Protein matrix retains most starch granules within corn fiber from corn wet-milling process

•Structures in fiber fraction that retain starch were identified and quantified.•Three structures were found to be related to the retention of starch granules.•The protein matrix contributed to 54 % of total starch retention.•Starch granules in the vitreous endosperm were embedded in the protein matrix.•Protein disruption would lead to the largest increase in starch extraction. Complete starch extraction has long been an issue in the wet-milling industry, and here structures in the fine and coarse fiber fractions that retain starch were identified and quantified for potential treatments to increase starch and protein extraction rates. Six main structures were identified in the fiber fraction and three of them were directly related to the retention of starch granules. Elemental composition analysis to quantify the contribution of structures responsible for starch retention showed that the protein matrix contributed to 54 % of total starch retention. Confocal microscopy showed that starch granules in the peripheral region of vitreous endosperm were embedded in the protein matrix, whereas the ones in the central region were either stuck in the cell wall polysaccharides or almost free to be liberated. Secondary structural composition of proteins showed differences in fine and coarse fiber fractions. Protein disruption would lead to the largest increase in starch extraction.