Capillary electrophoresis tandem mass spectrometry (CE-MS/MS) is an interesting tool for proteomic analysis as the separation principle is orthogonal to liquid chromatography tandem mass spectrometry (LC-MS/MS). The combination of both techniques can bring complementary information to enlarge proteome coverage. In this study, sample preconcentration techniques were investigated in order to improve sample loading and therefore sensitivity. Dynamic pH junction (DPJ) was found to be the most interesting approach by using 200 mM ammonium acetate (NH4Ac) adjusted to pH 10.0 as sample matrix. The use of DPJ allowed the identification of more peptides and proteins compared to conventional injections. Moreover, the sheath liquid (SL) composition was optimized in order to enhance signal intensity. A nanoflow SL interface (EMASS-II) was compared to the traditional coaxial SL interface (Triple tube) in terms of number of identified and proteins as well as detection sensitivity (peak area and peak height). MS acquisition was performed using both data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes. The results showed that the combined use of these two acquisition modes provided additional information in terms of identification. Moreover, the use of EMASS-II interface allowed the identification of approximately two times more peptides and proteins. Besides, there was an improvement in sensitivity using EMASS-II as peak height and peak area were improved by 4 and 6-fold, respectively, compared to the Triple tube. Altogether, by combining an efficient sample preconcentration method, a nanoflow CE-MS interface and a hybrid ion-mobility qTOF mass spectrometer, a satisfying sequence coverage was obtained by analyzing 1 µg of E. coli proteome digest.

中文翻译：

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质谱联用毛细管区带电泳进行蛋白质组学分析：两个偶联界面的优化和比较。

毛细管电泳串联质谱法（CE-MS / MS）是一种有趣的蛋白质组学分析工具，其分离原理与液相色谱串联质谱法（LC-MS / MS）正交。两种技术的结合可以带来补充信息，以扩大蛋白质组覆盖范围。在这项研究中，对样品预浓缩技术进行了研究，以提高样品装载量并因此提高灵敏度。动态pH结（DPJ）被发现是最有趣的方法，它使用200 mM的乙酸铵（NH4Ac）调节至pH 10.0作为样品基质。与常规注射相比，使用DPJ可以鉴定更多的肽和蛋白质。此外，优化了鞘液（SL）成分以增强信号强度。将纳流SL接口（EMASS-II）与传统的同轴SL接口（Triple tube）进行了比较，其中包括鉴定出的蛋白质数量以及检测灵敏度（峰面积和峰高）。使用数据相关采集（DDA）和数据独立采集（DIA）模式执行MS采集。结果表明，这两种采集模式的组合使用在识别方面提供了更多信息。而且，使用EMASS-II接口可以识别大约两倍以上的肽和蛋白质。此外，与三重管相比，使用EMASS-II可以提高灵敏度，因为峰高和峰面积分别提高了4倍和6倍。总之，通过结合有效的样品预浓缩方法，