|Title||»||File | Import | TransitionList... always gives charge state 1 if there is a peptide mass column to the left of the actual m/z column|
It naively stops at the first column of the first line whose value is a plausible m/z value - and the mass is plausible for z=1. We should keep looking for others that may yield a higher charge state.
Also note that even if we do this, if the first line happens to describe an actual z=1, we'll get the rest wrong. We should examine all lines.