Computer program (SEQPEP) to aid in the interpretation of high-energy collision tandem mass spectra of peptides

An algorithm (SEQPEP) that aids in the interpretation of high-energy (greater than 1 kV) collision-induced dissociation mass spectra of peptide ions generated by fast atom bombardment (FAB) ionization is described. The only required input is a list of product ion masses and relative abundances generated by the mass spectrometer data system, the mass of the precursor [M + H]+ ion, and the mass of any C-terminal modification, if present (e.g., amide). Possible N-terminal modifications and amino acid compositions are not required as input. In the output, sequences are ranked according to the fraction of total product ion current that can be accounted for as either sequence-specific or non-sequence-specific fragment ions. These are listed by ion type. One of the major advantages of this program over algorithms described earlier is the incorporation of ion types more recently discovered. Also, this program is much faster, requiring less than 5 min of central processing unit time for an input of as many as 100 product ions. The results obtained from 50 peptides, including some generated when sequencing a protein of previously unknown structure, are discussed.