SIAM Journal on Computing
Dictionary matching and indexing with errors and don't cares
STOC '04 Proceedings of the thirty-sixth annual ACM symposium on Theory of computing
Finding patterns with variable length gaps or don’t cares
COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics
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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.