Quantification of amyloid protein enrichment by mass spectrometry improves amyloidosis typing

Introduction Amyloidosis typing is crucial to determine the best therapeutic strategy for patients. Since conventional histological techniques often fail, the identification of amyloid precursors by mass spectrometry became the new standard. However, without quantification, selecting the amyloid precursor from proteins that may be ubiquitous under non-pathological conditions may be equivocal. Therefore, we quantified protein enrichment in amyloid deposits to improve typing. Methods Protein enrichment was measured by extracted ion chromatogram based label free quantification by comparing a microdissected amyloid area with a non-amyloid area. We assessed the discrimination ability of candidate precursors with this approach compared to the two practiced identification methods. Results As proof of concept, we selected seven cases, 5 typical of the most common amyloidosis subtypes and typed by immunostainings, 2 inconclusive after immunohistochemistry. Proteins associated with amyloid deposits were identified in all samples confirming the pathology. When the routine clinical mass spectrometric identification techniques allowed unambiguous conclusions for 2/3 of 7 cases, quantification of the enrichment ratio in the amyloid deposit allowed unambiguous precursor selection in all cases. Conclusion Quantification of precursor enrichment in amyloid deposits is a promising optimization for amyloidosis typing. Incorporated into routine clinical processes, it will improve patient care in difficult diagnostic situations. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Sylvaine Di Tommaso is funded by the association HepA. Cyril Dourthe was financed by the Canceropole Grand Sud Ouest. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: On 2023/03/17, the Research Ethics Committee of the Centre Hospitalier Universitaire de Bordeaux certifies that the submission for publication of the following article Quantification of amyloid protein enrichment by mass spectrometry improves amyloidosis typing - Dr Chauveau has received a favorable opinion. This favorable opinion bears the reference number CER-BDX-2023-02. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD039814.