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compomics / psm_utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
https://psm-utils.readthedocs.io
Apache License 2.0
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X!Tandem score is hyperscore instead of e-value #55

Closed tivdnbos closed 10 months ago

tivdnbos commented 10 months ago

In X!Tandem, the scoring scheme is the hyperscore. In the XTandemReader, however, the e-value was assigned (score=-np.log(peptide_entry["expect"])). The hyperscore is currently listed in the metadata.

RalfG commented 10 months ago

Hi Tim! I guess it really depends on what you want to do with the PSMs downstream on whether you would use the e-value or a hyperscore. I added a new argument to the XTandemReader 'score_key` to give the user the option to choose. (#57)