Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis

Although metaproteomics, the study
of the collective proteome of
microbial communities, has become increasingly powerful and popular
over the past few years, the field has lagged behind on the availability
of user-friendly, end-to-end pipelines for data analysis. We therefore
describe the connection from two commonly used metaproteomics data
processing tools in the field, MetaProteomeAnalyzer and PeptideShaker,
to Unipept for downstream analysis. Through these connections, direct
end-to-end pipelines are built from database searching to taxonomic
and functional annotation.