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levitsky / pyteomics

Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis.
http://pyteomics.readthedocs.io
Apache License 2.0
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Incorrect expasy rule #135

Closed Karl-Krauth closed 6 months ago

Karl-Krauth commented 6 months ago

This rule for thermolysin is incorrect: https://github.com/levitsky/pyteomics/blob/66dcd9d6d35e20c39e82c6c408e1b8ed05089ea6/pyteomics/parser.py#L844

it should be: r'[^DE](?=[AFILMV][^P])' If you check the summary of the cleavage rules here: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html the [^P] condition isn't included but it's included in the text above it and also seems to be implemented in their perl script.

I haven't checked other enzymes but there might be similar errors there too.

levitsky commented 6 months ago

Thank you for reporting. I made the change you proposed, seeing as the Proline effect is both mentioned in text and implemented in the tool itself.