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Does Trypsin Cut Before Proline?

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Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, Bioinformatics Program, University of California San Diego, La Jolla, California 92093, and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
* To whom correspondence should be addressed. E-mail: [email protected]
†Department of Computer Science and Engineering, University of California San Diego.
‡Bioinformatics Program, University of California San Diego.
§Pacific Northwest National Laboratory.
Cite this: J. Proteome Res. 2008, 7, 01, 300–305
Publication Date (Web):December 8, 2007
https://doi.org/10.1021/pr0705035
Copyright © 2008 American Chemical Society
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    Abstract

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    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.

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    Supplementary text provides an overview of the MS/MS data used and peptide identifications from this data set. This material is available free of charge via the Internet at http://pubs.acs.org.

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