Improving Spectral Validation Rates in Hydrogen–Deuterium Exchange Data Analysis

2021 ◽  
Author(s):  
Shaunak Raval ◽  
Vladimir Sarpe ◽  
Morgan Hepburn ◽  
D. Alex Crowder ◽  
Terry Zhang ◽  
...  
Keyword(s):  
Data Analysis ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Hydrogen Deuterium ◽  
Exchange Data

scholarly journals HD-eXplosion: visualization of hydrogen–deuterium exchange data as chiclet and volcano plots with statistical filtering

2020 ◽  
Author(s):  
Naifu Zhang ◽  
Xiaohe Yu ◽  
Xinchao Zhang ◽  
Sheena D’Arcy
Keyword(s):  
Source Code ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Web Based ◽  
Data Presentation ◽  
Software Packages ◽  
Volcano Plots ◽  
Hydrogen Deuterium ◽  
Exchange Data ◽  
Publication Quality

Abstract Summary Hydrogen–Deuterium eXchange coupled to mass spectrometry is a powerful tool for the analysis of protein dynamics and interactions. Bottom-up experiments looking at deuterium uptake differences between various conditions are the most common. These produce multi-dimensional data that can be challenging to depict in a single visual format. Each user must also set significance thresholds to define meaningful differences and make these apparent in data presentation. To assist in this process, we have created HD-eXplosion, an open-source, web-based application for the generation of chiclet and volcano plots with statistical filters. HD-eXplosion fills a void in available software packages and produces customizable plots that are publication quality. Availability and implementation The HD-eXplosion application is available at http://hd-explosion.utdallas.edu. The source code can be found at https://github.com/HD-Explosion.

scholarly journals Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability

2015 ◽  
Vol 44 (D1) ◽  
pp. D429-D434 ◽  
Author(s):  
Rita Pancsa ◽  
Mihaly Varadi ◽  
Peter Tompa ◽  
Wim F. Vranken
Keyword(s):  
Protein Folding ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Hydrogen Deuterium ◽  
Exchange Data

scholarly journals Methods for the analysis of high precision differential hydrogen–deuterium exchange data

2011 ◽  
Vol 302 (1-3) ◽  
pp. 59-68 ◽  
Author(s):  
Michael J. Chalmers ◽  
Bruce D. Pascal ◽  
Scooter Willis ◽  
Jun Zhang ◽  
Stephen J. Iturria ◽  
...  
Keyword(s):  
High Precision ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Hydrogen Deuterium ◽  
Exchange Data

Bottom-up hydrogen deuterium exchange mass spectrometry: data analysis and interpretation

The Analyst ◽  
2017 ◽  
Vol 142 (16) ◽  
pp. 2874-2886 ◽  
Author(s):  
Kerene A. Brown ◽  
Derek J. Wilson
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Deuterium Exchange ◽  
Mass Spectrometry Data ◽  
Hydrogen Deuterium Exchange ◽  
Bottom Up ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry ◽  
Hdx Ms

A tutorial review on the fundamentals of HDX-MS with an emphasis on data analysis and interpretation.

Probing the Nature of the Blue-Shifted Intermediate of Photoactive Yellow Protein in Solution by NMR:  Hydrogen−Deuterium Exchange Data and pH Studies†

Biochemistry ◽  
2000 ◽  
Vol 39 (47) ◽  
pp. 14392-14399 ◽  
Author(s):  
C. Jeremy Craven ◽  
Nocky M. Derix ◽  
Johnny Hendriks ◽  
Rolf Boelens ◽  
Klaas J. Hellingwerf ◽  
...  
Keyword(s):  
Deuterium Exchange ◽  
Photoactive Yellow Protein ◽  
Hydrogen Deuterium Exchange ◽  
Hydrogen Deuterium ◽  
Exchange Data
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