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Jonathan Krieger is the Head of Research at Bruker ProteoScape, where he has been contributing significantly since November 2021. His expertise spans various aspects of computational proteomics. Prior to his current role, Jonathan served as the Applications Manager and Core Facility Manager at Bioinformatics Solutions Inc., the creators of PEAKS software. He also gained valuable experience at the SPARC BioCentre, the core Mass Spectrometry facility at SickKids hospital. Based in Toronto, Canada, Jonathan's research at Bruker encompasses software development, data science, and computational proteomics.
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Combining Data-Independent Acquisition (DIA) with Trapped Ion Mobility Separation (TIMS) reduces sample complexity by providing an additional dimension of separation, thereby increasing overall system peak capacity. This scan mode, termed dia-PASEF, employs fixed quadrupole isolation windows for ion selection in both the m/z and mobility panes. To further enhance the analytical performance, diagonal-PASEF has been developed, which optimizes the acquisition of the precursor ion cloud by continuously tracking its diagonal shape.
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Although several data processing software tools currently support this innovative scan mode, none specifically focus on targeted data extraction. We present the implementation of diagonal-PASEF data processing in Skyline, demonstrating exceptional performance for targeted quantitation. The integration of diagonal-PASEF data acquisition with Skyline data processing shows significant promise for targeted quantitation due to its straightforward method setup and remarkably short cycle times.
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