This PR adds back support for integrated MS1 & MS2 scoring (level=ms1ms2). This mode can be used instead of level=ms2 and will write the results to SCORE_MS2 to maintain compatibility with downstream filters.
Further changes include input file sanity checks and removal of duplicate main_var score, which is why the regression tests needed to be updated.
This PR adds back support for integrated MS1 & MS2 scoring (
level=ms1ms2). This mode can be used instead oflevel=ms2and will write the results toSCORE_MS2to maintain compatibility with downstream filters.Further changes include input file sanity checks and removal of duplicate
main_varscore, which is why the regression tests needed to be updated.