Proteomic and Functional Profiling of Trichoderma reesei , Pichia guilliermondii , and Hericium erinaceus

Abstract Fungi relevant to food systems and biotechnology differ in physiology, yet their condition-specific intracellular proteomes have rarely been compared using a common workflow. We hypothesized that harmonized extraction and data-independent acquisition mass spectrometry would reveal distinct functional signatures across Trichoderma reesei, Pichia guilliermondii, and Hericium erinaceus. Overall, 199, 889, and 1456 proteins were identified, respectively, revealing species-associated differences in protein biosynthesis, bioenergetics, redox metabolism, carbohydrate catabolism, proteostasis, and RNA-associated functions. Orthogroup and enzyme analyses identified conserved and species-specific functional features. Proteomes displayed hydrophilic and acidic profiles. Crude extracts exhibited concentration-dependent ACE inhibitory, ABTS radical scavenging, reduced glutathione, and l-glutaminase readouts. In silico screening identified 119, 1035, and 1431 sequence-derived candidate assignments, respectively, without establishing endogenous peptide occurrence or causal links to extract activities. These strain- and condition-specific intracellular proteomic data sets provide hypotheses for food and biotechnology studies but do not represent complete species proteomes, secretomes, or validated endogenous bioactive peptides.