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Meng B, Huang Y, Lu A, Liao H, Zhai R, Gong X, Dong L, Jiang Y, Dai X, Fang X, Zhao Y. Enhanced Analysis of Low-Abundance Proteins in Soybean Seeds Using Advanced Mass Spectrometry. Int J Mol Sci 2025; 26:949. [PMID: 39940716 PMCID: PMC11817203 DOI: 10.3390/ijms26030949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 01/07/2025] [Accepted: 01/15/2025] [Indexed: 02/16/2025] Open
Abstract
This study presents an advanced approach for the comprehensive analysis of low-abundance proteins in soybean seeds, addressing challenges posed by high-abundance storage proteins. We compared the effectiveness of Data-Dependent Acquisition (DDA), Data-Independent Acquisition (DIA), and BoxCar mass spectrometry techniques to identify low-abundance proteins in two types of soybean seeds: High-Oil and High-Protein seeds. The results indicate that the DIA method, and particularly the BoxCar methods, significantly improve the detection of low-abundance proteins compared to DDA, offering deeper insights into soybean seed biology. Specifically, BoxCar-based analysis revealed distinct proteomic differences between High-Oil and High-Protein seeds, highlighting more active metabolic processes in High-Oil seeds. Additionally, several key proteins were identified and annotated as uniquely expressed in either High-Oil or High-Protein seeds. These findings emphasize the importance of advanced proteomic techniques, such as BoxCar, in deepening our understanding of soybean seed biology and supporting breeding strategies to improve nutritional qualities.
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Affiliation(s)
- Bo Meng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (B.M.); (A.L.); (H.L.); (R.Z.); (X.G.); (L.D.); (Y.J.); (X.D.)
| | - Yuanyuan Huang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China;
| | - Ao Lu
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (B.M.); (A.L.); (H.L.); (R.Z.); (X.G.); (L.D.); (Y.J.); (X.D.)
| | - Huanyue Liao
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (B.M.); (A.L.); (H.L.); (R.Z.); (X.G.); (L.D.); (Y.J.); (X.D.)
| | - Rui Zhai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (B.M.); (A.L.); (H.L.); (R.Z.); (X.G.); (L.D.); (Y.J.); (X.D.)
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (B.M.); (A.L.); (H.L.); (R.Z.); (X.G.); (L.D.); (Y.J.); (X.D.)
| | - Lianhua Dong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (B.M.); (A.L.); (H.L.); (R.Z.); (X.G.); (L.D.); (Y.J.); (X.D.)
| | - You Jiang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (B.M.); (A.L.); (H.L.); (R.Z.); (X.G.); (L.D.); (Y.J.); (X.D.)
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (B.M.); (A.L.); (H.L.); (R.Z.); (X.G.); (L.D.); (Y.J.); (X.D.)
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (B.M.); (A.L.); (H.L.); (R.Z.); (X.G.); (L.D.); (Y.J.); (X.D.)
| | - Yang Zhao
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China; (B.M.); (A.L.); (H.L.); (R.Z.); (X.G.); (L.D.); (Y.J.); (X.D.)
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Linhuan H, Liangying Z, Shaobin L, Caixia Z, Danlei C, Siqi H, Peiming H, Shu K, Yingjun X, Yanmin L. Effect of MSX1 on the cellular function of cardiomyocytes. Gene 2024; 916:148419. [PMID: 38556116 DOI: 10.1016/j.gene.2024.148419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
MSX1 (Muscle Segment Homeobox 1) has pleiotropic effects in various tissues, including cardiomyocytes, while the effect of MSX1 on cardiomyocyte cellular function was not well known. In this study, we used AC16 cell culture, real-time fluorescence quantitative PCR (qPCR), protein blotting (Western blot), flow cytometry apoptosis assay and lactate dehydrogenase (LDH) ELISA (Enzyme-Linked Immunosorbnent Assay) to investigate the effect of the MSX1 gene on cardiomyocyte function. The results showed that MSX1 plays a protective role against hypoxia of cardiomyocytes. However, further studies are required to fully understand the role of MSX1 in the regulation of LDH expression in different cell types and under different conditions.
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Affiliation(s)
- Huang Linhuan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510100, Guangdong Province, PR China.
| | - Zhong Liangying
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510100, Guangdong Province, PR China.
| | - Lin Shaobin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510100, Guangdong Province, PR China.
| | - Zhu Caixia
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510100, Guangdong Province, PR China.
| | - Cai Danlei
- Department of Ultrasound, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510100, Guangdong Province, PR China.
| | - Huang Siqi
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, Guangdong Province, PR China.
| | - Hong Peiming
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, Guangdong Province, PR China.
| | - Kong Shu
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, Guangdong Province, PR China.
| | - Xie Yingjun
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, Guangdong Province, PR China.
| | - Luo Yanmin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510100, Guangdong Province, PR China.
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