Comparative analysis of high-throughput metaproteomics data in Unipept

Metaproteomics is the study of the proteins expressed by all organisms in complex environments or ecosystems such as the human gut or a water treatment plant. Based on protein fragments (peptides) found in the environment, we can infer which proteins these peptides originated from, which organisms created them, and which biological functions they perform. These analyses are done with specialised software tools such as Unipept. Unipept is developed by the Computational Biology Lab at Ghent University to derive the taxonomic and functional signature of samples from an analysis of metaproteomics data. Unipept is widely used in the field because of its performance, user-friendliness and interactive data visualisations. Recently, the field of metaproteomics has been moving towards bigger, high-throughput experiments. Unipept, as a web-based tool, is not an ideal fit to handle this data deluge. Its set of command line tools, on the other hand, are specifically created for high-throughput experiments, but they lack the user-friendliness and interactive visualisations of the web application. This research proposal aims to solve these shortcomings by creating a Unipept desktop application. This tool will allow researchers to manage, analyse, and compare huge datasets while maintaining complete control over their data. In addition, it will create the opportunity to use custom databases tailored to specific experiments.