Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome

Pascal Schlage, Fabian E. Egli, Paolo Nanni, Lauren W. Wang, Jayachandran N. Kizhakkedathu, Suneel S. Apte, Ulrich Auf Dem Keller*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Proteolysis is an irreversible post-translational modification that affects intra- and intercellular communication by modulating the activity of bioactive mediators. Key to understanding protease function is the system-wide identification of cleavage events and their dynamics in physiological contexts. Despite recent advances in mass spectrometry- based proteomics for high-throughput substrate screening, current approaches suffer from high false positive rates and only capture single states of protease activity. Here, we present a workflow based on multiplexed terminal amine isotopic labeling of substrates for timeresolved substrate degradomics in complex proteomes. This approach significantly enhances confidence in substrate identification and categorizes cleavage events by specificity and structural accessibility of the cleavage site. We demonstrate concomitant quantification of cleavage site spanning peptides and neo-N and/or neo-C termini to estimate relative ratios of noncleaved and cleaved forms of substrate proteins. By applying this strategy to dissect the matrix metalloproteinase 10 (MMP10) substrate degradome in fibroblast secretomes, we identified the extracellular matrix protein ADAMTS-like protein 1 (ADAMTSL1) as a direct MMP10 substrate and revealed MMP10-dependent ectodomain shedding of platelet-derived growth factor receptor alpha (PDGFR=) as well as sequential processing of type I collagen. The data have been deposited to the ProteomeXchange Consortium with identifier PXD000503.

Original languageEnglish
JournalMolecular and Cellular Proteomics
Volume13
Issue number2
Pages (from-to)580-593
ISSN1535-9476
DOIs
Publication statusPublished - 2014
Externally publishedYes

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