You can use this script with the following example:
Rscript inst/scripts/prepare_annotations_spectra.R --fil-ann-raw-spe-spe data/interim/annotations/example_isdb.tsv.gz --fil-ann-pre-str data/interim/annotations/example_isdbPrepared.tsv.gz

Usage:
  prepare_annotations_spectra.R [--fil-ann-raw-spe=<fil-ann-raw-spe>] [--fil-ann-pre-str=<fil-ann-pre-str>]

Arguments:
  fil-ann-raw-spe-spe        List of spectral matching results. STRING
  fil-ann-pre-str            List of prepared structural annotations. STRING

Options:
  -h --help                  Shows this screen.
  -v --version               Shows version.