Background: The identification of non-specifically cleaved peptides in proteomics and
peptidomics poses a significant computational challenge. Current strategies for the identification of such
peptides are typically time consuming and hinder routine data analysis.
Objective: We aimed to design an algorithm that would improve the speed of semi- and non-specific
enzyme searches and could be applicable to existing search programs.
Method: We developed a novel search algorithm that leverages fragment-ion redundancy to
simultaneously search multiple non-specifically cleaved peptides at once. Briefly, a theoretical peptide
tandem mass spectrum is generated using only the fragment-ion series from a single terminus. This
spectrum serves as a proxy for several shorter theoretical peptides sharing the same terminus. After
database searching, amino acids are removed from the opposing terminus until the observed and
theoretical precursor masses match within a given mass tolerance.
Results: The algorithm was implemented in the search program MetaMorpheus and found to perform
an order of magnitude faster than the traditional MetaMorpheus search and produce superior results.
Conclusion: We report a speedy non-specific enzyme search algorithm which is open-source and
enables search programs to utilize fragment-ion redundancy to achieve a notable increase in search