msgf+ and fragmentation mode

[ypriverol]

Hi @alchemistmatt @FarmGeek4Life,

In quantms (see issue #532), we've encountered a challenge: if we don't explicitly filter by fragmentation mode (e.g., HCD or CID), we end up with TMT3 identifications based on MS3 spectra, which is not ideal. To address this, we considered passing the fragmentation mode (CID, HCD, etc.) directly to MS-GF+. However, many of the datasets we analyze contain thousands of files with mixed fragmentation modes, making it difficult to annotate everything correctly.

Interestingly, both Comet and SAGE offer the ability to filter spectra for identification based on MS level (e.g., MS2 only). This is quite helpful, as it selects the correct spectra regardless of fragmentation mode and also resolves the issue with TMT3 identifications.

Would you be open to adding support for filtering by MS level in MS-GF+?