pepFunk, functional enrichment analysis of metaproteomic gut microbiome data

Abstract

Metaproteomics can be used to study the gut microbiome to better understand its composition and functional contributions to health. To acquire metaproteomic data, researchers typically perform enzymatic digestion of proteins into smaller and more easily detectable peptides. The peptides are processed by a mass spectrometer and the spectra acquired are matched to a peptide sequence database before identifying a potential parent protein. Enzymatic digestion, however, can produce peptides that are found in multiple proteins preventing unambiguous protein identification and challenges to functional analyses. To circumvent this challenge, we present pepFunk, a software tool for peptide-level functional analysis of metaproteomic data. pepFunk considers a custom gut microbiome peptide sequence database annotated with functional terms and a functional enrichment analysis adapted for peptide-level data. pepFunk is able to identify more functional changes than protein-level analyses for a more in-depth look at the biological processes taking place in microbiomes. Our tool is open source and is available as a Shiny web application at https://shiny.imetalab.ca/pepFunk

Caitlin Simopoulos

PhD, Sr. Computational Biologist

I use computational biology and machine learning to understand the world around me!