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

ABSTRACT: We present 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-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 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-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.

SUBMITTER: Filandr F

PROVIDER: S-EPMC10928179 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

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

Filandr Frantisek F Sarpe Vladimir V Raval Shaunak S Crowder D Alex DA Khan Morgan F MF Douglas Pauline P Coales Stephen S Viner Rosa R Syed Aleem A Tainer John A JA Lees-Miller Susan P SP Schriemer David C DC

Nature communications 20240311 1

We present a hydrogen/deuterium exchange workflow coupled to tandem mass spectrometry (HX-MS<sup>2</sup>) 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<sup>1</sup>-based deuteration calculations. The high redundancy provided by the fragments su ...[more]

PMID: 38467655

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Project description:Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to interrogate protein structure and dynamics. With the ability to study almost any protein without a size limit, including intrinsically disordered ones, HDX-MS has shown fast growing importance as a complement to structural elucidation techniques. Current experiments compare two or more related conditions (sequences, interaction partners, excipients, conformational states, etc.) to determine statistically significant differences at a number of fixed time points and highlight areas of changed structural dynamics in the protein. The work presented here builds on the fundamental research performed in the early days of the technique and re-examines exchange rate calculations with the aim of establishing HDX-MS as an absolute and quantitative, rather than relative and qualitative, measurement. We performed millisecond HDX-MS experiments on a mixture of three unstructured peptides (angiotensin, bradykinin, and atrial natriuretic peptide amide rat) and compared experimental deuterium uptake curves with theoretical ones predicted using established exchange rate calculations. With poly-dl-alanine (PDLA) commonly used as a reference,, we find that experimental rates are sometimes faster than theoretically possible, while they agree much better, and are never faster, with the fully unstructured trialanine peptide (3-Ala). Molecular dynamics (MD) simulations confirm the high helical propensity of the longer and partially structured PDLA peptides, which need as few as 15 residues to form a stable helix and are therefore not suitable as an unstructured reference. Reanalysis of previously published data by Weis et al. at 100 mM NaCl however still shows a discrepancy with predictions based on 3-Ala in the absence of salt, highlighting the need for a better understanding of salt effects on exchange rates. Such currently unquantifiable salt effects prevent us from proposing a comprehensive, universal calibration framework at the moment. Nevertheless, an accurate recalibration of intrinsic exchange rate calculations is crucial to enable kinetic modeling of the exchange process and to ultimately allow HDX-MS to move toward a direct link with atomistic structural models.

Dataset Information

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

Publications

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

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