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ToolsSimopoulos, Caitlin M.A., Ning, Zhibin, Zhang, Xu, Li, Leyuan, Walker, Krystal, Lavallée-Adam, Mathieu and Figeys, Daniel (2020) pepFunk:A tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies. Bioinformatics, 36 (14). pp. 4171-4179. ISSN 1367-4803
Full text not available from this repository. (Request a copy)Abstract
Motivation: Enzymatic digestion of proteins before mass spectrometry analysis is a key process in metaproteomic workflows. Canonical metaproteomic data processing pipelines typically involve matching spectra produced by the mass spectrometer to a theoretical spectra database, followed by matching the identified peptides back to parent-proteins. However, the nature of enzymatic digestion produces peptides that can be found in multiple proteins due to conservation or chance, presenting difficulties with protein and functional assignment. Results: To combat this challenge, we developed pepFunk, a peptide-centric metaproteomic workflow focused on the analysis of human gut microbiome samples. Our workflow includes a curated peptide database annotated with Kyoto Encyclopedia of Genes and Genomes (KEGG) terms and a gene set variation analysis-inspired pathway enrichment adapted for peptide-level data. Analysis using our peptide-centric workflow is fast and highly correlated to a protein-centric analysis, and can identify more enriched KEGG pathways than analysis using protein-level data. Our workflow is open source and available as a web application or source code to be run locally.
| Item Type: | Article |
|---|---|
| Additional Information: | Publisher Copyright: © The Author(s) 2020. |
| Uncontrolled Keywords: | statistics and probability,biochemistry,molecular biology,computer science applications,computational theory and mathematics,computational mathematics ,/dk/atira/pure/subjectarea/asjc/2600/2613 |
| Faculty \ School: | Faculty of Medicine and Health Sciences > Norwich Medical School |
| UEA Research Groups: | Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 27 Mar 2026 12:30 |
| Last Modified: | 27 Mar 2026 12:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/102615 |
| DOI: | 10.1093/bioinformatics/btaa289 |
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