title: Digestion and depletion of abundant proteins improves proteomic coverage.
abstract: Two major challenges in proteomics are the large number of proteins and their broad dynamic range in the cell. We exploited the abundance-dependent Michaelis-Menten kinetics of trypsin digestion to selectively digest and deplete abundant proteins with a method we call DigDeAPr. We validated the depletion mechanism with known yeast protein abundances, and we observed greater than threefold improvement in low-abundance human-protein identification and quantitation metrics. This methodology should be broadly applicable to many organisms, proteases and proteomic pipelines.
authors.affiliation: Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA.
authors.forename: Bryan R
authors.initials: BR
authors.lastname: Fonslow
authors.forename: Benjamin D
authors.initials: BD
authors.lastname: Stein
authors.forename: Kristofor J
authors.initials: KJ
authors.lastname: Webb
authors.forename: Tao
authors.initials: T
authors.lastname: Xu
authors.forename: Jeong
authors.initials: J
authors.lastname: Choi
authors.forename: Sung Kyu
authors.initials: SK
authors.lastname: Park
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
mesh_terms: D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D010446:Peptide Fragments / Q000032:analysis*; D011506:Proteins / Q000378:metabolism*; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*
chemical_list: D010446:Peptide Fragments; D011506:Proteins; D020543:Proteome