Two-dimensional nano-liquid chromatography–mass spectrometry system for applications in proteomics

This work demonstrates the development of a method for the analysis of complex proteome samples by two-dimensional nano-liquid chromatography–mass spectrometry. This approach includes strong cation-exchange, sample enrichment, reversed-phase chromatography and nanospray ion trap mass spectroscopy with data dependent tandem mass spectrometry spectra acquisition, and subsequent database search. The new methodology was first evaluated using standard protein digest samples. Finally, data for the analysis of a total Escherichia coli proteome are provided.