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Assessing a commercial capillary electrophoresis interface (ZipChip) for shotgun proteomi applications

Capillary electrophoresis coupled electrospray ionization mass spectrometry (CE-MS) has long existed as a theoretical alternative to liquid chromatography coupled mass spectrometry (LC-MS). Until recently, however, the coupling of these technologies has occupied only a small niche within specific applications. A recent innovation in CE-MS is the ZipChip interface system from 908 devices that was pioneered by the Ramsay lab at NC State. This newly available source offers advantages over previous CE-MS interfaces including both relative ease of use and direct compatibility to thousands of mass spectrometers currently in use throughout the world with no hardware alterations. The ZipChip CE-MS has been demonstrated in recent studies to provide high resolution and rapid separations for the analysis of intact proteins, glycoproteins and glycosylated peptides, with more applications likely on the way. In this study we assess the capabilities of the ZipChip system in the context of high throughput global shotgun proteomics experiments. We find that on a high field Orbitrap system we can repeatedly identify as many as 800 unique protein groups in an experiment using a run time of 12 minutes. We find the ZipChip CE-MS system to be widely applicable for both data dependent and data independent acquisition experiments as well as targeted experiments. We conclude that the ZipChip is an attractive alternative solution to traditional nanoflow ESI-MS/MS for the analysis of the genomes of single celled organisms and for offline fractionation of eukaryotic proteomes.