As a tool, conventional mass spectrometry is a good method for differentiating between proteins with different masses. However, as different folded forms of a particular protein have identical masses, it is virtually impossible to differentiate them by conventional means. That's where the Waters Synapt HDMS system and its embedded ion mobility technology can help.
Even though different 3D structures have the same mass and mass-to-charge (m/z) ratio, the ion mobility capability of the Synapt system can separate them and identify how much of the protein is in its folded form versus the unfolded form. As the cross-sectional areas of the two protein conformers are different, the system allows users to distinguish between the various protein forms by separating them by shape.
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