Introduction: The last decade has yielded significant developments in the field of proteomics, especially in mass spectrometry (MS) and data analysis tools. In particular, a shift from gel-based to MS-based proteomics has been observed, thereby providing a platform with which to construct proteome atlases for all life forms. Nevertheless, the analysis of plant proteomes, especially those of samples that contain high-abundance proteins (HAPs), such as soybean seeds, remains challenging.

Areas covered: Here, we review recent progress in soybean seed proteomics and highlight advances in HAPs depletion methods and peptide pre-fractionation, identification, and quantification methods. We also suggest a pipeline for future proteomic analysis, in order to increase the dynamic coverage of the soybean seed proteome.

Expert opinion: Because HAPs limit the dynamic resolution of the soybean seed proteome, the depletion of HAPs is a prerequisite of high-throughput proteome analysis, and owing to the use of two-dimensional gel electrophoresis-based proteomic approaches, few soybean seed proteins have been identified or characterized. Recent advances in proteomic technologies, which have significantly increased the proteome coverage of other plants, could be used to overcome the current complexity and limitation of soybean seed proteomics.

简介：过去十年在蛋白质组学领域取得了重大进展，尤其是在质谱（MS）和数据分析工具方面。特别地，已经观察到从基于凝胶的蛋白质组学向基于MS的蛋白质组学的转变，从而提供了一个平台，可用于构建所有生命形式的蛋白质组图谱。然而，植物蛋白质组的分析，尤其是那些包含高丰度蛋白（HAP）的样品（例如大豆种子）的分析仍然具有挑战性。

涵盖的领域：在这里，我们回顾了大豆种子蛋白质组学的最新进展，并重点介绍了HAP消耗方法以及肽预分离，鉴定和定量方法方面的进展。我们还建议了用于将来蛋白质组学分析的管道，以增加大豆种子蛋白质组的动态覆盖范围。

专家意见：由于HAP限制了大豆种子蛋白质组的动态分辨率，因此HAP的消耗是高通量蛋白质组分析的先决条件，并且由于使用了基于二维凝胶电泳的蛋白质组学方法，几乎​​没有大豆种子蛋白质具有被识别或表征。蛋白质组学技术的最新进展已大大提高了其他植物的蛋白质组覆盖率，可以用来克服目前大豆种子蛋白质组学的复杂性和局限性。