State-of-the-art quantification in proteomics is performed by extracting the precursor ion chromatogram of identified peptides. When using data independent acquisition (DIA) the profiles of the fragment ions can also be used to increase quantification confidence, or sometimes in alternative to the precursor ion signal. We recently demonstrated that in both phosphoproteomics (PubMedID: 27301801) and histone peptide analysis (PubMedID: 26505526) many modified peptides are erroneously quantified using both approaches, because they have isobaric forms that cannot be discriminated when co-eluting by liquid chromatography. These peptides have the same mass, but modifications on different residues. We thus developed templates that use DIA data and the Skyline (v3.6) output to assign the correct intensity on co-eluting isobaric modified peptides. These templates select unique fragment ions to determine the relative ratio of such peptides. This approach is imperative for samples where isobaric forms are common, i.e. histone peptides, for proper biological interpretation.