Software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry
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README.md

Deuteros

History

Version 1.07
  • Added number of peptides to Flattened Data Map
  • Upgraded legends on Woods plot
  • Fixed bug with importing data with modifications in difference file
  • Fixed bug with exporting Woods plot without figure legends
  • Fixed bug with y-axis limits for Woods plots

Summary

Software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry

See also: https://www.biorxiv.org/content/early/2018/09/14/417998

Andy M. C. Lau, Zainab Ahdash, Chloe Martens, Argyris Politis

King's College London, Department of Chemistry, Britannia House, 7 Trinity Street, London, SE1 1DB, United Kingdom

Hydrogen deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful technique for interrogating the conformational dynamics of proteins and their complexes. Currently, analysis of HDX-MS data remains a laborious procedure, mainly due to the lack of streamlined software to process the large datasets. We present Deuteros which is a standalone soft-ware designed to be coupled with Waters DynamX HDX data analysis software, allowing the rapid analysis and visualization of data from differential HDX-MS.

Deuteros is available for any machine capable of running MATLAB, and requires Ghostscript for figure exporting.

Ghostscript for Windows: https://www.ghostscript.com/download/gsdnld.html

Ghostscript for Mac: with homebrew installed, use brew install ghostscript

Usage

The easiest method of running Deuteros is to open the Deuteros.m script using MATLAB and press 'Run'. This will initialise the Deuteros GUI directly.

Inputs

XylE WT apo vs E397Q difference.csv                     DynamX 'difference' file
XylE WT apo vs E397Q state.csv                          DynamX 'state' file

Outputs

XylE WT apo vs E397Q difference_peptide_list.csv        List of deprotected and protected peptides  
XylE WT apo vs E397Q difference coverage.pdf            Vector: global coverage
XylE WT apo vs E397Q difference redundancy.pdf          Vector: peptide redundancy
XylE WT apo vs E397Q difference heatmap 5 min.pdf       Vector: heatmap of global deuterium uptake for t=5min
XylE WT apo vs E397Q difference_WoodsPlot.pdf           Vector: grid of Woods plots 
XylE WT apo vs E397Q difference_coverage.pml            PyMOL: coverage data for PDB
XylE WT apo vs E397Q difference_redundancy.pml          PyMOL: redundancy data for PDB 
XylE WT apo vs E397Q difference_uptake...scale.pml      PyMOL: Woods plot data (per timepoint) for PDB

Tutorial Video

Deuteros Tutorial