3D Proteomics: Structural, Functional, Chemical and Biomarker Discovery Proteomics With LiP-MS.

Area of Science:

• Proteomics
• Structural Biology
• Biochemistry

Background:

• Protein structural dynamics are crucial for biological functions.
• Understanding these dynamics is essential for biological system interrogation.
• Limited proteolysis coupled to mass spectrometry (LiP-MS) is a key method for profiling protein structure.

Purpose of the Study:

• To review the applications and methodological variants of LiP-MS.
• To highlight LiP-MS's role in structural, functional, chemical, and biomarker discovery proteomics.
• To introduce the concept of 3D proteomics for comprehensive biological system analysis.

Main Methods:

• Limited proteolysis coupled to mass spectrometry (LiP-MS) was employed.
• The method profiles proteome-wide protein structural changes using protease cleavage susceptibility.
• Peptide-level resolution was achieved within complex biological samples.

Main Results:

• LiP-MS has been widely adopted for structural proteomics over the past decade.
• It successfully identified drug targets and delineated cellular pathways.
• The method revealed structural information for challenging protein targets and demonstrated structural biomarkers of disease.

Conclusions:

• LiP-MS enables the simultaneous probing of diverse molecular events like binding, modifications, and conformational changes.
• It supports a novel 3D proteomics workflow for detecting functional sites altered by perturbations.
• LiP-MS significantly enhances the information content of functional proteomics screens, providing peptide-level resolution for comprehensive biological system probing.