Unipept in 2024: Expanding Metaproteomics Analysis with Support for Missed Cleavages and Semitryptic and Nontryptic Peptides

Unipept,
a pioneering software tool in metaproteomics, has significantly
advanced the analysis of complex ecosystems by facilitating both taxonomic
and functional insights from environmental samples. From the onset,
Unipept’s capabilities focused on tryptic peptides, utilizing
the predictability and consistency of trypsin digestion to efficiently
construct a protein reference database. However, the evolving landscape
of proteomics and emerging fields like immunopeptidomics necessitate
a more versatile approach that extends beyond the analysis of tryptic
peptides. In this article, we present a significant update to the
underlying index structure of Unipept, which is now powered by a Sparse
Suffix Array index. This advancement enables the analysis of semitryptic
peptides, peptides with missed cleavages, and nontryptic peptides
such as those encountered in other research fields such as immunopeptidomics
(e.g., MHC- and HLA-peptides). This new index benefits all tools in
the Unipept ecosystem such as the web application, desktop tool, application
programming interface (API), and command line interface. A benchmark
study highlights significantly improved performance in handling missed
cleavages, preserving the same level of accuracy.