Computationally Analyzing Mass Spectra of Hydrogen Deuterium Exchange Experiments

Kevin S. Drew. 29 August, 2005.
Communicated by Janos Simon.


Hydrogen deuterium exchange (HDX) using Mass Spectrometers (MS) has become a useful experiment in Proteomics which can probe structural characteristics of proteins. The data analysis of such experiments can be difficult and laborious to do by hand. First, peptides of the protein must first be matched to their corresponding mass spectrum. Second, mass spectra must be analyzed to determine the amount of deuterium in the peptides. Two computer algorithms which automate much of the data analysis of HDX experiments are described. The first, SpectralMatch, matches peptide mass spectra to the corresponding sequence in the subject protein. The second algorithm, HDXRates, computes the amount of deuterium in a peptide represented by a given spectrum. The two algorithms are shown to work on MS data from a quadropole time of flight mass spectrometer. Runtime analysis are shown for each algorithm and time trials are shown for implementations of the two algorithms.

Original Document

The original document is available in PDF (uploaded 29 August, 2005 by Janos Simon).