We initially benchmarked the performance of IsoDec on a set of complex intact protein fragmentation spectra. These averaged spectra were selected because of their complexity and because they covered three different common mass analyzers (Orbitrap, FT-ICR, and ToF) and fragmentation types (UVPD, ETD, and ECD). Different instrument vendors, mass analyzers, and fragmentation strategies produce data with different characteristics, and it was important to ensure that model performance was consistent across different platforms.