The growing demand for plant-based foods is reshaping the global food system, driven by rising consumer concerns related to health, environmental sustainability, and animal welfare [1]. However, the success of this transition depends not only on the availability of plant-based alternatives but also on their ability to match or surpass animal-based products in terms of texture, flavor, appearance, and nutritional value [2]. Despite market growth, most plant-based products underperform because simple protein substitution cannot replicate the complex structure and functionality of animal proteins [3,4]. Plant proteins possess diverse isoforms, post-translational modifications (PTMs), and interaction networks that directly influence functional properties such as solubility, emulsification, gelling, binding, and structural integrity [5]. Achieving foods with desirable texture, flavor, and nutritional profiles therefore requires a deep, molecular-level understanding of these protein characteristics [6]. Emerging analytical and computational technologies, including high-throughput screening, machine learning, and systems biology, complement proteomics by enabling the identification of specific protein features and interactions that can be linked to functional performance in complex food matrices, providing a foundation for rational design strategies [7].

To develop next-generation plant-based foods that deliver superior sensory and nutritional performance, processing and formulation strategies must adopt data-driven, molecular-level approaches [8,9]. Proteomics, initially developed for biomedical research, has rapidly evolved due to advances in mass spectrometry, bioinformatics, and systems biology, allowing comprehensive characterization of plant proteins, including isoforms, PTMs, and interaction networks [10]. These analyses directly inform functional properties such as solubility, emulsification, gelling, and binding, which are essential for achieving desirable textures, stable structures, controlled flavor release, and improved nutritional attributes, including digestibility and allergenic potential [11,12]. By integrating proteomic analysis with processing strategies such as enzymatic treatments, fermentation, or physical modification, researchers can rationally optimize protein behavior and interactions, reducing trial-and-error formulation while enhancing texture, stability, and sensory appeal [13].

Proteomics also provides practical guidance for the selection and processing of conventional and novel protein sources such as legumes, cereals, and algae to achieve targeted functionality in real food matrices. The main mass spectrometry (MS)-based methods applied in this context include discovery proteomics and targeted mass spectrometry. These approaches enable both qualitative and quantitative insights into protein composition, modifications, and interactions, which are critical for designing functional analogs that mimic animal protein properties. By focusing on MS-based proteomics and peptidomics within real food systems, this framework allows for precise modulation of plant protein functionality while excluding unrelated applications such as marketing strategies or generalized sustainability claims [14].

While proteomics, particularly LC-MS/MS–based approaches, is well established in nutrition, agricultural, and plant protein research, its systematic and design-oriented integration into plant-based food formulation remains underdeveloped [15,16]. Many studies apply proteomic tools for compositional or descriptive purposes, but fewer leverage these datasets to directly guide processing, formulation, and multi-attribute optimization of texture, flavor, and nutritional performance [17,18]. This review therefore focuses on how proteomics can be used as a rational design framework for functional plant-based foods. It is structured to introduce key proteomic approaches and illustrate their application in improving texture, flavor, and nutritional quality. By integrating these perspectives, this review outlines a path toward next-generation plant-based foods that combine analytical rigor with practical innovation.