1. Fundamentals and instrumentation. Ion formation (EI, CI, ESI/APCI, MALDI), ambient ionization (DESI, REIMS); quadrupole, TOF, ion traps, Orbitrap and FT-ICR; resolving power, mass accuracy, dynamic range and ion mobility. 2. Tandem MS and spectral interpretation. CID/HCD, ETD/ECD; isotope envelopes, accurate mass, molecular formula assignment, fragmentation rules, MSn, spectral libraries and database searching. 3. Quantitative clinical MS. LC-MS/MS and GC-MS; internal standards, calibration, matrix effects, carry-over, accuracy and precision, LOD/LOQ, reference materials, method validation, QC/EQA and harmonization. Examples include therapeutic drug monitoring, steroid analysis, toxicology and newborn screening. 4. Peptides, proteins and structural MS. Deconvolution, bottom-up and top-down analysis, targeted proteomics, post-translational modifications, native MS, HDX-MS and chemical cross-linking. 5. Metabolomics and lipidomics. Targeted and untargeted workflows, biofluids, metabolite annotation and dereplication, normalization and multivariate analysis; requirements for translating a biomarker into a clinical test. 6. Clinical microbiology and infection. MALDI-TOF microbial identification, direct analysis of clinical samples and positive blood cultures, opportunities and limitations for resistance detection and strain typing; microbial metabolites and metallophores. 7. Spatial and intraoperative MS. MALDI-MSI, DESI and SIMS principles; spatial metabolomics/proteomics, multimodal imaging, REIMS/iKnife and SpiderMass; trade-offs among spatial resolution, sensitivity and molecular-identification confidence. 8. Data, software and AI. CycloBranch, mMass and public databases; data-quality control, reproducibility, machine-learning classification and responsible reporting of results. Practical training and learning outcomes ? Data acquisition on MALDI/ESI instruments using model or student-provided samples; charge-state and molecular-mass calculations; MS/MS interpretation and software/database work. ? After completing the course, students will be able to select an appropriate MS strategy for a clinical question, justify analyte identification, outline a basic validation/QC plan, and distinguish biomarker discovery from a clinically validated diagnostic test. ? The colloquium assesses theory, calculations, spectrum interpretation and critical appraisal of a selected clinical application.
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Lee W. et al. Clinical metabolomics: analytical workflows, data interpretation, and translational considerations. J. Anal. Sci. Technol. 17, 46 (2026). doi:10.1186/s40543-026-00567-8..
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Lira K.E., May J.C., McLean J.A. Ion mobility spectrometry and ion mobility-mass spectrometry in clinical chemistry. Adv. Clin. Chem. 124, 123?160 (2025). doi:10.1016/bs.acc.2024.10.003..
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Weiss Z.F., Basu S.S. The Mass Spectrometry Revolution in Clinical Microbiology Part 2: Emerging Applications. Clin. Lab. Med. 45, 15?26 (2025). doi:10.1016/j.cll.2024.10.012..
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