A method of analyzing a biological sample in a fully automated and validated analysis system (100, 300, 400) comprising an analyzer, wherein the analyzer is configured for accepting a cartridge with a valid identifier and rejecting a cartridge with an invalid identifier whose associated analysis protocol is not listed in a set of valid analysis protocols, comprising the steps of: a) providing a cartridge comprising an invalid identifier and containing at least one reagent for analyzing the biological sample; b) generating a custom analysis protocol with a protocol creation system, wherein steps a) and b) are interchangeable or may be performed in parallel; c) linking the custom analysis protocol to a protocol identifier corresponding to the invalid identifier; d) changing the invalid identifier into a valid identifier by transferring said custom analysis protocol associated with the protocol identifier from the protocol creation system to the set of valid analysis protocols stored by an analyzer controller of the analyzer, wherein the analyzer controller comprises a controller memory containing the set of analysis protocols, wherein each of the set of analysis protocols defines protocols and parameters for performing the analysis of a biological sample and is referenced by a protocol identifier, and wherein said analyzer controller permits the analyzer to accept the cartridge if the invalid identifier corresponds to the protocol identifier by comparing the identifier to the set of analysis protocols; e) selecting said custom analysis protocol linked to the protocol identifier corresponding to the now valid identifier, f) loading said cartridge with said now valid identifier into said analyzer; g) reading said identifier, wherein the identifier is read by an identification unit comprising an identifier reader comprised in the analyzer; and h) analyzing said biological sample using at least one aliquot of said at least one reagent comprised in said cartridge according to the selected custom analysis protocol. a) providing a cartridge comprising an invalid identifier and containing at least one reagent for analyzing the biological sample; b) generating a custom analysis protocol with a protocol creation system, wherein steps a) and b) are interchangeable or may be performed in parallel; c) linking the custom analysis protocol to a protocol identifier corresponding to the invalid identifier; d) changing the invalid identifier into a valid identifier by transferring said custom analysis protocol associated with the protocol identifier from the protocol creation system to the set of valid analysis protocols stored by an analyzer controller of the analyzer, wherein the analyzer controller comprises a controller memory containing the set of analysis protocols, wherein each of the set of analysis protocols defines protocols and parameters for performing the analysis of a biological sample and is referenced by a protocol identifier, and wherein said analyzer controller permits the analyzer to accept the cartridge if the invalid identifier corresponds to the protocol identifier by comparing the identifier to the set of analysis protocols; e) selecting said custom analysis protocol linked to the protocol identifier corresponding to the now valid identifier, f) loading said cartridge with said now valid identifier into said analyzer; g) reading said identifier, wherein the identifier is read by an identification unit comprising an identifier reader comprised in the analyzer; and h) analyzing said biological sample using at least one aliquot of said at least one reagent comprised in said cartridge according to the selected custom analysis protocol.