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This article complements an earlier work published in 2015 Baron et al. (2015) that showed the interest of a shrimp shells bio-refining process. We compare here the effect of eleven commercial proteases at pH 3.5 or 4.0 on a residual amount of shrimp shells proteins after 6 h at 50 °C. The two pH are obtained when respectively 40 and 25 mmol of formic acid are added to 5 g of mild dried shell. Deproteinisation yield above 95% are obtained. Residual amino acids profile in the solid phase was identical for the eleven proteases except for pepsin which was similar to the raw material profile. A significant relative increase in the proportion of Glycine is observed for the ten other cases. Likewise, shapes of size exclusion chromatograms of the dissolved phase are similar except with pepsin.