Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology

Filandr, F.; Sarpe, V.; Raval, S.; Crowder, D. A.; Khan, M. F.; Douglas, P.; Coales, S.; Viner, R.; Syed, A.; Tainer, J. A.; Lees-MIller, S. P.; Schriemer, D. C.

doi:10.1101/2023.08.25.554852

bioRxiv · 10.1101/2023.08.25.554852

Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology

Filandr, F.·Sarpe, V.·Raval, S.·Crowder, D. A.·Khan, M. F.·Douglas, P.·Coales, S.·Viner, R.·Syed, A.·Tainer, J. A.·Lees-MIller, S. P.·Schriemer, D. C.

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Abstract

We developed a hydrogen/deuterium exchange workflow coupled to tandem mass spectrometry (HX-MS2) that supports the acquisition of peptide fragment ions alongside their peptide precursors. The approach enables true auto-validation of HX data by mining a rich set of deuterated fragments, generated by collisional-induced dissociation (CID), to simultaneously confirm the peptide ID and authenticate MS1-based deuteration calculations. The high redundancy provided by the fragments supports a confidence assessment of deuterium calculations using a combinatorial strategy. The approach requires data-independent acquisition (DIA) methods that are available on most MS platforms, making the switch to HX-MS2 straightforward. Importantly, we find that HX-DIA enables a proteomics-grade approach and wide-spread applications. Considerable time is saved through auto-validation and complex samples can now be characterized and at higher throughput. We illustrate these advantages in a drug binding analysis of the ultra-large protein kinase DNA-PKcs, isolated directly from mammalian cells.

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Filandr, F., Sarpe, V., Raval, S., Crowder, D. A., Khan, M. F., Douglas, P., Coales, S., Viner, R., Syed, A., Tainer, J. A., Lees-MIller, S. P., Schriemer, D. C.. 2023-08-26. Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology. https://doi.org/10.1101/2023.08.25.554852

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