MINING GENOMES - CORRELATING TANDEM MASS-SPECTRA OF MODIFIED AND UNMODIFIED PEPTIDES TO SEQUENCES IN NUCLEOTIDE DATABASES

The correlation of uninterpreted tandem mass spectra of modified and u nmodified peptides, produced under low-energy (10-50 eV) collision con ditions, with nucleotide sequences is demonstrated. In this method nuc leotide databases are translated in six reading frames, and the result ing amino acid sequences are searched ''on the fly'' to identify and f it linear sequences to the fragmentation patterns observed in the tand em mass spectra of peptides. A cross-correlation function is then used to provide a measurement of similarity between the mass-to-charge rat ios for the fragment ions predicted by amino acid sequences translated from the nucleotide database and the fragment ions observed in the ta ndem mass spectrum. In general, a difference greater than 0.1 between the normalized cross-correlation functions for the first- and second-r anked search results indicates a successful match between sequence and spectrum. Measurements of the deviation from maximum similarity emplo ying the spectral reconstruction method are made. The search method em ploying nucleotide databases is also demonstrated on the spectra of ph osphorylated peptides. Specific sites of modification are identified e ven though no specific information relevant to sites of modification i s contained in the character-based sequence information of nucleotide databases.