This short note highlights a procedure to distinguish the residues having similar masses, oxidized methionine and phenylalanine containing peptides using MALDI TOF/TOF. The isotope intensities give a preliminary recognition of peptides containing oxidized methionine. In the peptides with partial oxidation of methionine a mass difference of 16 Da can be observed in the mass finger print of the peptide. Neutral loss of methane sulphenate (CH3 SOH) in the MS/MS spectra is the most abundant ion in the peptide containing oxidized methionine, whereas this fragment ion is not produced from phenylalanine containing peptide. The mass spectra of methionine, oxidized methionine and phenylalanine containing peptides were examined from the proteins of Pseudomonas syringae Lz4W, whose genome sequence is not known.
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