Abstract: Computer-implemented methods and non-transitory computer readable storage media for isobaric amino acid differentiation, where an MS/MS data set may be processed, wherein the processing includes determining whether a protein sample comprises at least one isobaric amino acid, analyzing whether any diagnostic fragment ions of the at least one isobaric amino acid are present in the protein sample, assigning a score to the at least one isobaric amino acid based on the diagnostic fragment ions present in the MS/MS data set, evaluating the identity of the at least one isobaric amino acid present in the protein sample based on the assigned score, and reporting the evidence of the identity of the at least one isobaric amino acid present in the protein sample.