UNKNOWN PEPTIDE SEQUENCING USING MATRIX-ASSISTED-LASER-DESORPTION IONIZATION AND IN-SOURCE DECAY/

The results of a study to determine the utility of in-source decay fra gmentation of matrix-assisted laser-desorbed ions for obtaining useful sequence information on unknown peptides are presented. Six peptides were purified by high-performance liquid chromatography and submitted as single blind unknowns. The in-source decay fragment ion data were c ollected on a linear time-of-flight mass spectrometer equipped with de layed extraction. These fragment ion data were manually interpreted on the basis of known fragmentation pathways to determine a proposed seq uence. The proposed sequences for three of the unknowns were essential ly correct, with a few minor errors. A fourth unknown had significant errors associated with its proposed sequence due to misinterpretation of the fragmentation data. Two unknowns were found to have undergone s ignificant sample degradation prior to naalysis, which compromised the results for these samples. An example of the use of protein database searching of a partial peptide sequence to aid in a sequence determina tion is also presented.