OpenMS
FeatureFinderMetaboIdent: allow quantifying charge 0 seeds (single traces)?
In the MTBLS733 dataset where FFM can detect 784 features, FFMident only extracts 712 of them- many of the missing features were annotated with charge 0 from FFM and that charge is skipped by FFMident. FFM assigns zero charges when: "Mass traces that could not be assembled or low-intensity metabolites with only a monoisotopic mass trace to observe are left in the resulting @ref FeatureMap as singletons with the undefined charge state of 0."
In the case of the dataset above, this is causing a lot of zero charges and so missing values. Does it make more sense to assign the value 0 than to assign those features with the charge 1?
By default, FFM should also ignore charges below 1 (see param charge_lower_bound 1 Lowest charge state to consider in FFM but I can still see a huge chunk of the features assigned as 0 charged). Or does this mean that it simply doesn't search for isotopes/reduce information for those features?
