Faculty, Staff and Student Publications
Publication Date
3-11-2024
Journal
Nature Communications
DOI
10.1038/s41467-024-46610-3
PMID
38467655
PMCID
PMC10928179
PubMedCentral® Posted Date
March 2024
PubMedCentral® Full Text Version
Post-print
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
Published Open-Access
yes
Recommended Citation
Filandr, Frantisek; Sarpe, Vladimir; Raval, Shaunak; et al., "Automating Data Analysis for Hydrogen/Deuterium Exchange Mass Spectrometry Using Data-Independent Acquisition Methodology" (2024). Faculty, Staff and Student Publications. 2163.
https://digitalcommons.library.tmc.edu/uthgsbs_docs/2163
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