His work is focused on developing tools and in proteomics and he specializes in mass spectrometry. He is best known for the development of the SEQUEST algorithm for automated peptide sequencing[1][2] and Multidimensional Protein Identification Technology (MudPIT)[3] and data independent acquisition (DIA).[4] His laboratory has made important contributions to understanding the biochemical mechanisms behind the failure of DF508 cystic fibrosis ion transport regulator (CFTR) to mature.[5][6]
^Washburn, Michael P.; Wolters, Dirk; Yates, John R. (March 2001). "Large-scale analysis of the yeast proteome by multidimensional protein identification technology". Nature Biotechnology. 19 (3): 242–247. doi:10.1038/85686. ISSN1087-0156. PMID11231557. S2CID16796135.