Copyright Notice

compareMS2 is Copyright (C) 2010 Magnus Palmblad

compareMS2 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.

About compareMS2

compareMS2 is a simple tool developed to compare, globally, all MS/MS spectra between two datasets (in Mascot Generic Format or MGF) acquired under similar conditions. This may be useful for differentiating samples or molecular phylogenetics based on shared peptide sequences quantified by the number or frequency of highly similar tandem mass spectra. The similarity between a pair of tandem mass spectra is calculated essentially as in SpectraST [see Lam et al. Proteomics 2007, 7, 655-667 (2007)].

This is a simplified, minimum, version of compareMS2. A more advanced version of compareMS2 with several experimental (non-stable) features is available upon request. These features include smoothing (windowing) the spectra before taking the dot product, extraction and use of retention times, working with mzXML/mzML instead of MGF etc.

Download compareMS2 here. (Right-click and choose "Save Link As...".)

Compiling compareMS2

Compile compareMS2 with: gcc -o compareMS2 compareMS2.c under GNU/Linux or Microsoft Windows with Cygwin or MinGW.

Using compareMS2

Usage: compareMS2 -1 <first dataset filename> -2 <second dataset filename> [-o <output filename> -p <precursor tolerance>]