A program to aid the interpretation of the MS/MS spectra of peptides

The combination of Collision Activated Decomposition (CAD) and linked-scan measurement has demonstrated its utility for sequencing unknown and chemically modified peptides. Various computer algorithms has been described in order to aid the peptide sequencing but few of them behave well for peptides with molecular weight over 1 000. Our algorithm based on the graphos theory was modified on to obtain faster and reliable results of the "N" sequences with the best scores. To compare it we used a computer with lower performances than the previous papers. The program needed less than 1 minute to analyze very complicated spectrum it can also differentiate two isobaric amino acid such as Leu and Ile when the side chain fragmentation were observed in the spectrum.