A method for controlling an analysis system is presented. The method comprises receiving, by an encryption unit, authentication data of a user. In the case of a successful authentication, a user-specific security code is generated by the encryption unit. The security code is outputted by the encryption unit to the authenticated user. The security code and the user-ID are received by an authentication unit coupled to the analysis system via a user-interface coupled to the authentication unit. The security code is decrypted by the authentication unit. If the decrypted security code matches with the user-ID, the user is authenticated at the authentication unit and an authentication signal is generated by the authentication unit for permitting the user to initialize at least one function of the analysis system.