Concepts and strategies of soybean seed proteomics using the shotgun proteomics approach. (2nd September 2019)

• Record Type: Journal Article
• Authors: Min, Cheol Woo; Gupta, Ravi; Agrawal, Ganesh Kumar; Rakwal, Randeep; Kim, Sun Tae
• Is Part Of: Expert review of proteomics. Volume 16:Number 9(2019)
• Page Start: 795
• Page End: 804
• Publication Date: 2019-09-02
• Subjects: Basic pH reversed phase -- filter-aided sample preparation -- low-abundance proteins -- MaxQuant -- perseus -- shotgun proteomics -- soybean seed -- tandem mass tag; Proteins -- Biotechnology -- Periodicals; Proteomics -- Periodicals; 572.6
• DOI: 10.1080/14789450.2019.1654860
• Languages: English
• ISSNs: 1478-9450

Abstract

ABSTRACT: 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.