Emerging opportunities for intact and native protein analysis using chemical proteomics

Area of Science:

• Proteomics
• Chemical Biology
• Mass Spectrometry

Background:

• Chemical proteomics advances small molecule ligand discovery and medicinal chemistry.
• Mass spectrometry is the primary analytical technique in chemoproteomics.
• High-resolution mass spectrometry has driven interest in proteoform-level analysis.

Purpose of the Study:

• To review recent advancements in MS-based proteomics for chemoproteomics.
• To detail the capabilities and limitations of intact mass analysis (IMA) and top-down proteomics (TDMS).
• To explore the complementary roles of native mass spectrometry (nMS) and ion mobility mass spectrometry (IM-MS).

Main Methods:

• Intact mass analysis (IMA) for proteoform-level analysis.
• Top-down proteomics (TDMS) for proteoform-level analysis.
• Mass spectrometry (MS)-based approaches including native MS (nMS) and ion mobility MS (IM-MS).

Main Results:

• IMA and TDMS provide proteoform-level insights, overcoming challenges in protein inference and modification stoichiometry compared to bottom-up proteomics (BUMS).
• Review details strengths and considerations for IMA and TDMS in chemoproteomic studies.
• nMS and IM-MS offer complementary capabilities for advancing functional proteomics.

Conclusions:

• Proteoform-level MS methods like IMA and TDMS are crucial for understanding protein-ligand interactions and drug development.
• Native MS and ion mobility MS enhance chemoproteomic investigations.
• Continued development of MS techniques will further advance functional proteomics and drug discovery.