Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics Analyses

Unipept Desktop 2.0 is the most recent iteration of theUnipeptDesktop tool that adds support for the analysis of metaproteogenomicsdatasets. Unipept Desktop now supports the automatic constructionof targeted protein reference databases that only contain proteins(originating from the UniProtKB resource) associated with a predeterminedlist of taxa. This improves both the taxonomic and functional resolutionof a metaproteomic analysis and yields several technical advantages.By limiting the proteins present in a reference database, it is alsopossible to perform (meta)proteogenomics analyses. Since the proteinreference database resides on the user's local machine, theyhave complete control over the database used during an analysis. Datano longer need to be transmitted over the Internet, decreasing thetime required for an analysis and better safeguarding privacy-sensitivedata. As a proof of concept, we present a case study in which a humangut metaproteome dataset is analyzed with Unipept Desktop 2.0 usingdifferent targeted databases based on matched 16S rRNA gene sequencingdata.