Biodiversity analysis of metaproteomics samples with Unipept: a comprehensive tutorial

TL;DR

This tutorial provides a comprehensive guide to using the Unipept ecosystem for analyzing metaproteomic data, covering key concepts, practical steps, and insights into microbiome biodiversity.

Contribution

It introduces detailed methodologies and practical workflows for leveraging Unipept in metaproteomics, enhancing microbiome research capabilities.

Findings

Guides on LCA determination and handling missed cleavages

Step-by-step instructions for Unipept Web and Desktop tools

Empowers researchers with practical knowledge for microbiome analysis

Abstract

Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as an invaluable resource for analyzing metaproteomic data. It offers in-depth insights into both taxonomic distributions and functional characteristics of complex ecosystems. This tutorial explains essential concepts like Lowest Common Ancestor (LCA) determination and the handling of peptides with missed cleavages. It also provides a detailed, step-by-step guide on using the Unipept Web application and Unipept Desktop for thorough metaproteomics analyses. By integrating theoretical principles with practical methodologies, this tutorial empowers researchers with the essential knowledge and tools needed to fully utilize metaproteomics in their microbiome studies.