Rapid Sample Preparation Workflow for Serum Sample Analysis with Different Mass Spectrometry Acquisition Strategies,Analytical Chemistry

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Rapid Sample Preparation Workflow for Serum Sample Analysis with Different Mass Spectrometry Acquisition Strategies
Analytical Chemistry ( IF 6.7 ) Pub Date : 2020-12-29 , DOI: 10.1021/acs.analchem.0c03985
Fenglin Shen _{1,

2} , Yueting Xiong ₁ , Lei Zhang ₁ , Hengchao Li ₃ , Huanhuan Zhao ₁ , Xiaohui Liu _{1,

2} , Pengyuan Yang _{1,

2}

Affiliation

Fast, robust, and high-throughput mass spectrometry-based serum proteomic pipelines have great potential to yield information for biomarker discovery and daily clinical practice. Here, we developed a simple and rapid sample preparation (RSP) workflow by reducing the classical pretreatment time from overnight to less than 1.5 h in an ordinary system. In HeLa cell lysates and serum samples, the number of proteins and tryptic peptides generated using the RSP was comparable to that generated using conventional methods. For fast scanning of the serum proteome, the RSP-supported pipeline could complete a test in less than 2 h with 30 min of LC–MS/MS analysis. Nearly 390 proteins spanning 8 magnitudes of abundance range were identified with high reproducibility, containing over 90 cancer-associated proteins and over 50 FDA-approved biomarkers. For fast assay development, eight candidate biomarker peptides for cardiovascular disease (CVD) were quantified by MRM with high accuracy (CV% <10). After a simple highly abundant protein removal, a deep serum proteome of over 1400 proteins was reached. By analyzing the depleted serum in DIA acquisition mode, over 700 proteins were quantified. The differentially expressed proteins could help us unambiguously distinguish the serum samples from healthy people and patients with pancreatic cancer (PC). Potential biomarkers for PC were also found. The new RSP method, which is rapid and simple, meets the demands of both deep mining and fast analysis of serum proteins. We believe that it will be widely used in serum protein studies and accelerate the transformation from biomarker discovery to clinical application.

中文翻译：

使用不同的质谱采集策略进行血清样品分析的快速样品制备工作流程

基于质谱的快速，强大和高通量的血清蛋白质组学管道具有巨大的潜力，可为生物标记物发现和日常临床实践提供信息。在这里，我们通过在常规系统中将经典的预处理时间从过夜减少到不到1.5小时，从而开发了一种简单而快速的样品制备（RSP）工作流程。在HeLa细胞裂解液和血清样品中，使用RSP产生的蛋白质和胰蛋白酶肽的数量与使用常规方法产生的蛋白质和胰蛋白酶肽的数量相当。为了快速扫描血清蛋白质组，支持RSP的管线可以在不到2小时的时间内完成30分钟的LC-MS / MS分析。经鉴定，具有8个丰度范围的近390种蛋白质具有很高的重现性，其中包含90多种与癌症相关的蛋白质和50多种FDA批准的生物标记。为了快速进行分析开发，通过MRM以高精度（CV％<10）对8种候选心血管疾病生物标志物肽进行了MRM定量。简单去除高度丰富的蛋白质后，即可获得超过1400种蛋白质的深层血清蛋白质组。通过以DIA采集模式分析耗尽的血清，定量了700多种蛋白质。差异表达的蛋白质可以帮助我们明确区分血清样本与健康人和胰腺癌（PC）患者。还发现了潜在的PC生物标志物。快速简便的新RSP方法可满足深度挖掘和血清蛋白快速分析的需求。我们相信它将被广泛用于血清蛋白研究中，并加速从生物标记物发现到临床应用的转化。通过MRM以高准确度（CV％<10）定量了8种候选心血管疾病生物标志物肽（CVD）。简单去除高度丰富的蛋白质后，即可获得超过1400种蛋白质的深层血清蛋白质组。通过以DIA采集模式分析耗尽的血清，定量了700多种蛋白质。差异表达的蛋白质可以帮助我们明确区分血清样本与健康人和胰腺癌（PC）患者。还发现了潜在的PC生物标志物。快速简便的新RSP方法可满足深度挖掘和血清蛋白快速分析的需求。我们相信它将被广泛用于血清蛋白研究中，并加速从生物标记物发现到临床应用的转化。通过MRM以高准确度（CV％<10）定量了8种候选心血管疾病生物标志物肽（CVD）。简单去除高度丰富的蛋白质后，即可获得超过1400种蛋白质的深层血清蛋白质组。通过以DIA采集模式分析耗尽的血清，定量了700多种蛋白质。差异表达的蛋白质可以帮助我们明确区分血清样本与健康人和胰腺癌（PC）患者。还发现了潜在的PC生物标志物。快速简便的新RSP方法可满足深度挖掘和血清蛋白快速分析的需求。我们相信它将被广泛用于血清蛋白研究中，并加速从生物标记物发现到临床应用的转化。

更新日期：2021-01-26

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