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Elsevier, Molecular and Cellular Proteomics, 10(9), p. 2327-2333, 2010

DOI: 10.1074/mcp.m110.001271

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A Quantitative Proteomics Design for Systematic Identification of Protease Cleavage Events*

Journal article published in 2010 by Francis Impens ORCID, Niklaas Colaert, Kenny Helsens, Bart Ghesquière ORCID, Evy Timmerman, Pieter-Jan De Bock, Benjamin M. Chain, Joël Vandekerckhove, Kris Gevaert ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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.