This dataset contains mass spectrometry-based proteomics data generated for the clinical identification and subtyping of amyloid deposits from formalin-fixed, paraffin-embedded (FFPE) tissue biopsies. The study evaluates a rapid sample preparation workflow coupled with high-flow liquid chromatography–tandem mass spectrometry (LC-MS/MS) for the characterization of amyloid-associated proteins. FFPE tissue sections were processed using Congo red staining and targeted microdissection of amyloid-positive regions. Proteins were extracted using a heat-assisted extraction procedure followed by rapid tryptic digestion. The resulting peptide mixtures were analyzed using high-flow liquid chromatography coupled to a Q Exactive Orbitrap mass spectrometer operated in data-dependent acquisition mode. The dataset includes representative proteomic data generated from clinical amyloid tissue specimens. Protein identification and characterization were performed based on peptide-spectrum matches, unique peptide identification,