Evaluation of a 'plug and play' nanoflow liquid chromatography system for MS-based proteomic characterization of clinical FFPE specimens.

IF 3.8 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS Expert Review of Proteomics Pub Date : 2023-04-01 DOI:10.1080/14789450.2023.2219844

Georgia Mitsa, Vincent R Richard, Yasamin Majedi, Josiane Lafleur, Adriana Aguilar-Mahecha, Mark Basik, Christoph H Borchers

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Abstract

Introduction: Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tumor tissue specimens has gained interest in the last 5 years due to technological advances and improved sample collection, as well as biobanking for clinical trials. The real-world implementation of clinical proteomics to these specimens, however, is hampered by tedious sample preparation steps and long instrument acquisition times.

Areas covered: To advance the translation of quantitative proteomics into the clinic, we are comparing the performance of the leading commercial nanoflow liquid chromatography (nLC) system (based on literature reviews), the Easy-nLC 1200 (Thermo Fisher Scientific, Waltham, MA, U.S.A.), to the Evosep One HPLC (Evosep Biosystems, Odense, Denmark). We measured FFPE-tissue digests from 21 biological replicates with a similar gradient on both of the LC systems while keeping the on-column amount (1 µg total protein) and the single-shot data-dependent acquisition-based MS/MS method constant.

Expert opinion: Overall, the Evosep One facilitates robust and sensitive high-throughput sample acquisition, making it suitable for clinical MS. We found the Evosep One to be a useful platform for positioning mass spectrometry-based proteomics in the clinical setting. The clinical application of nLC/MS will inform clinical decision-making in oncology and other diseases.

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评价“即插即用”纳米流液相色谱系统用于临床FFPE标本的MS-based蛋白质组学表征。

导读:在过去的5年里，由于技术的进步和样品收集的改进，以及用于临床试验的生物银行，福尔马林固定石蜡包埋(FFPE)肿瘤组织标本的蛋白质组学分析引起了人们的兴趣。然而，对这些标本进行临床蛋白质组学的实际实施受到繁琐的样品制备步骤和较长的仪器获取时间的阻碍。涉及领域:为了推进定量蛋白质组学的临床应用，我们比较了领先的商用纳米流液相色谱(nLC)系统的性能(基于文献综述)，Easy-nLC 1200 (Thermo Fisher Scientific, Waltham, MA, usa)和Evosep One HPLC (Evosep Biosystems, Odense, Denmark)。我们在两种LC系统上以相似的梯度测量了21个生物重复的ffpe组织消化物，同时保持柱上量(1µg总蛋白)和单次数据依赖获取的MS/MS方法不变。专家意见:总体而言，Evosep One促进了稳健和敏感的高通量样品采集，使其适用于临床质谱。我们发现Evosep One是在临床环境中定位基于质谱的蛋白质组学的有用平台。nLC/MS的临床应用将为肿瘤及其他疾病的临床决策提供依据。

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来源期刊

Expert Review of Proteomics 生物-生化研究方法

CiteScore

7.60

自引率

0.00%

发文量

审稿时长

6-12 weeks

期刊介绍： Expert Review of Proteomics (ISSN 1478-9450) seeks to collect together technologies, methods and discoveries from the field of proteomics to advance scientific understanding of the many varied roles protein expression plays in human health and disease. The journal coverage includes, but is not limited to, overviews of specific technological advances in the development of protein arrays, interaction maps, data archives and biological assays, performance of new technologies and prospects for future drug discovery. The journal adopts the unique Expert Review article format, offering a complete overview of current thinking in a key technology area, research or clinical practice, augmented by the following sections: Expert Opinion - a personal view on the most effective or promising strategies and a clear perspective of future prospects within a realistic timescale Article highlights - an executive summary cutting to the author''s most critical points.