modloss_importance in modification.tsv

[yangkl96]

Were the modloss_importance values derived from somewhere or just arbitrary? I noticed they were only set to non-zero values for phospho and glygly. Does this mean that unless manually changed in modification.tsv to be 1, b/y ions with modlosses will be ignored?

Thanks,
Kevin

[jalew188]

1. In AlphaPeptDeep, modloss_importance is controlled by modloss_importance_level in the settings: https://github.com/MannLabs/alphapeptdeep/blob/main/peptdeep/constants/default_settings.yaml#L41
2. The fragment masses and predicted intensities will be zero for all PTMs with modloss_importance < modloss_importance_level
3. To change the modloss_importance values, you can either modify the tsv or do it programmingly:

from alphabase.constants.modification import MOD_DF, update_all_by_MOD_DF, MOD_LOSS_IMPORTANCE

MOD_DF.loc['Oxidation@M','modloss_importance'] = 1000
update_all_by_MOD_DF()
print(MOD_LOSS_IMPORTANCE['Oxidation@M'])

[yangkl96]

Thanks for explaining!