Automating Data Analysis for Hydrogen/Deuterium Exchange Mass Spectrometry Using Data-Independent Acquisition Methodology

Authors

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

Publication Date

3-11-2024

Journal

Nature Communications

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.

Keywords

Animals, Deuterium, Deuterium Exchange Measurement, Hydrogen, Tandem Mass Spectrometry, Peptides, Mammals

DOI

10.1038/s41467-024-46610-3

PMID

38467655

PMCID

PMC10928179

PubMedCentral® Posted Date

March 2024

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes