Skip to content

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

@jjcarver

Description

@jjcarver

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.

Metadata

Metadata

Assignees

Labels

Type

No type

Projects

No projects

Milestone

No milestone

Relationships

None yet

Development

No branches or pull requests

Issue actions