Meta-PepView: a metaproteomics performance evaluation and visualization platform

Abstract

Microbial community proteomics is rapidly gaining traction as it allows exploration of functional processes in microbial ecosystems. Consequently, there is a growing need for user-friendly tools that enable performance evaluation and interactive visualization of the increasingly complex community proteomics data. We introduce meta-PepView, a web-based platform that enables performance evaluation and interactive visualization of metaproteomics data, ensuring transparent and reproducible metaproteomics experiments. Meta-PepView integrates spectral sequencing outputs and databases from common proteomics search engines and classification tools. It runs efficiently on laptop or desktop PCs and can be deployed as a Docker container or installed with pip, from which it is operated through the web browser. Its modular design allows easy expansion with new data sources and annotation databases. Meta-PepView is an open-source Python platform that is freely available under the Apache License 2.0. The code is available on GitHub: https://github.com/ramonzwaan/metapepview/. Here, we showcase the meta-PepView platform with data from synthetic communities and previously published microbiome studies.