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Shotgun proteomics: tools for the analysis of complex biological systems.
Wu CC, MacCoss MJ. Wu CC, et al. Among authors: maccoss mj. Curr Opin Mol Ther. 2002 Jun;4(3):242-50. Curr Opin Mol Ther. 2002. PMID: 12139310 Review.
Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems.
Claw KG, George RD, MacCoss MJ, Swanson WJ. Claw KG, et al. Among authors: maccoss mj. BMC Genomics. 2018 Jun 22;19(1):488. doi: 10.1186/s12864-018-4872-x. BMC Genomics. 2018. PMID: 29929489 Free PMC article.
Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development.
Prakash A, Tomazela DM, Frewen B, Maclean B, Merrihew G, Peterman S, Maccoss MJ. Prakash A, et al. Among authors: maccoss mj. J Proteome Res. 2009 Jun;8(6):2733-9. doi: 10.1021/pr801028b. J Proteome Res. 2009. PMID: 19326923 Free PMC article.
Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures.
Hoopmann MR, Merrihew GE, von Haller PD, MacCoss MJ. Hoopmann MR, et al. Among authors: maccoss mj. J Proteome Res. 2009 Apr;8(4):1870-5. doi: 10.1021/pr800828p. J Proteome Res. 2009. PMID: 19256536 Free PMC article.
Identification of peptide features in precursor spectra using Hardklör and Krönik.
Hoopmann MR, MacCoss MJ, Moritz RL. Hoopmann MR, et al. Among authors: maccoss mj. Curr Protoc Bioinformatics. 2012 Mar;Chapter 13:Unit13.18. doi: 10.1002/0471250953.bi1318s37. Curr Protoc Bioinformatics. 2012. PMID: 22389013 Free PMC article.
High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry.
Hoopmann MR, Finney GL, MacCoss MJ. Hoopmann MR, et al. Among authors: maccoss mj. Anal Chem. 2007 Aug 1;79(15):5620-32. doi: 10.1021/ac0700833. Epub 2007 Jun 21. Anal Chem. 2007. PMID: 17580982 Free PMC article.
Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data.
Ting YS, Egertson JD, Payne SH, Kim S, MacLean B, Käll L, Aebersold R, Smith RD, Noble WS, MacCoss MJ. Ting YS, et al. Among authors: maccoss mj. Mol Cell Proteomics. 2015 Sep;14(9):2301-7. doi: 10.1074/mcp.O114.047035. Epub 2015 Jul 27. Mol Cell Proteomics. 2015. PMID: 26217018 Free PMC article.
Comparison of data acquisition strategies on quadrupole ion trap instrumentation for shotgun proteomics.
Canterbury JD, Merrihew GE, MacCoss MJ, Goodlett DR, Shaffer SA. Canterbury JD, et al. Among authors: maccoss mj. J Am Soc Mass Spectrom. 2014 Dec;25(12):2048-59. doi: 10.1007/s13361-014-0981-1. Epub 2014 Sep 27. J Am Soc Mass Spectrom. 2014. PMID: 25261218 Free PMC article.
Computational and statistical analysis of protein mass spectrometry data.
Noble WS, MacCoss MJ. Noble WS, et al. Among authors: maccoss mj. PLoS Comput Biol. 2012 Jan;8(1):e1002296. doi: 10.1371/journal.pcbi.1002296. Epub 2012 Jan 26. PLoS Comput Biol. 2012. PMID: 22291580 Free PMC article. Review.
Semi-supervised learning for peptide identification from shotgun proteomics datasets.
Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ. Käll L, et al. Among authors: maccoss mj. Nat Methods. 2007 Nov;4(11):923-5. doi: 10.1038/nmeth1113. Epub 2007 Oct 21. Nat Methods. 2007. PMID: 17952086
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