If the PEPREC contains modifications that are not configured in the config file (or in the form on iomics.ugent.be/ms2pip), MS²PIP currently just skips those peptides. This can lead to a wall of warnings for a unknown modification and an output that only contains a fraction of the input peptides.
Should we check for unknown modifications and raise an exception before starting the predictions?
If the PEPREC contains modifications that are not configured in the config file (or in the form on iomics.ugent.be/ms2pip), MS²PIP currently just skips those peptides. This can lead to a wall of warnings for a unknown modification and an output that only contains a fraction of the input peptides.
Should we check for unknown modifications and raise an exception before starting the predictions?