biostudies-literatureMin CWNational Research Foundation of KoreaDepartment of Biotechnology, Ministry of Science and Technology, IndiaE1517https://www.ebi.ac.uk/biostudies/studies/S-EPMC7349688biostudies-literatureUnknown9(6)Despite the significant technical advancements in mass spectrometry-based proteomics and bioinformatics resources, dynamic resolution of soybean seed proteome is still limited because of the high abundance of seed storage proteins (SSPs). These SSPs occupy a large proportion of the total seed protein and hinder the identification of low-abundance proteins. Here, we report a TMT-based quantitative proteome analysis of matured and filling stages seeds of high-protein (Saedanbaek) and low-protein (Daewon) soybean cultivars by application of a two-way pre-fractionation both at the levels of proteins (by PS) and peptides (by basic pH reverse phase chromatography). Interestingly, this approach led to the identification of more than 5900 proteins which is the highest number of proteins reported tCellsIn-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of <i>Glycine max</i> Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis.PMC7349688BT/HRD/35/02/20062019R1A6A3A130956552019R1A2C2085868Gupta RBae JWPark JRakwal RKim STYang PKim YMin CWAgrawal GKfalseIn-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of <i>Glycine max</i> Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis.Despite the significant technical advancements in mass spectrometry-based proteomics and bioinformatics resources, dynamic resolution of soybean seed proteome is still limited because of the high abundance of seed storage proteins (SSPs). These SSPs occupy a large proportion of the total seed protein and hinder the identification of low-abundance proteins. Here, we report a TMT-based quantitative proteome analysis of matured and filling stages seeds of high-protein (Saedanbaek) and low-protein (Daewon) soybean cultivars by application of a two-way pre-fractionation both at the levels of proteins (by PS) and peptides (by basic pH reverse phase chromatography). Interestingly, this approach led to the identification of more than 5900 proteins which is the highest number of proteins reported t2020-01-01T00:00:00Z2020 Jun2026-04-08T13:55:44.061Z2021-02-19T23:55:59ZS-EPMC73496883258039210.3390/cells9061517