Protein quality and identification of the storage protein subunits of tofu and null soybean genotypes, using amino acid analysis, one- and two-dimensional gel electrophoresis, and tandem mass spectrometry

The protein quality of 11 null and 2 tofu soybean genotypes were determined from their total protein content, their amino acid composition, and their glycinin and β-conglycinin contents. There were highly significant differences (P < 0.001) in their total storage proteins, and amino acid contents. Total protein among these genotypes ranged from 33 to 37%, with arginine being the third highest amino acid (7.4–10.9 g/100 g protein) followed by glutamic and aspartic acids. Methionine accounted for only 1.6–2.4 g/ 100 g of protein. All genotypes contained a good balance of essential amino acids (EAA9), ranging from 43.5 to 47.3% of the total protein, limited only in methionine and possibly threonine and valine. Two-dimensional gel electrophoretic (2-DE) reference maps, using narrow range immobilized pH gradient (IPG) strips, revealed unique differences in the proteome, and subunit expression of glycinin and β-conglycinin, among these null genotypes, which can then be correlated with their protein quality. Out of a total of 111 basic (pH 6–11), and 223 acidic (pH 4–7) protein spots separated by 2-DE, 41 soybean storage protein spots were excised, and identified by liquid chromatography on-line with electro spray LCQ DecaXP tandem quadrupole time-of-flight mass spectrometry (LC/MS/MS). These methods will enable accurate evaluation of protein quality in soybeans, based on their protein digestibility-corrected amino acid score, assessment of the genetic variability of soybean genotypes, and serve as very effective tools for assisting plant breeders in their selection of high quality soybean varieties.