Revisiting the effect of trypsin digestion buffers on artificial deamidation

Deamidation of asparagine and glutamine residues occurs spontaneously, accelerated by adjacent amino acid residues and influenced by pH, temperature, and incubation time. Standard proteolytic digestion induces significant deamidation, which is especially problematic in bottom-up proteomic studies. Trypsin digestion protocol modifications, including shorter incubation times and specific lysis buffers are shown to minimize deamidation. Herein, HEPES is proven to be most optimal due to reduced deamidation coupled with its compatibility for both proteins and trypsin digestion, highlighting its suitability for maintaining sample integrity in biological research contexts.