A method of operating and diagnosing faults in a laboratory instrument, the method comprising: a) performing an analytic sequence of steps to analyze a biological sample, wherein the analytic sequence of steps comprises: i) transferring a portion of the biological sample from a sample vessel to a reaction vessel; ii) creating an analytic mixture by transferring a first reagent comprising alkaline phosphatase from a reagent pack to the reaction vessel; iii) removing portions of the analytic mixture that are not bound to an analyte from the reaction vessel using a assay washing subsystem; and iv) adding a substrate adapted to generate chemiluminescent light in reaction with ALP to the reaction vessel and detecting chemiluminescent light generated by the substrate in reaction with the ALP using a luminometer; b) performing a set of diagnostic steps that comprises evaluating the assay washing subsystem by, for each of a set of one or more vessels, performing a set of wash efficiency check steps comprising: i) adding a combination of: A) an ALP solution; B) a second reagent comprising paramagnetic particles; and C) a wash buffer to the one or more vessels; ii) performing a set of washing steps comprising: A) subjecting the one or more vessels to a magnetic field; B) adding additional wash buffer to the one or more vessels; and C) spinning the contents of the one or more vessels one or more times; iii) aspirating fluid from the one or more vessels; iv) after aspirating fluid from the one or more vessels, adding the substrate adapted to generate chemiluminescent light in reaction with ALP; v) incubating the one or more vessels; and vi) using the luminometer, measuring chemiluminescent light from the one or more vessels after it has been placed in a luminometer vessel chamber. a) performing an analytic sequence of steps to analyze a biological sample, wherein the analytic sequence of steps comprises: i) transferring a portion of the biological sample from a sample vessel to a reaction vessel; ii) creating an analytic mixture by transferring a first reagent comprising alkaline phosphatase from a reagent pack to the reaction vessel; iii) removing portions of the analytic mixture that are not bound to an analyte from the reaction vessel using a assay washing subsystem; and iv) adding a substrate adapted to generate chemiluminescent light in reaction with ALP to the reaction vessel and detecting chemiluminescent light generated by the substrate in reaction with the ALP using a luminometer; i) transferring a portion of the biological sample from a sample vessel to a reaction vessel; ii) creating an analytic mixture by transferring a first reagent comprising alkaline phosphatase from a reagent pack to the reaction vessel; iii) removing portions of the analytic mixture that are not bound to an analyte from the reaction vessel using a assay washing subsystem; and iv) adding a substrate adapted to generate chemiluminescent light in reaction with ALP to the reaction vessel and detecting chemiluminescent light generated by the substrate in reaction with the ALP using a luminometer; b) performing a set of diagnostic steps that comprises evaluating the assay washing subsystem by, for each of a set of one or more vessels, performing a set of wash efficiency check steps comprising: i) adding a combination of: A) an ALP solution; B) a second reagent comprising paramagnetic particles; and C) a wash buffer to the one or more vessels; ii) performing a set of washing steps comprising: A) subjecting the one or more vessels to a magnetic field; B) adding additional wash buffer to the one or more vessels; and C) spinning the contents of the one or more vessels one or more times; iii) aspirating fluid from the one or more vessels; iv) after aspirating fluid from the one or more vessels, adding the substrate adapted to generate chemiluminescent light in reaction with ALP; v) incubating the one or more vessels; and vi) using the luminometer, measuring chemiluminescent light from the one or more vessels after it has been placed in a luminometer vessel chamber. i) adding a combination of: A) an ALP solution; B) a second reagent comprising paramagnetic particles; and C) a wash buffer to the one or more vessels; A) an ALP solution; B) a second reagent comprising paramagnetic particles; and C) a wash buffer ii) performing a set of washing steps comprising: A) subjecting the one or more vessels to a magnetic field; B) adding additional wash buffer to the one or more vessels; and C) spinning the contents of the one or more vessels one or more times; A) subjecting the one or more vessels to a magnetic field; B) adding additional wash buffer to the one or more vessels; and C) spinning the contents of the one or more vessels one or more times; iii) aspirating fluid from the one or more vessels; iv) after aspirating fluid from the one or more vessels, adding the substrate adapted to generate chemiluminescent light in reaction with ALP; v) incubating the one or more vessels; and vi) using the luminometer, measuring chemiluminescent light from the one or more vessels after it has been placed in a luminometer vessel chamber.