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An Algorithm to Improve the Speed of Semi- and Non-Specific Enzyme Searches in Proteomics

Author(s):

Zach Rolfs, Robert J. Millikin and Lloyd M. Smith*   Pages 1 - 9 ( 9 )

Abstract:


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 speed.

Keywords:

Proteomics, Algorithm, Peptidomics, Non-specific, Nonspecific, No-enzyme, Semi-specific, Open-Source

Affiliation:

Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706



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