pepAlign
Copyright Notice
pepAlign is Copyright (C) 2001- Magnus Palmblad and Jeroen de Bruin
pepAlign 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 pepAlign
pepAlign aligns LC-MS/MS data, through peptide identifications, with accurate mass LC-MS data, for instance from a TOF, Orbitrap or FTICR mass spectrometer. This version of pepAlign is primarily meant
for inclusion and use with scientific workflow managers such as Taverna.
Download pepAlign here. (Right-click and choose "Save Link As...".)
Compiling pepAlign
Compile pepAlign with: gcc -O3 -o pepAlign pepAlign.c -lm
Using pepAlign
Usage: pepAlign -p <pepXML file to be aligned> -m <accurate mass LC-MS data in mzXML> -e <max. mass measurement error>
-R <first mzXML scan>,<last mzXML scan>
-P <first pepXML scan>,<last pepXML scan>
-L <lower peptide score bound> -U <upper peptide bound> -t <threshold score variable (probability, E-value...)>
-M <alignment mode (time/scan)>
[-o <output file>]
magnus.palmblad@gmail.com