HaDeX: an R Package and Web-server for Analysis of Data from Hydrogen-deuterium Exchange Mass Spectrometry Experiments

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2020 Jun 25

PMID 32579220

Citations 11

Authors

Weronika Puchala

Michal Burdukiewicz

Michal Kistowski

Katarzyna A Dabrowska

Aleksandra E Badaczewska-Dawid

Dominik Cysewski

Michal Dadlez

Affiliations

Soon will be listed here.

Abstract

Motivation: Hydrogen-deuterium mass spectrometry (HDX-MS) is a rapidly developing technique for monitoring dynamics and interactions of proteins. The development of new devices has to be followed with new software suites addressing emerging standards in data analysis.

Results: We propose HaDeX, a novel tool for processing, analysis and visualization of HDX-MS experiments. HaDeX supports a reproducible analytical process, including data exploration, quality control and generation of publication-quality figures.

Availability And Implementation: HaDeX is available primarily as a web-server (http://mslab-ibb.pl/shiny/HaDeX/), but its all functionalities are also accessible as the R package (https://CRAN.R-project.org/package=HaDeX) and standalone software (https://sourceforge.net/projects/HaDeX/).

Supplementary Information: Supplementary data are available at Bioinformatics online.

Citing Articles

Computational Tools for Hydrogen-Deuterium Exchange Mass Spectrometry Data Analysis.

Stofella M, Grimaldi A, Smit J, Claesen J, Paci E, Sobott F Chem Rev. 2024; 124(21):12242-12263.

PMID: 39481095 PMC: 11565574. DOI: 10.1021/acs.chemrev.4c00438.

HDXBoxeR: an R package for statistical analysis and visualization of multiple Hydrogen-Deuterium Exchange Mass-Spectrometry datasets of different protein states.

Janowska M, Reiter K, Magala P, Guttman M, Klevit R Bioinformatics. 2024; 40(8).

PMID: 39078213 PMC: 11310453. DOI: 10.1093/bioinformatics/btae479.

Deciphering the dual nature of nesfatin-1: a tale of zinc ion's Janus-faced influence.

Lenda R, Zhukova L, Ozyhar A, Bystranowska D Cell Commun Signal. 2024; 22(1):298.

PMID: 38812013 PMC: 11134965. DOI: 10.1186/s12964-024-01675-x.

Recruitment of trimeric eIF2 by phosphatase non-catalytic subunit PPP1R15B.

Fatalska A, Hodgson G, Freund S, Maslen S, Morgan T, Thorkelsson S Mol Cell. 2023; 84(3):506-521.e11.

PMID: 38159565 PMC: 7615683. DOI: 10.1016/j.molcel.2023.12.011.

Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein.

Jelen M, Grochowina I, Grabinska-Rogala A, Ciesielski S, Dabrowska K, Tomiczek B J Mol Biol. 2023; 435(21):168283.

PMID: 37730084 PMC: 11457148. DOI: 10.1016/j.jmb.2023.168283.

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