ArticleCurrent bioinformatics2020
An Algorithm to Improve the Speed of Semi and Non-Specific Enzyme Searches in Proteomics.
Article in Current bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed.
- Enhanced Proteomic Data Analysis with MetaMorpheus.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A Hybrid Spectral Library and Protein Sequence Database Search Strategy for Bottom-Up and Top-Down Proteomic Data Analysis.Journal of proteome research · 2022Article
- Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus.Journal of proteome research · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundThe 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.
objectiveWe 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.
methodWe 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.
resultsThe 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.
conclusionWe 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.
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