MetaLab 2.0 Enables Accurate Post-Translational Modifications Profiling in Metaproteomics

Studying
the structure and function of microbiomes is an emerging
research field. Metaproteomic approaches focusing on the characterization
of expressed proteins and post-translational modifications (PTMs)
provide a deeper understanding of microbial communities. Previous
research has highlighted the value of examining microbiome-wide protein
expression in studying the roles of the microbiome in human diseases.
Nevertheless, the regulation of protein functions in complex microbiomes
remains underexplored. This is mainly due to the lack of efficient
bioinformatics tools to identify and quantify PTMs in the microbiome.
We have developed comprehensive software termed MetaLab for the data
analysis of metaproteomic data sets. Here, we build an open search
workflow within MetaLab for unbiased identification and quantification
of unmodified peptides as well as peptides with various PTMs from
microbiome samples. This bioinformatics platform provides information
about proteins, PTMs, taxa, functions, and pathways of microbial communities.
The performance of the workflow was evaluated using conventional proteomics,
metaproteomics from mouse and human gut microbiomes, and modification-specific
enriched data sets. Superior accuracy and sensitivity were obtained
simultaneously by using our method compared with the traditional closed
search strategy.