SEMQuant: Extending Sipros-Ensemble with Match-Between-Runs for Comprehensive Quantitative Metaproteomics.

Metaproteomics, utilizing high-throughput LC-MS, offers a profound understanding of microbial communities. Quantitative metaproteomics further enriches this understanding by measuring relative protein abundance and revealing dynamic changes under different conditions. However, the challenge of missing peptide quantification persists in metaproteomics analysis, particularly in data-dependent acquisition mode, where high-intensity precursors for MS2 scans are selected.