Clinical and Laboratory Standards Institute guideline M58—Methods for the Identification of Cultured Microorganisms Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry provides guidance to the end user for adopting matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in the medical laboratory setting. Included are procedures and guidelines for preparing and analyzing cultured patient isolates, interpreting and reporting results, and troubleshooting. Best practices are described for ensuring quality and safety, and guidelines are provided for the initial introduction of MALDI-TOF MS into an existing laboratory, including method verification, training development and competence assessment programs, and operational considerations.

This guideline establishes best practices for applying and integrating matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technology into the diagnostic microbiology laboratory. It presents preexamination considerations, such as selecting appropriate isolates for analysis and isolate preparation from solid or liquid media, and postexamination activities, such as results interpretation, indications for supplemental testing, and results reporting. Practical recommendations are provided for integrating MALDI-TOF MS into an existing traditional laboratory operation; for establishing QC procedures, safety procedures, and a competence assessment program; and for designing a method verification protocol. The intended users of this guideline are microbiologists in private, academic, and commercial diagnostic laboratory settings, including public health laboratories and veterinary diagnostic laboratories. This guideline: • Is not intended for use in the research setting • Is not intended to provide guidance pertaining to identifying microorganisms directly from patient specimens (before culture) • Does not cover antimicrobial susceptibility testing (AST) using MALDI-TOF MS – Although several studies have demonstrated that MALDI-TOF MS can be adapted for this purpose, its utility in a diagnostic laboratory setting remains undefined, and the methods are still in development.