Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra*

Generating all plausible de novo interpretations of a peptide tandem mass (MS/MS) spectrum (Spectral Dictionary) and quickly matching them against the database represent a recently emerged alternative approach to peptide identification However, the sizes of the Spectral Dictionaries quickly grow with the peptide length making their generation impractical for long peptides We introduce Gapped Spectral Dictionaries (all plausible de novo interpretations with gaps) that can be easily generated for any peptide length thus addressing the shortcoming of the Spectral Dictionary approach We show that Gapped Spectral Dictionaries are small thus opening a possibility of using them to speed-up MS/MS database searches Our MS-GappedDictionary algorithm (based on Gapped Spectral Dictionaries) enables proteogenomics applications that are prohibitively time consuming with existing approaches We further introduce gapped tags that have advantages over the conventional peptide sequence tags in filtration-based MS/MS database searches.