Target Deconvolution by Limited Proteolysis Coupled to Mass Spectrometry.

Viviane Reber, Matthias Gstaiger

Methods in molecular biology (Clifton, N.J.) 2023

filter terms:

Limited proteolysis coupled to mass spectrometry (LiP-MS) is a recent proteomics technique that allows structure-based target engagement profiling on a proteome-wide level. To achieve this, native lysates are first incubated with a compound, followed by a short incubation with a nonspecific protease. Binding of a compound can change accessibility at the binding site or induce other structural changes in the target. This leads to treatment-specific proteolytic fingerprints upon limited proteolysis, which can be analyzed by standard bottom-up MS-based proteomics. Here, we describe a basic LiP-MS protocol using the natural product rapamycin as an example compound. Along with the provided LiP-MS reference data available via ProteomeXchange with identifier PXD035183, this enables the straightforward implementation of the method by scientists with a basic biochemistry and mass spectrometry background. We describe how the procedure can easily be adapted to other protein samples and small molecules. © 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Citation

Viviane Reber, Matthias Gstaiger. Target Deconvolution by Limited Proteolysis Coupled to Mass Spectrometry. Methods in molecular biology (Clifton, N.J.). 2023;2706:177-190