Abstract: A method for the selective fragmentation of peptides using free radical initiator-peptide conjugates is provided. Free radical initiated peptide sequencing, or FRIPS, consists of covalently attaching a free radical initiator to a peptide and collisionally activating this conjugate. This results in fragment formation. Subsequent collision-activated dissociation further dissociates the fragments, producing a group of ions based on the interaction of the free radical initiator and the target molecule. The methodology is applied to the fundamental study of biologically relevant reactions of free radicals with peptides and proteins in the gas phase, as well as to a completely gas-phase approach to protein sequencing.