Does trypsin cut before proline?

TitleDoes trypsin cut before proline?
Publication TypeJournal Article
Year of Publication2008
AuthorsRodriguez J, Gupta N, Smith RD, Pevzner PA
JournalJ Proteome Res
Volume7
Issue1
Pagination300-5
Date Published2008 Jan
ISSN1535-3893
KeywordsBinding Sites, Proline, Substrate Specificity, Tandem Mass Spectrometry, Trypsin
Abstract

Trypsin is the most commonly used enzyme in mass spectrometry for protein digestion with high substrate specificity. Many peptide identification algorithms incorporate these specificity rules as filtering criteria. A generally accepted "Keil rule" is that trypsin cleaves next to arginine or lysine, but not before proline. Since this rule was derived two decades ago based on a small number of experimentally confirmed cleavages, we decided to re-examine it using 14.5 million tandem spectra (2 orders of magnitude increase in the number of observed tryptic cleavages). Our analysis revealed a surprisingly large number of cleavages before proline. We examine several hypotheses to explain these cleavages and argue that trypsin specificity rules used in peptide identification algorithms should be modified to "legitimatize" cleavages before proline. Our approach can be applied to analyze any protease, and we further argue that specificity rules for other enzymes should also be re-evaluated based on statistical evidence derived from large MS/MS data sets.

DOI10.1021/pr0705035
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/18067249?dopt=Abstract
Alternate TitleJ. Proteome Res.
PubMed ID18067249