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Current Bioinformatics

Editor-in-Chief

ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

General Research Article

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*

Volume 15 , Issue 9 , 2020

Page: [1065 - 1074] Pages: 10

DOI: 10.2174/1574893615999200429123334

Price: $65

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 nonspecific enzyme searches and could be applied to existing search programs.

Methods: 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 that 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.

Graphical Abstract

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