Active peptides pursuit from complicated matrices via tracing ligand-protein complex with MS/MS: Chaperone screening for lysozyme as a pilot study

• A refined workflow was designed for high-throughput screening of active peptides in complicated matrices. • Confidence was enhanced by directly capturing peptide-protein complex in MS 1 , assisted by MS 2 . • Lysozyme (Lyz) and Bacillus licheniformis fermentation broth were utilized for utility illustration and justification. • Fifteen potential peptides were detected, of which bacitracins A and B3 (Bacs A and B3) were annotated. • The interactions between Lyz and Bac A dramatically advanced the antibacterial performance of Lyz.