FragPro is meant to assist in assigning observed fragments in mass spectra with those of a known isotopic sequence.
Although the program is expecting PIR format files, it's not too demanding about the exact format. You can create a PIR style file for you peptide if it's not listed in the PIR data base. The program ignores everything in the PIR file until it sees the characters "SEQUENCE". After this, everything it sees is considered part of the sequence using single letter amino acid abreviations. Invalid characters and letters not associated with amino acids are ignored.