Tandem Mass Spectrometry-Based Amyloid Typing Using Manual Microdissection and Open-Source Data Processing.

Autor:	Phipps WS; Department of Laboratory Medicine and Pathology, Seattle, WA, USA., Smith KD; Department of Laboratory Medicine and Pathology, Seattle, WA, USA.; Department of Medicine, Seattle, WA, USA., Yang HY; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Henderson CM; Department of Laboratory Medicine and Pathology, Seattle, WA, USA.; Seagen, Bothel, WA, USA., Pflaum H; Department of Laboratory Medicine and Pathology, Seattle, WA, USA.; Seattle Children's Hospital, Seattle, WA, USA., Lerch ML; Department of Laboratory Medicine and Pathology, Seattle, WA, USA., Fondrie WE; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Emrick MA; Department of Laboratory Medicine and Pathology, Seattle, WA, USA., Wu CC; Department of Genome Sciences, University of Washington, Seattle, WA, USA., MacCoss MJ; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Noble WS; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Hoofnagle AN; Department of Laboratory Medicine and Pathology, Seattle, WA, USA.; Department of Medicine, Seattle, WA, USA.
Jazyk:	angličtina
Zdroj:	American journal of clinical pathology [Am J Clin Pathol] 2022 May 04; Vol. 157 (5), pp. 748-757.
DOI:	10.1093/ajcp/aqab185
Abstrakt:	Objectives: Standard implementations of amyloid typing by liquid chromatography-tandem mass spectrometry use capabilities unavailable to most clinical laboratories. To improve accessibility of this testing, we explored easier approaches to tissue sampling and data processing. Methods: We validated a typing method using manual sampling in place of laser microdissection, pairing the technique with a semiquantitative measure of sampling adequacy. In addition, we created an open-source data processing workflow (Crux Pipeline) for clinical users. Results: Cases of amyloidosis spanning the major types were distinguishable with 100% specificity using measurements of individual amyloidogenic proteins or in combination with the ratio of λ and κ constant regions. Crux Pipeline allowed for rapid, batched data processing, integrating the steps of peptide identification, statistical confidence estimation, and label-free protein quantification. Conclusions: Accurate mass spectrometry-based amyloid typing is possible without laser microdissection. To facilitate entry into solid tissue proteomics, newcomers can leverage manual sampling approaches in combination with Crux Pipeline and related tools. (© American Society for Clinical Pathology, 2021. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Databáze:	MEDLINE
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