DeNovoID is a program that has been specifically designed to use degenerate amino acid sequence and mass data derived from MS experiments to search a peptide database. Since the algorithm employed depends on the amino acid composition of the peptide and not its sequence, DeNovoID does not have to consider all possible sequences, but rather a smaller number of compositions consistent with a spectrum. DeNovoID also uses a geometric indexing scheme that reduces the number of calculations required to determine the best peptide match in the database. The user selects a database to search and inputs data for a series of peptides consisting of ordered sequence tags, non-ordered sequence tags, and mass tags in the following format:
 
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    ORDEREDSEQUENCE[NONORDREDSEQUENCE][200.4]
 
The DeNovoID program then searches the database for near and exact matches and emails the results to the user.