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DOE OSTI · 2470753

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

Filandr, Frantisek·Sarpe, Vladimir·Raval, Shaunak·Crowder, D. Alex·Khan, Morgan F.·Douglas, Pauline·Coales, Stephen·Viner, Rosa·Syed, Aleem·Tainer, John A.·Lees-Miller, Susan P.·Schriemer, David C.
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Abstract

We present a hydrogen/deuterium exchange workflow coupled to tandem mass spectrometry (HX-MS 2 ) that supports the acquisition of peptide fragment ions alongside their peptide precursors. The approach enables true auto-curation 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 MS 1 -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-MS 2 straightforward. Importantly, we find that HX-DIA enables a proteomics-grade approach and wide-spread applications. Considerable time is saved through auto-curation 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, Frantisek, Sarpe, Vladimir, Raval, Shaunak, Crowder, D. Alex, Khan, Morgan F., Douglas, Pauline, Coales, Stephen, Viner, Rosa, Syed, Aleem, Tainer, John A., Lees-Miller, Susan P., Schriemer, David C.. 2024-03-11. Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology. https://doi.org/10.1038/s41467-024-46610-3

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