title: A quantitative proteomics design for systematic identification of protease cleavage events.
abstract: We present here a novel proteomics design for systematic identification of protease cleavage events by quantitative N-terminal proteomics, circumventing the need for time-consuming manual validation. We bypass the singleton detection problem of protease-generated neo-N-terminal peptides by introducing differential isotopic proteome labeling such that these substrate reporter peptides are readily distinguished from all other N-terminal peptides. Our approach was validated using the canonical human caspase-3 protease and further applied to mouse cathepsin D and E substrate processing in a mouse dendritic cell proteome, identifying the largest set of protein protease substrates ever reported and gaining novel insight into substrate specificity differences of these cathepsins.
authors.affiliation: Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium.
authors.forename: Francis
authors.initials: F
authors.lastname: Impens
authors.forename: Niklaas
authors.initials: N
authors.lastname: Colaert
authors.forename: Kenny
authors.initials: K
authors.lastname: Helsens
authors.forename: Bart
authors.initials: B
authors.lastname: Ghesquière
authors.forename: Evy
authors.initials: E
authors.lastname: Timmerman
authors.forename: Pieter-Jan
authors.initials: PJ
authors.lastname: De Bock
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Chain
authors.forename: Joël
authors.initials: J
authors.lastname: Vandekerckhove
authors.forename: Kris
authors.initials: K
authors.lastname: Gevaert
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D053148:Caspase 3 / Q000378:metabolism*; D002402:Cathepsin D / Q000378:metabolism; D020059:Cathepsin E / Q000378:metabolism; D006801:Humans; D006868:Hydrolysis; D051379:Mice; D008969:Molecular Sequence Data; D040901:Proteomics; D013379:Substrate Specificity
chemical_list: D053148:Caspase 3; D020059:Cathepsin E; D002402:Cathepsin D