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In a recent presentation at the World HUPO Congress 2024, Ludwig Sinn from the Ralser lab shared exciting advancements in proteomics research, focusing on the innovative ZT Scan DIA acquisition modes developed in collaboration with SCIEX. Let us explore the key highlights and benefits of this innovative technology.

The evolution of SWATH DIA

Ludwig began by discussing the evolution from the traditional SWATH DIA approach to the more advanced Zeno trap-enabled scanning DIA (ZT Scan DIA). While SWATH DIA has been a cornerstone in proteomics, it has limitations, particularly the time-consuming filling and emptying of the collision cell for each SWATH isolation window. ZT Scan DIA addresses this by leveraging a sliding Q1 quadrupole, which enhances specificity and speed by correlating fragment ions across the scanning quadrupole dimension.

Introducing the ZenoTOF system family

When SCIEX launched the ZenoTOF 7600 system in 2021, it came with two significant innovations:

1. The electron-activated dissociation (EAD) collision cell allows versatile fragmentation mechanisms.
2. The Zeno trap: trapping ions to improve the duty cycle in TOF MS/MS scans significantly boosts low-abundance signals’ intensity.

These enhancements translated to better coverage of low-abundance ions, increased sensitivity and more robust system performance.

Then, SCIEX introduced Zeno SWATH DIA, capitalizing on the Zeno trap capabilities and significant sensitivity gains to MS/MS data acquisition. Zeno SWATH DIA could reveal tens, hundreds and even thousands more identified and quantified analytes in a shorter time and with higher precision.

Combining the scanning quadrupole dimension with Zeno trapping

The natural progression was to combine the benefits of the scanning quadrupole dimension with the Zeno trap capabilities in the new ZenoTOF 7600+ system. Ludwig shared initial data showing impressive gains in identification consistency and data completeness, particularly at lower loads and faster gradients. For example, using a mere five nanograms of K562 proteome digestion standard, the ZT Scan DIA approach showed a significant increase in IDs compared to Zeno SWATH DIA.

Performance across different gradients and loads

Ludwig’s team rigorously tested ZT Scan DIA across separation speeds and loading inputs. The results were compelling, with ZT Scan DIA consistently outperforming Zeno SWATH DIA, especially at lower loads and faster gradients. This makes ZT Scan DIA an excellent choice for high-throughput proteomics, offering speed and depth without compromising quantitative precision.

Advancing quantitative precision

One of the standout features of ZT Scan DIA is its ability to maintain high quantitative precision. Ludwig highlighted that ZT Scan DIA effectively removes ratio compression and quantitative bias, providing reliable results across a wide dynamic range. This was evident in their LFQ benchtop test analysis, where ZT Scan DIA outperformed Zeno SWATH DIA in terms of quantitative precision.

Exploring glycoproteomics with ZT Scan DIA

Ludwig also touched upon the potential of ZT Scan DIA in the emerging field of glycoproteomics. By leveraging the scanning quadrupole dimension to identify oxonium ions, the team could achieve high-resolution analysis of glycopeptide features, making ZT Scan DIA a powerful tool for studying glycoproteins.

Conclusion

Ludwig’s presentation at the World HUPO Congress 2024 highlighted the remarkable advancements brought by ZT Scan DIA. With enhanced specificity, speed and quantitative precision, ZT Scan DIA is set to revolutionize proteomics research, offering unparalleled performance for high-throughput and detailed analyses.

Watch Ludwig’s presentation here.

Related links:

Technical overview: Continuing the data-independent acquisition (r)evolution: Introducing ZT Scan DIA for quantitative proteomics

Nature Portfolio article: Fast, sensitive or accurate? Proteomics researchers can now have all three.