Capillary zone electrophoresis-tandem mass spectrometry for in-depth proteomics analysis via data-independent acquisition

IF 3.8 2区化学 Q1 BIOCHEMICAL RESEARCH METHODS Analytical and Bioanalytical Chemistry Pub Date : 2024-08-28 DOI:10.1007/s00216-024-05502-7

Rong Liu, Gang Lu, Xiaozhong Hu, Junhui Li, Zhenbin Zhang, Keqi Tang

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Abstract

A capillary zone electrophoresis (CZE) system was coupled to an Orbitrap mass spectrometer operating in a data-independent acquisition (DIA) mode for in-depth proteomics analysis. The performance of this CZE-DIA-MS system was systemically evaluated and optimized under different operating conditions. The performance of the fully optimized CZE-DIA-MS system was subsequently compared to the one by using the same CZE-MS system operating in a data-dependent acquisition (DDA) mode. The experimental results show that the numbers of identified peptides and proteins acquired in the DIA mode are much higher than the ones acquired in the DDA mode, especially with the small sample loading amount. Specifically, the numbers of identified peptides and proteins acquired in the DIA mode are 1.8-fold and 2-fold higher than the ones acquired in the DDA mode by using 12.5 ng Hela digests. The proteins identified in the DIA mode also cover almost all the proteins identified in the DDA mode. In addition, a potential cancer biomarker protein, carbohydrate antigen 125, undetected in the DDA mode, can be easily identified in the DIA mode even with 12.5 ng Hela digests. The performance of the CZE-DIA-MS system for in-depth proteomics analysis with a limited sample amount has been fully demonstrated for the first time through this study.

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毛细管区带电泳-串联质谱法，通过数据独立采集进行深入的蛋白质组学分析。

将毛细管区带电泳（CZE）系统与 Orbitrap 质谱仪耦合，以数据独立采集（DIA）模式进行深入的蛋白质组学分析。在不同的操作条件下，对该 CZE-DIA-MS 系统的性能进行了系统评估和优化。随后，将经过全面优化的 CZE-DIA-MS 系统的性能与在数据依赖采集（DDA）模式下运行的相同 CZE-MS 系统的性能进行了比较。实验结果表明，在 DIA 模式下获得的肽段和蛋白质鉴定数量远远高于在 DDA 模式下获得的肽段和蛋白质鉴定数量，尤其是在样品装载量较小的情况下。具体来说，使用 12.5 毫微克的 Hela 消化液，DIA 模式获得的鉴定肽段和蛋白质数量分别是 DDA 模式的 1.8 倍和 2 倍。在 DIA 模式下鉴定的蛋白质也几乎涵盖了在 DDA 模式下鉴定的所有蛋白质。此外，在 DDA 模式下未检测到的潜在癌症生物标志蛋白--碳水化合物抗原 125，即使使用 12.5 毫微克的 Hela 消化液，也能在 DIA 模式下轻松鉴定出来。这项研究首次充分展示了 CZE-DIA-MS 系统在有限样品量下进行深入蛋白质组学分析的性能。

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来源期刊

Analytical and Bioanalytical Chemistry 化学-分析化学

CiteScore

8.00

自引率

4.70%

发文量

638

审稿时长

2.1 months

期刊介绍： Analytical and Bioanalytical Chemistry’s mission is the rapid publication of excellent and high-impact research articles on fundamental and applied topics of analytical and bioanalytical measurement science. Its scope is broad, and ranges from novel measurement platforms and their characterization to multidisciplinary approaches that effectively address important scientific problems. The Editors encourage submissions presenting innovative analytical research in concept, instrumentation, methods, and/or applications, including: mass spectrometry, spectroscopy, and electroanalysis; advanced separations; analytical strategies in “-omics” and imaging, bioanalysis, and sampling; miniaturized devices, medical diagnostics, sensors; analytical characterization of nano- and biomaterials; chemometrics and advanced data analysis.