DEX

Abstract | Example Results | Documentation | Get DEX | References

Abstract

DEX (Deconvolution of EXchange data) is a complete package for calculating the backbone amide exchange populations of Hydrogen/Deuterium exchange (H/D exchange) experiments from high resolution mass spectrometry data. This determination is accomplished by extracting a calculated natural isotopic profile for a peptide using a deconvolution calculation to reveal the level of deuteration present. If a fast exchanging side chain deuteration profile is also present (as in MALDI-TOF), this profile may also be removed by the deconvolution. DEX is written in ANSI C/C++ languages, and the source code is available. It runs in a command line environment, and executes the calculations in seconds. It is capable of high-throughput calculation, and greatly improves the data collection process over simpler methods. Included in the package are programs to automatically evaluate the deconvoluted results by visual inspection, population weights or centroids. This program will handle both singly charged species from MALDI-TOF as well as multiply charged species from ESI-TOF and other instruments.

DEX is described in the publication Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments 1 by Hotchko et. al 2006, who wrote the program along with Lynn Ten Eyck.


Example Results

Deconvolution of an undeuterated sample (B) by the theoretical natural isotope profile (A) reveals a single peak at the monoisotopic mass (C). All graphs were produced with the program GRACE.
(A) A deuterated mass envelope. (B) Total deuteration profile consisting of side chain and backbone amide deuterons. (C) Backbone amide deuteration shows only populations with 0 and 1 sites. (D) Reconstructed mass envelope spectra shows accurate modeling of all parts (isotopic distribution, sidechain and backbone exchange profiles) of the original spectrum (part A).


Documentation


Get DEX

DEX is Free Software in the technical sense as defined by the Free Software Foundation (see Categories of Free and Non-Free Software). DEX is distributed under the terms of the GNU General Public License (GPL). Non-free licenses for DEX are also available that permit different terms of use other than the GPL. Contact Lynn Ten Eyck concerning Non-Free licenses.

San Diego Supercomputer Center-0505
University of California, San Diego
9500 Gilman Drive, La Jolla, CA 92103-8382.

Phone: (858) 534-5141
Fax: (858) 822-3610


A source code distribution is available through the e-mailer responder; you may modify the code under the GNU Public License. Commerical users who do not want to release their software under the GPL (which would require them to release source code and allow free redistribution) should contact Lynn Ten Eyck for more information.

Please cite Hotchko et al. 2006 (reference #1 below) if this software is used for any scientific purpose.

Upon submission of this form, you will receive email instructions on how to get a copy of the DEX source code and binaries.

First name
Last name
Organization
E-mail address


References

[1] Hotchko, M., Komives, E. A., and Ten Eyck, T. F. (2006) "Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments". Protein Sci.15: 583-601.

Other References

[1] Law, D, Hotchko M, and Ten Eyck, T. F. (2005) "Progress in computation and amide hydrogen exchange for prediction of protein - protein complexes". Proteins 60: 302-307.