb 15; 4(78)1337-44
Peptide charge state determination for low-resolution tandem mass spectra.
Klammer AA, Wu CC, MacCoss MJ, Noble WS.
Proc IEEE Comput Syst Bioinform Conf. 2005; 175-85
MacCoss MJ, Wu CC, Matthews DE, Yates JR 3rd.
Anal Chem. 2005 Dec 1; 23(77)7646-53
Quantitative MS for proteomics: teaching a new dog old tricks.
MacCoss MJ, Matthews DE.
Anal Chem. 2005 Aug 1; 15(77)294A-302A
Aminoglycoside antibiotics induce bacterial biofilm formation.
Hoffman LR, D'Argenio DA, MacCoss MJ, Zhang Z, Jones RA, Miller SI.
Nature. 2005 Aug 25; 7054(436)1171-5
Computational analysis of shotgun proteomics data.
MacCoss MJ
Curr Opin Chem Biol. 2005 Feb; 1(9)88-94
Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis.
Wu CC, MacCoss MJ, Howell KE, Matthews DE, Yates JR 3rd.
Anal Chem. 2004 Sep 1; 17(76)4951-9
McDonald WH, Tabb DL, Sadygov RG, MacCoss MJ, Venable J, Graumann J, Johnson JR, Cociorva D, Yates JR 3rd.
Rapid Commun Mass Spectrom. 2004; 18(18)2162-8
Anderson LB, Ouellette AJ, Eaton-Rye J, Maderia M, MacCoss MJ, Yates JR 3rd, Barry BA.
J Am Chem Soc. 2004 Jul 14; 27(126)8399-405
Organellar proteomics reveals Golgi arginine dimethylation.
Wu CC, MacCoss MJ, Mardones G, Finnigan C, Mogelsvang S, Yates JR 3rd, Howell KE.
Mol Biol Cell. 2004 Jun; 6(15)2907-19
A correlation algorithm for the automated quantitative analysis of shotgun proteomics data.
MacCoss MJ, Wu CC, Liu H, Sadygov R, Yates JR 3rd.
Anal Chem. 2003 Dec 15; 24(75)6912-21
Tabb DL, MacCoss MJ, Wu CC, Anderson SD, Yates JR 3rd.
Anal Chem. 2003 May 15; 10(75)2470-7
A method for the comprehensive proteomic analysis of membrane proteins.
Wu CC, MacCoss MJ, Howell KE, Yates JR 3rd.
Nat Biotechnol. 2003 May; 5(21)532-8
Code developments to improve the efficiency of automated MS/MS spectra interpretation.
Sadygov RG, Eng J, Durr E, Saraf A, McDonald H, MacCoss MJ, Yates JR 3rd.
J Proteome Res. 2002 May-Jun; 3(1)211-5
Probability-based validation of protein identifications using a modified SEQUEST algorithm.
MacCoss MJ, Wu CC, Yates JR 3rd.
Anal Chem. 2002 Nov 1; 21(74)5593-9
Posttranslational modifications in the CP43 subunit of photosystem II.
Anderson LB, Maderia M, Ouellette AJ, Putnam-Evans C, Higgins L, Krick T, MacCoss MJ, Lim H, Yates JR 3rd, Barry BA.
Proc Natl Acad Sci U S A. 2002 Nov 12; 23(99)14676-81
Shotgun proteomics: tools for the analysis of complex biological systems.
Wu CC, MacCoss MJ.
Curr Opin Mol Ther. 2002 Jun; 3(4)242-50
Shotgun identification of protein modifications from protein complexes and lens tissue.
MacCoss MJ, McDonald WH, Saraf A, Sadygov R, Clark JM, Tasto JJ, Gould KL, Wolters D, Washburn M, Weiss A, Clark JI, Yates JR 3rd.
Proc Natl Acad Sci U S A. 2002 Jun 11; 12(99)7900-5
Proteomics: analytical tools and techniques.
MacCoss MJ, Yates JR 3rd.
Curr Opin Clin Nutr Metab Care. 2001 Sep; 5(4)369-75
MacCoss MJ, Toth MJ, Matthews DE.
Anal Chem. 2001 Jul 1; 13(73)2976-84
Recovery of (13)CO(2) from infused [1-(13)C]leucine and [1,2-(13)C(2)]leucine in healthy humans.
Toth MJ, MacCoss MJ, Poehlman ET, Matthews DE.
Am J Physiol Endocrinol Metab. 2001 Aug; 2(281)E233-41
Measurement of intracellular sulfur amino acid metabolism in humans.
MacCoss MJ, Fukagawa NK, Matthews DE.
Am J Physiol Endocrinol Metab. 2001 Jun; 6(280)E947-55
Toth MJ, Poehlman ET, Matthews DE, Tchernof A, MacCoss MJ.
Am J Physiol Endocrinol Metab. 2001 Mar; 3(280)E496-501
Measurement of homocysteine concentrations and stable isotope tracer enrichments in human plasma.
MacCoss MJ, Fukagawa NK, Matthews DE.
Anal Chem. 1999 Oct 15; 20(71)4527-33
Direct database searching with MALDI-PSD spectra of peptides.
Griffin PR, MacCoss MJ, Eng JK, Blevins RA, Aaronson JS, Yates JR 3rd.
Rapid Commun Mass Spectrom. 1995; 15(9)1546-51
Research Summary
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) increasing the dynamic range of liquid chromatography-mass spectrometry for the analysis of peptides; and 3) developing computational tools for the automated conversion of mass spectrometry data into biologically meaningful results.