An example of uniquely phosphorylated peptide (A) and workflows for qualitative and quantitative data processing (B, C). The crosses mark the samples from which the corresponding peptides have been identified. The red peptides have a phosphoserine (bolded red S) that occurs only in the case sample: these peptides are deemed to be uniquely phosphorylated in the case sample. Note that the red peptides are considered as the same peptide in the report (counted as two) –despite having slightly different amino acid sequence lengths – because they have identical phosphosites. Their shared sequence is reported. The black peptides are not uniquely phosphorylated, because the same phosphosite (bolded black S) has been identified once in both the case and the control samples. Again, their shared sequence is reported. The single blue peptide is uniquely phosphorylated (bolded blue S) in the control sample.