| Title |
HRaDeX: R package and web server for computing high-resolution deuterium uptake rates for HDX-MS data |
| Authors |
Puchała, Weronika ; Kistowski, Michał ; Zhukova, Liliya ; Burdukiewicz, Michal Jan ; Dadlez, Michał |
| DOI |
10.1021/acs.jproteome.4c00700 |
| Full Text |
|
| Is Part of |
Journal of proteome research.. Washington : American Chemical Society. 2025, vol. 24, iss. 4, p. 1688-1700.. ISSN 1535-3893. eISSN 1535-3907 |
| Keywords [eng] |
HDX-MS ; hydrogen−deuterium exchange ; structural proteomics ; web server |
| Abstract [eng] |
Hydrogen-deuterium exchange monitored by mass spectrometry (HDX-MS) is a well-established and powerful technique used to study protein dynamics and stability by capturing local and global unfolding events in protein structures. However, in this technique, obtaining region-specific information requires proteolytic digestion that breaks the protein into peptide fragments, causing the HDX data to reflect averages over these fragments rather than individual amino acids. We propose a new computational method that provides deuterium uptake kinetic parameters with high resolution, considering deuterium uptake trajectories of superimposed peptides. Our algorithm, HRaDeX, is available as a web server and an R package capable of processing data from single-state and comparative HDX-MS studies. Utilizing eight benchmark data sets, we demonstrate that HRaDeX reaches an average root-mean-square error of 7.15% in the reconstitution of experimental normalized deuterium uptake curves. |
| Published |
Washington : American Chemical Society |
| Type |
Journal article |
| Language |
English |
| Publication date |
2025 |
| CC license |
|
