# Capturing protein-protein interactions in plants: recent advances, challenges, and opportunities

## TL;DR

This paper reviews recent technologies for studying protein interactions in plants, aiming to improve understanding of plant biology and crop improvement.

## Contribution

The paper provides an updated practical guide for selecting and combining advanced tools to study plant protein interactions.

## Key findings

- Proximity labeling, yeast-3-hybrid, AlphaFold 3, and data-independent acquisition MS are promising for studying plant PPIs.
- These technologies address limitations of classical methods and offer new opportunities for plant research.
- Combining these tools can enhance coverage of the plant protein interactome.

## Abstract

Plants rely on dynamic protein-protein interaction (PPI) networks to carry out routine functions (such as photosynthesis and respiration) and responses to environmental cues. Therefore, capturing dynamic PPIs is critical for understanding molecular processes underlying the plant life cycle. Recent technological advances have significantly expanded the experimental and computational toolkit available for studying PPIs in plants. In this review, emerging and advanced technologies are presented, including proximity labeling, yeast-3-hybrid, AlphaFold 3, and data-independent acquisition mass spectrometry (MS). How these technologies address critical limitations posed by classical techniques, and their strengths, challenges, and opportunities, are discussed. The goal is to provide an updated practical guide that informs researchers on selecting, optimizing, and combining these tools to maximize protein interactome coverage. Together, these complementary tools and approaches promise to advance mechanistic understanding of plant biological processes and enable more informed manipulation of complex biological networks toward improving crop quality and yield.