There are many powerful workflows available for proteomics research on today’s mass spectrometry systems, depending on project goals. They cover a wide range that includes fully untargeted data-dependent acquisition approaches for protein identification, comprehensive data-independent acquisition strategies for large-scale quantification, and fully targeted quantitative assays for the highest specificity and sensitivity. As proteomics samples are some of the most complex samples analyzed by mass spectrometry, the MS system must be able to collect high-quality MS/MS with high sensitivity at very high acquisition rates, in order to identify large numbers of peptide and protein identifications and quantify large panels of peptides.
The ZenoTOF 7600 system is a QTOF system that can collect high-resolution, high mass accuracy, full-scan MS and MS/MS data at very high acquisition rates. The ZenoTOF 7600 system delivers a ~5-fold gain in MS/MS sensitivity when analyzing peptides using the novel Zeno trap technology (Figure 1). This sensitivity gain is achieved while maintaining high mass accuracy and high resolution in the MS/MS spectra.
This work investigates the impact of this large MS/MS sensitivity gain on protein and peptide identifications, as well as targeted peptide quantitation. Here, information-dependent IDA workflows were developed for four microflow gradient lengths and the impact of Zeno MS/MS was assessed. Also, a large-scale targeted assay for peptides in human plasma was developed to explore the quantitative capability of Zeno MS/MS on the ZenoTOF 7600 system.