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27 Feb 2014 (Updated )

QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with isotopic fine structure

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Hydrogen-deuterium exchange coupled to mass spectrometry permits analysis of structural dynamics, stability, and molecular interactions of proteins. Resolving isotopic fine structure during mass spectrometry has been recently demonstrated to allow direct detection and quantification of deuterium incorporation distinct from peaks corresponding to non-deuterium incorporated natural abundance heavy isotopomers. Here, we present a graphical tool that allows for a rapid and automated estimation of deuterium incorporation from a spectrum with isotopic fine structure resolved. Given a peptide sequence or elemental formula, the distribution of deuterium-associated mass-to-charge ratios is calculated based on a particular charge state corresponding to the molecular species resolved in an input mass spectrum. Peaks in the input mass spectrum fitting within bins corresponding to these values are used to determine the distribution of deuterium incorporated. A theoretical spectrum can then be calculated within the program based on the estimated distribution of deuterium incorporated to confirm interpretation of the spectrum. Deuterium incorporation can also be detected for ion signals without a priori specification of an elemental formula, permitting detection of exchange in complex samples of unidentified material such as natural organic matter.
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Required Products Bioinformatics Toolbox
Statistics and Machine Learning Toolbox
MATLAB release MATLAB 8.3 (R2014a)
MATLAB Search Path
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27 Feb 2014 1.1

Added link to manual.

17 Jun 2014 1.2

Fixed an error where m/z values were displaying incorrectly after exchange calculation.

22 Aug 2014 1.3

Fixing file attachments

07 Oct 2014 1.4

+ Digest Tool, Preprocessing Tool.
+ Manual in Help.
+ Editable peak picking thresholds, new zoom features.
+ Displays observed vs calculated m/z, corresponding mass error.
+ Reformatted exported exchange results, spectrum can be exported as graphic.

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