Cotton Genomics and Genetics 2025, Vol.16, No.5, 241-248 241 Review Article Open Access Label-Free Quantitative Proteomics Reveals Key Enzymes in Fiber Maturation Jiayi Wu, Yuxin Zhu, Tianze Zhang Modern Agriculture Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: tianze.zhang@cuixi.org Cotton Genomics and Genetics, 2025, Vol.16, No.5 doi: 10.5376/cgg.2025.16.0024 Received: 06 Aug., 2025 Accepted: 17 Sep., 2025 Published: 09 Oct., 2025 Copyright © 2025 Wu et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Wu J.Y., Zhu Y.X., and Zhang T.Z., 2025, Label-free quantitative proteomics reveals key enzymes in fiber maturation, Cotton Genomics and Genetics, 16(5): 241-248 (doi: 10.5376/cgg.2025.16.0024) Abstract Cotton fibers are important natural textile raw materials, and their maturation process directly affects the length, strength and quality of the fibers. However, the molecular regulatory mechanisms during the fiber maturation period remain unclear, which limits the genetic improvement of high-quality cotton varieties. To deeply reveal the protein regulatory network related to fiber maturation, in this study, Label-Free Quantitative Proteomics technology was adopted to systematically analyze the protein expression profiles in cotton fibers at different developmental stages. Further functional enrichment and protein-protein interaction network analysis indicated that cellulose synthase (CESA), sucrose synthase (SUS), peroxidase, heat shock protein, etc. play a core role in the process of fiber maturation. This study systematically analyzed the developmental biological basis of cotton fiber maturation, the types and expression characteristics of key enzymes, and verified the expression patterns of key genes through case studies. Finally, it explored the application potential of proteomics data in breeding. This research not only enriches the understanding of the maturation mechanism of cotton fibers, but also provides potential functional gene resources for molecular breeding of high-quality cotton. Keywords Cotton fiber maturation; Label-free quantitative proteomics; Key enzyme; Cell wall synthesis; Molecular breeding 1 Introduction Why is cotton important? It's not because it is widely grown, but because the fibers it produces support a multi-billion-dollar global market. The length, strength and fineness of fibers-these seemingly technical indicators-actually directly determine the quality of clothes and fabrics, as well as the commercial value of cotton. For industry and agriculture, cotton is both the protagonist and the foundation (Lee et al., 2024). From this perspective, to maintain the stability and competitiveness of the textile industry, merely having output is not enough; the quality of fibers must keep up. But it's easy to say, but it's not easy to actually improve cotton fibers at the genetic level. Although we have gained a considerable understanding of the development mechanism of cotton fibers, when it comes to the "maturity" stage, the regulatory details at the molecular level remain unclear. For instance, how the structure of the cell wall changes and what specific roles proteins play have not yet been fully clarified. Traditional research methods have also made attempts, but they are relatively limited in terms of dynamic monitoring of protein changes. At this point, label-free quantitative proteomics emerged as a breakthrough. It does not rely on preset labels and can comprehensively and systematically analyze the abundance and function of proteins in fibers, and is less likely to miss important information (Distler et al., 2016; Ankney et al., 2018). Through it, key enzymes and regulatory proteins involved in fiber development are also more easily identified, which has greatly promoted our understanding of fiber maturation. Although this method seems to have a relatively high technical threshold, it can indeed provide many clues for the cultivation of superior cotton varieties in the future. This study utilized a label-free quantitative proteomics process to analyze the proteome of cotton fibers at different developmental stages. By isolating fibroblasts and employing advanced mass spectrometry techniques, proteins crucial for fiber maturation were identified and located. This study aims to reveal the key enzymes and regulatory pathways that drive fiber development, providing a comprehensive framework for future crop improvement. These findings are of great significance to both basic plant biology and the agricultural industry, providing new strategies for improving fiber quality and yield.
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