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Comparative Analysis of Soybean Seed Proteome Based on Different Mass Spectrometry Acquisition Strategies

ABSTRACT: This study established a soybean seed proteome database and analyzed the raw mass spectrometry data of BoxCar and DIA on MaxQuant based on this database. Subsequently, the three mass spectrometry acquisition strategies, DDA, DIA and BoxCar, were compared for their depth of protein identification, data stability, and effectiveness of their use in differential proteomics.

ORGANISM(S): Glycine Max

SUBMITTER: Yang Zhao

PROVIDER: PXD052278 | iProX | Thu May 16 00:00:00 GMT+01:00 2024

REPOSITORIES: iProX

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Enhanced Analysis of Low-Abundance Proteins in Soybean Seeds Using Advanced Mass Spectrometry.

Meng Bo B Huang Yuanyuan Y Lu Ao A Liao Huanyue H Zhai Rui R Gong Xiaoyun X Dong Lianhua L Jiang You Y Dai Xinhua X Fang Xiang X Zhao Yang Y

International journal of molecular sciences 20250123 3

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, ...[more]

PMID: 39940716

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