Detergents and high concentrations of chaotropic agents, such as SDS, urea, and guanidine hydrochloride, are often used to denature protein samples before protease treatment. However, high concentrations of chaotropic agents and ionic detergents (such as SDS at > 0.1%) inhibit trypsin. Denatured samples need to be buffer-exchanged or dialyzed into a suitable trypsin reaction buffer before trypsin is added for digestion. Some non-ionic detergents, such as NP-40 and Triton, can be compatible with trypsin digestion at low levels but must be removed from the sample before mass spectrometry analysis.
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