DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes

Area of Science:

• Proteomics
• Molecular Biology
• Biochemistry

Background:

• Proteins function in macromolecular assemblies, crucial for cellular processes.
• Affinity purification coupled with mass spectrometry (AP-MS) identifies protein interactions.
• Resolving complex protein isoforms from AP-MS data requires computationally intensive reciprocal experiments.

Purpose of the Study:

• Introduce deep interactome profiling by mass spectrometry (DIP-MS) for resolving complex protein isoforms.
• Enable the analysis of protein complex composition in a single experiment.
• Overcome limitations of traditional AP-MS for isoform resolution.

Main Methods:

• DIP-MS combines affinity purification (AP) with blue-native-PAGE separation.
• Utilizes data-independent acquisition with mass spectrometry.
• Employs deep-learning-based signal processing for data analysis.

Main Results:

• DIP-MS successfully resolved distinct prefoldin holo- and subcomplex variants.
• Identified complex-complex interactions and novel complex isoforms with new subunits.
• Demonstrated experimental validation of newly identified subunits and interactions.

Conclusions:

• DIP-MS offers unprecedented depth and resolution for analyzing proteome modularity.
• Provides a powerful tool for dissecting complex protein interactions and isoforms.
• Advances the understanding of cellular organization and function.