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MassIVE search import does not correctly negate mass values for "loss" CV terms #13

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jjcarver opened this issue Dec 20, 2021 · 0 comments
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When importing an mzTab file to MassIVE search, the code currently parses modifications from each PSM row and uses them to build a "variant" or modified peptide string to write to the database. When doing so, it handles "neutral loss" CV terms (e.g. MS:1001524 - "fragment neutral loss") by simply parsing the numeric value of the CV tuple and adding it to the mass at the indicated peptide position.

However, this is semantically inappropriate for such CV terms, as their intention is obviously to encode a negative mass (hence "loss"). The negativity of the numeric CV value is implied even if not explicitly written. The code must be updated to always interpret these terms as negative mass offsets, whether the negative sign is explicitly written into the value or not.

@jjcarver jjcarver added the bug label Dec 20, 2021
@jjcarver jjcarver self-assigned this Dec 20, 2021
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