Fragment ions were identified using Proteo-SAFARI; a schematic workflow for fragment identification is shown in Figure . Theoretical fragment ions were generated based on a userprovided amino acid sequence. Any modification can be specified on the peptide backbone nitrogen, amino acid side chain, or backbone carbonyl based on its chemical formula or a predefined encoding listed in the 'Prerequisites and Helpers.R' file of the application. Based on the sequence and any modifications, the chemical formulas of theoretical fragment ions are calculated as cumulative sums of each element from the N-or C-terminus for a/b/c or x/y/z fragments, respectively. From these chemical formulas corresponding to all theoretical fragment ions, fine isotopic distributions are generated using the IsoSpecR package and collated by nominal mass.