FDA and manufacturer's recommendations dictate that a biological test standard (BTS) is run with each target and must be acceptable prior to reading the unknown samples.
For research use only (RUO) and laboratory developed tests (LDTs), laboratories must develop their own quality control (QC) measures. Laboratories typically include a bacterial test standard (BTS) and series of reference-level identified organisms. Consideration may be given to include a rotating schedule of microorganisms that would be tested to ensure that the system performs to standard. Most laboratories also included negative reagent controls. These are controls in which blank reagents are added and the wells are assessed to ensure that no contaminated peaks are present. This control helps to ensure that reagents have not been contaminated and, for those laboratories re-using target plates, it ensures the cleaning process has been successful. It takes approximately 105 colony forming units (CFUs) to generate an identification with MALDI-TOF MS (Croxatto et al. 2012), so it is unlikely that a reagent or target plate would become so completely contaminated that it would generate a false identification. However, contaminating protein generates additional spectra that can lower identification scores and reduce the chances of successfully identifying a microorganism.
When QC fails, repeat testing is recommended and, if not resolved, the manufacturer should be notified immediately to assist in troubleshooting. The laboratory must have provisions for alternative methods of identification if an instrument fails or downtime occurs.