Pitfalls in the desulphation of glucosinolates in a high-throughput assay

► Effect of sulphatase preparation on glucosinolate analysis in microtiter plates was tested. ► High amounts of sulphatase decreased glucotropaeolin concentration. ► High amounts of sulphatase hardly affected other glucosinolates than glucotropaeolin. ► Hence, too high recoveries were calculated when glucotropaeolin is used as internal standard. ► Purified sulphatase is applicable for glucosinolate analysis in a diversity of samples.