Mass Spectrometry in Anatomic Pathology: From Amyloid Typing to Reproducible Tissue Assays

Tissue protein diagnosis relies heavily on immunohistochemistry, whose results can be affected by tissue processing, antibodies, and platforms. Since 2022, our clinical amyloid typing service has used peptide-based mass spectrometry to analyze tissue specimens. This presentation reviews that experience, the use of the same platform for other diagnostic questions, and newer data-independent and targeted approaches, including an assay under development for Hirschsprung disease. It also examines how validation, detailed standard operating procedures, and reproducible data processing can help make tissue mass spectrometry assays more transferable.

After viewing this lecture, participants should be able to:

1. Explain how peptide-based mass spectrometry complements immunohistochemistry in tissue protein analysis.
2. Compare the roles of data-dependent, data-independent, and targeted acquisition in anatomic pathology assays.
3. Identify validation and data-processing practices needed for reproducible, transferable tissue mass spectrometry assays.

William Phipps, MD
Assistant Professor, Chemistry
Director, Tissue Mass Spectrometry
Assistant Director, Clinical Chemistry
Department of Laboratory Medicine & Pathology
University of Washington

10/14/26




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