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

Unipept Desktop 2.0 is the most recent iteration of the
Unipept
Desktop tool that adds support for the analysis of metaproteogenomics
datasets. Unipept Desktop now supports the automatic construction
of targeted protein reference databases that only contain proteins
(originating from the UniProtKB resource) associated with a predetermined
list of taxa. This improves both the taxonomic and functional resolution
of a metaproteomic analysis and yields several technical advantages.
By limiting the proteins present in a reference database, it is also
possible to perform (meta)proteogenomics analyses. Since the protein
reference database resides on the user’s local machine, they
have complete control over the database used during an analysis. Data
no longer need to be transmitted over the Internet, decreasing the
time required for an analysis and better safeguarding privacy-sensitive
data. As a proof of concept, we present a case study in which a human
gut metaproteome dataset is analyzed with Unipept Desktop 2.0 using
different targeted databases based on matched 16S rRNA gene sequencing
data.