The protein inference problem arises because peptides can be shared among homologous proteins, making it ambiguous which protein generated a particular peptide spectrum match.
- ProteoAnalyst relies on protein-level grouping performed by upstream software (MaxQuant, DIA-NN, FragPipe, Spectronaut) which applies parsimony principles to assign peptides to protein groups.
- During data filtering, users can further filter proteins based on their confidence or probability scores provided by different tools