Automated injection of uncleaned samples using a ten-port switching valve and a strong cation-exchange trap column for proteome analysis

Nanoliter flow rate is optimum for separation in capillary column liquid chromatography coupled with tandem mass spectrometry (μHPLC–MS/MS). In order to develop a high-performance automated proteome analysis system allowing direct injection sample containing detergents, the influence of void volume varied from 0 to 5 μL on the separation performance and proteomic coverage of sample injection system using strong cation-exchange (SCX) trap column was investigated, it was found the void volume hardly affects the separation performance by using SCX trap column. Thus, a fully automated sample injection system using SCX trap column and ten-port switching valve was established for efficient shotgun proteome analysis. In this system, a nanoflow switching valve and a microtee were used to connect the SCX trap and analytical columns, and the uncleaned samples of proteolytic digests containing contaminants could be directly injected with minor influence on the separation performance, which was demonstrated to be a useful strategy in proteome analysis.