A comprehensive review on tandem mass tag based proteomics deciphering molecular insights of fruit development and ripening

Fruit development, ripening, and post-harvest physiology are regulated by intricate molecular networks that directly impact its quality, shelf-life, and consumer appeal. Tandem Mass Tag (TMT)-based quantitative proteomics has emerged as a powerful approach for high-throughput, multiplexed analysis of protein abundance, modifications, and interactions across developmental and ripening stages and environmental conditions. TMT-based studies have uncovered key regulators including hormone-responsive proteins, transcription factors, epigenetic modifiers, and stress-related proteins that coordinate ripening and senescence. The integration of TMT proteomics with other omics approaches such as transcriptomics and metabolomics has facilitated systems-level insights, revealing layers of regulation beyond gene expression. Despite limitations such as cost and ratio compression, TMT offers notable advantages in quantification accuracy, reproducibility, and temporal resolution. Overall, TMT-based proteomics stands as a critical tool for advancing fruit biology research and supporting innovations in precision breeding, quality enhancement, and post-harvest management. This review summarizes the recent TMT-based proteomic studies in diverse fruit species, with an emphasis on tissue-specific, developmental, and organelle-targeted analyses.