title: Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion.
abstract: Trypsin is the popular protease to digest proteins into peptides in shotgun proteomics, but few studies have attempted to systematically investigate the kinetics of trypsin-catalyzed protein digestion in proteome samples. In this study, we applied quantitative proteomics via triplex stable isotope dimethyl labeling to investigate the kinetics of trypsin-catalyzed cleavage. It was found that trypsin cleaves the C-terminal to lysine (K) and arginine (R) residues with higher rates for R. And the cleavage sites surrounded by neutral residues could be quickly cut, while those with neighboring charged residues (D/E/K/R) or proline residue (P) could be slowly cut. In a proteome sample, a huge number of proteins with different physical chemical properties coexists. If any type of protein could be preferably digested, then limited digestion could be applied to reduce the sample complexity. However, we found that protein abundance and other physicochemical properties, such as molecular weight (Mw), grand average of hydropathicity (GRAVY), aliphatic index, and isoelectric point (pI) have no notable correlation with digestion priority of proteins.
authors.affiliation: Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
authors.forename: Yanbo
authors.initials: Y
authors.lastname: Pan
authors.forename: Kai
authors.initials: K
authors.lastname: Cheng
authors.forename: Jiawei
authors.initials: J
authors.lastname: Mao
authors.forename: Fangjie
authors.initials: F
authors.lastname: Liu
authors.forename: Jing
authors.initials: J
authors.lastname: Liu
authors.forename: Mingliang
authors.initials: M
authors.lastname: Ye
authors.forename: Hanfa
authors.initials: H
authors.lastname: Zou
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D055162:Biocatalysis; D007700:Kinetics; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D008970:Molecular Weight; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D016415:Sequence Alignment; D014357:Trypsin / Q000737:chemistry*
chemical_list: D011506:Proteins; D014357:Trypsin