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arXiv · 2311.07494

Biodiversity analysis of metaproteomics samples with Unipept: a comprehensive tutorial

Tim Van Den Bossche·Pieter Verschaffelt·Tibo Vande Moortele·Peter Dawyndt·Lennart Martens·Bart Mesuere
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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.

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Tim Van Den Bossche, Pieter Verschaffelt, Tibo Vande Moortele, Peter Dawyndt, Lennart Martens, Bart Mesuere. 2023-11-13. Biodiversity analysis of metaproteomics samples with Unipept: a comprehensive tutorial. https://arxiv.org/abs/2311.07494

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