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

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

doi:10.1038/s41467-024-46610-3

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

Nat Commun. 2024 Mar 11;15(1):2200. doi: 10.1038/s41467-024-46610-3.

Authors

Frantisek Filandr^#¹, Vladimir Sarpe^#¹, Shaunak Raval^#^{1

2}, D Alex Crowder¹, Morgan F Khan¹, Pauline Douglas¹, Stephen Coales³, Rosa Viner⁴, Aleem Syed⁵, John A Tainer^{6

7}, Susan P Lees-Miller¹, David C Schriemer^{8

9}

Affiliations

¹ Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada.
² Department of Chemistry, University of Calgary, Calgary, AB, T2N 4N1, Canada.
³ Trajan Scientific & Medical - Raleigh, Morrisville, NC, USA.
⁴ Thermo Fisher Scientific, San Jose, CA, USA.
⁵ Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
⁶ Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
⁷ Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
⁸ Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada. [email protected].
⁹ Department of Chemistry, University of Calgary, Calgary, AB, T2N 4N1, Canada. [email protected].

^# Contributed equally.

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.

MeSH terms

Animals
Deuterium / chemistry
Deuterium Exchange Measurement* / methods
Hydrogen* / chemistry
Mammals
Peptides / chemistry
Tandem Mass Spectrometry / methods

Substances

Deuterium
Hydrogen
Peptides

Abstract

MeSH terms

Substances

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