Pout2Prot: an efficient tool to create protein (sub)groups from Percolator output files

The protein inference problem is complicated in metaproteomics due to the presence of homologous proteins from closely related species. Nevertheless, this process is vital to assign taxonomy and functions to identified proteins of microbial species, a task for which specialized tools such as Prophane have been developed. We here present Pout2Prot, which takes Percolator Output (.pout) files from multiple experiments and creates protein (sub)group output files (.tsv) that can be used directly with Prophane. Pout2Prot offers different grouping strategies, allows distinction between sample categories and replicates for multiple files, and uses a weighted spectral count for protein (sub)groups to reflect (sub)group abundance. Pout2Prot is available as a web application at https://pout2prot.ugent.be and is installable via pip as a standalone command line tool and reusable software library. All code is open source under the Apache License 2.0 and is available at https://github.com/compomics/pout2prot. Logo O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY