Proteomics-driven innovations in plant-based foods: Current advances, emerging technologies, and future perspectives

Despite rapid market growth, plant-based foods such as meat analogs, plant-based milk, yogurt alternatives, and fermented products still fall short of matching the sensory, structural, and nutritional qualities of animal-based counterparts, primarily due to simple ingredient substitution that fails to reproduce the molecular structure, interactions, and functional properties required for optimal texture, flavor, and nutritional performance. Proteomics, using advanced mass spectrometry (MS) and label-free quantification methods, provides an approach to analyze plant protein composition, structure, interactions, and modifications, enabling targeted functional improvements. This review describes how proteomic workflows inform formulation across three areas. First, protein compositional and structural characterization employs techniques such as liquid chromatography-tandem mass spectrometry (LC-MS/MS) and differential scanning calorimetry (DSC) coupled with MS to map protein composition and structural behavior, supporting decisions on protein sources, fractionation, and purification. Second, indirect proteomic methods coupled with other non-proteomic complementary tools are used to determine structure-function relationships induced by processing to examine processing-induced crosslinking, enzymatic modifications, and lipid-protein interactions that influence texture. Third, targeted MS methods, including selected reaction monitoring (SRM) and parallel reaction monitoring (PRM), are applied to profile off-flavor compounds and identify protein modification sites relevant to sensory and nutritional properties. By integrating proteomic data with processing strategies, this review outlines how proteomics can be used to examine key functional attributes related to texture, flavor, and nutritional quality in plant-based foods. SIGNIFICANCE: This review highlights the pivotal role of proteomics in advancing next-generation plant-based foods. Proteomic analysis enables an in-depth understanding of plant protein structure, composition, interactions, and bioactivity, providing critical insights for the development of functionally enhanced and consumer-acceptable alternatives. By integrating proteomics with AI, machine learning, multi-omics approaches, and cutting-edge analytical tools such as spatial proteomics and mass spectrometry imaging, the review demonstrates how protein functionality, flavor, texture, nutrition, and allergenicity can be optimized. Furthermore, it emphasizes the potential of proteomics to accelerate innovation in personalized nutrition, support sustainable and circular food systems, improve food safety, and reduce waste by valorizing plant-based by-products. This work serves as a roadmap for researchers and industry stakeholders seeking to leverage proteomics to design novel, high-quality, and sustainable plant-based protein products.