Copyright Notice

AUTOHD is Copyright (C) 2000 Magnus Palmblad

AUTOHD is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.


AUTOHD identifies and characterizes peptides or proteins from hydrogen/deuterium exchange experiments analyzed by mass spectrometry using rapid calculation of isotopic distributions to fit a model for deuterium exchange with amide hydrogens. The model used for amide hydrogen/deuterium exchange could be replaced with any model for any other isotope. The algorithm was first presented at the Asilomar Conference in 2000 and later described in Palmblad et al., J. Am. Soc. Mass Spectrom., 12(11), 1153-1162 (2001). Originally, AUTOHD was reposited here. Although this site is no longer maintained, it contains a tutorial and some sample data.

Download AUTOHD here. AUTOHD also uses the FFTW library for the rapid calculation of isotopic distributions.

Compiling AUTOHD

Compile AUTOHD with: gcc -o autohd autohd.c -lrfftw -lfftw -lm


Usage: AUTOHD <peaklist> <theoretical peptides> <sequence> <max charge> <fraction D> [<RL value threshold>]

where <peaklist> is a peak list from a mass spectrum, the <theoretical peptides> a list of theoretical peptides from the digest and <sequence> the full protein sequence in FASTA format. The <fraction D> is the fraction incorporated deuterium in slowly exchanging hydrogens (C-H). The formats are easily derived by inspecting the source code, and more information on using AUTOHD is still available here.