A streamlined mass spectrometry-based proteomics workflow for large-scale FFPE tissue analysis
A streamlined mass spectrometry-based proteomics workflow for large-scale FFPE tissue analysis
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DOI：
10.1002/path.5420
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发表时间：
2020-05-01
影响因子：
7.3
通讯作者：
Mann, Matthias
中科院分区：
文献类型：
--
作者：
Coscia, Fabian;Doll, Sophia;Mann, Matthias
福尔马林固定和石蜡包埋（FFPE）是保存人体组织用于临床诊断的最常用方法，FFPE档案是生物医学研究的宝贵资源。FFPE材料中的蛋白质在几十年内是稳定的，但迄今为止，通过基于质谱（MS）的蛋白质组学对其进行有效提取和简化分析已被证明具有挑战性。在此，我们描述了一种基于MS的蛋白质组学工作流程，用于直接从组织病理学载玻片定量分析大型FFPE组织队列。我们证明了工作流程对临床病理学标本和可变样本量的广泛适用性，包括通过激光显微切割分离的低输入癌症组织。使用最先进的数据相关采集（DDA）和数据独立采集（DIA）MS工作流程，我们在100分钟的单次运行分析中始终如一地定量了大部分蛋白质组。在一个包含100多个样本的腺瘤队列中，总检查时间不到一天。我们观察到在长期储存的样品（>15年）中蛋白质鉴定较低的适度趋势，但聚类成不同的蛋白质组亚型与存档时间无关。我们的研究结果强调了FFPE组织使用无偏见蛋白质组学进行患者表型分析的巨大前景，并且它们证明了以稳健，及时和简化的方式分析大型组织队列的可行性。(c)2020年，任作家。病理学杂志由John Wiley & Sons Ltd代表大不列颠和爱尔兰病理学会出版。
Formalin fixation and paraffin-embedding (FFPE) is the most common method to preserve human tissue for clinical diagnosis, and FFPE archives represent an invaluable resource for biomedical research. Proteins in FFPE material are stable over decades but their efficient extraction and streamlined analysis by mass spectrometry (MS)-based proteomics has so far proven challenging. Herein we describe a MS-based proteomic workflow for quantitative profiling of large FFPE tissue cohorts directly from histopathology glass slides. We demonstrate broad applicability of the workflow to clinical pathology specimens and variable sample amounts, including low-input cancer tissue isolated by laser microdissection. Using state-of-the-art data dependent acquisition (DDA) and data independent acquisition (DIA) MS workflows, we consistently quantify a large part of the proteome in 100 min single-run analyses. In an adenoma cohort comprising more than 100 samples, total workup took less than a day. We observed a moderate trend towards lower protein identification in long-term stored samples (>15 years), but clustering into distinct proteomic subtypes was independent of archival time. Our results underscore the great promise of FFPE tissues for patient phenotyping using unbiased proteomics and they prove the feasibility of analyzing large tissue cohorts in a robust, timely, and streamlined manner. (c) 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.