msgf+ needs the disassociation method/fragmentation methods

### Description of feature

SAGE and Comet use the MS level to target identifications, while MSGF+ uses fragmentation mode HCD, CID, etc. In the current version of the pipeline, if we put HCD in the SDRF and the file is CID, we will not identify any peptide. This is now making me go inside the MS/MS file and try to see which method is used at MS2. I think would be good to contact MSGF team and define the spectrum level that would be used for identification, similar to Comet and SAGE, rather than using the fragmentation mode.

Opinions @jpfeuffer @daichengxin @timosachsenberg

Start by tracing how the pipeline reads fragmentation methods from the SDRF and passes them to MSGF+, then compare that behavior with the Comet and SAGE handling described in the issue. Clarify with the MSGF team which spectrum level should control identification and define tests or example files that demonstrate correct behavior for HCD and CID.

Written by the indexing model from the issue text.