Interestingly, NRPs can be characterized using the same experimental set-up, except that specific pre-enrichment should be carried out (e.g., for glycopeptides) . Once the peptides are characterized, the monitoring of lowly abundant entities or cheap routine analysis of protein marker panels with targeted proteomics through selected reaction monitoring (SRM) mode can be straightforwardly developed for hundreds of samples. Fully harnessing the cutting-edge metaproteomics technology represents a major breakthrough for microbiome functional analysis, marking a transformative step forward in microbiome research .