For PTM quantitation, the same parameters for peptide sequence coverage were applied. PTMs were identified automatically in BPF by their mass differences compared to unmodified peptides generated from pepsin digestion. Relative PTM abundance was expressed in BPF as a percentage of PTM presence on a peptide to all forms of said peptide present. Manual validation of peptides selected for relative PTM quantitation was performed in addition to automatic software assignment to ensure accurate quantitation.