Mass Spectrometry-Based Diagnosis and Typing of Amyloidosis: Analytical Workflows, Interpretation and Clinical Implementation

Accurate molecular typing of amyloid deposits is essential because morphologically similar deposits arise from clinically distinct precursor proteins that require different investigations and treatment. Mass spectrometry (MS)-based proteomics has become a reference approach for amyloid typing, but reliable diagnosis depends on the entire tissue-to-report workflow rather than on instrumentation alone. This review examines specimen selection and fixation, Congo red-guided enrichment and laser microdissection, protein extraction and digestion, LC–MS/MS acquisition, database searching, protein inference, precursor assignment, diagnostic ambiguity, quality control, reporting and clinical implementation. Established evidence supports bottom-up LC–MS/MS, particularly on enriched formalin-fixed paraffin-embedded tissue, for identifying common, hereditary, rare and unexpected amyloid precursors. However, inadequate sampling, low peptide recovery, incomplete sequence representation, competing amyloidogenic proteins and inappropriate interpretation can produce inconclusive or misleading results despite technically successful MS acquisition. Emerging strategies, including data-independent acquisition, targeted proteomics, variant-aware and patient-specific sequence analysis, spatial proteomics and machine-learning-supported interpretation, are promising but remain variably validated. The principal challenge is therefore shifting from demonstrating that MS can identify amyloid precursors to ensuring reproducible, transparent and clinically integrated typing across specimens, laboratories and health-care systems.