As the field of quantitative proteomics continues to evolve, larger biological cohorts are being studied, often using precious samples obtained from biobanks or other difficult-to-obtain sources. This creates 2 workflow requirements: the need to acquire quantitative data on the digested samples faster and the need to use smaller amounts of sample. For these types of studies, data-independent acquisition (DIA) continues to grow as the workflow of choice for reproducible quantitative analysis of large numbers of proteins from a proteomic sample.
Previously, the combination of fast microflow chromatography and SWATH DIA enabled large numbers of proteins to be quantified from complex proteomics samples at very high rates, up to 100 samples per day.1 The activation of the Zeno trap has been shown to improve MS/MS sensitivity for peptide quantification by improving the duty cycle of the ZenoTOF 7600 system.2,3 Coupling SWATH DIA with Zeno MS/MS and microflow LC therefore has the potential to significantly enhance a core quantitative proteomics workflow.
Here, the use of microflow chromatography in combination with Zeno SWATH DIA was optimized and evaluated compared to traditional SWATH DIA to characterize the impact of the Zeno MS/MS sensitivity gains. Four different gradient lengths (5, 10, 20 and 45 minutes) were tested to cover a range of application needs.
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