An updated perspective on deconvoluting chimeric MS/MS spectra by LC and precursor isolation and their subsequent assignment by the CharmeRT mPSM search strategy

Considering the recent advances in LC and mPSM methodologies, we aimed to provide a systematic comparison and in-depth analysis of the effects that standard and specialized LC setups, as well as different isolation windows, have on the occurrence and assignment of chimeric spectra derived from a complex peptide mixture. To this end, we provide a comprehensive analysis of how these factors influence the chromatographic resolution, isolation interference, and the subsequent identification of MS/MS spectra by a traditional or mPSM algorithm.