Proteomic analysis using capillary electrophoresis hyphenated with high resolution mass spectrometry: comparison of two coupling interfaces

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. The use of dynamic pH junction allowed the identification of more peptides and proteins compared to conventional injections. The sheath liquid composition was also optimized in order to enhance signal intensity. A nanoflow sheath liquid interface (EMASS-II) was compared to the traditional coaxial sheath liquid interface (Triple tube) in terms of number of identified peptides and proteins as well as in terms of sensitivity (peak area and peak height). 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 a factor of 4 and 6-fold, respectively, compared to the Triple tube