Fragment ion m/z values are then calculated based on the charge state of the precursor, where fragment ions with charge densities closest to the precursor ion are considered (default 3 fragment ion charge states). For EThcD spectra that also employ PTCR, these parameters were significantly increased (lower expected precursor charge state and up to 14 fragment ion charge states) to more accurately capture the charge-reduced ions in these spectra. Theoretical fragment ions are searched against peak centroids recorded within ".raw" spectrum files read into R via the rawrr package.