Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

Journal of Proteomics
Setsuko KomatsuKatsumi Sakata

Abstract

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolom...Continue Reading

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Citations

Feb 18, 2018·Biometals : an International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine·Rout George KerryJyoti Ranjan Rout
Aug 12, 2020·The Plant Journal : for Cell and Molecular Biology·Cornelia M HooperA Harvey Millar
Dec 5, 2020·International Journal of Molecular Sciences·Galina SmolikovaAndrej Frolov
Oct 16, 2020·International Journal of Molecular Sciences·Xin Wang, Setsuko Komatsu
Aug 14, 2021·Plant Biotechnology Journal·Min ZhangZhixi Tian

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