Release v2.0.2 of the Unipept Desktop application provides support for using the new suffix array based backend of Unipept (see this post for more information on what changed internally).
This means that missed cleavage handling is always enabled (cannot be disabled anymore) and is much faster than before. Please note that the Windows version of Unipept will not automatically update to this release. It is recommended to download the installer here and install the newest version manually on Windows.