Paired with MSFragger for identifying peptides with PTMs , it effectively identified rare modifications like the sulfur-to-selenium (S-Se) mass shift, crucial for detecting selenocysteine, a key adaptation mechanism to oxidative stress in microbial communities. By incorporating DIAMOND for peptide alignment and a reverse decoy strategy, the pipeline maintained a strict 5% FDR, improving identification confidence and greatly speeding up processing compared to BLAST+ .