recal2
Copyright Notice
recal2 is Copyright (C) 2005- Magnus Palmblad
recal2 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 recal2
recal2 recalibrates LC-FTICR-MS datasets using peptides identified by MS/MS as internal calibrants, together with polydimethylcyclosiloxanes, first described in Palmblad et al., Rapid Commun. Mass Spectrom., 20, 3076-3080 (2006).
Download recal2 here.
Using recal2 typically requires a tool such as combine_masslist_and_Mascot_for_recalibration (available here) and a filter to format Mascot output (an example in AWK is availble here). If combining recal2 with chromatographic alignment by msalign, use awk '{print $1, $4}' xxx.alignment > xxx.training to generate the xxx.training file as calibration list for recal2.
Compiling recal2
Compile recal2 with: gcc -o recal2 recal2.c -lm -lgsl -lgslcblas
Using recal2
Usage: recal2 -m <mzXML file> -r <list of calibrants> -o <output> -s <scan range> -b <background> -O <offset> -M <modifications> where <mzXML> is the mzXML file to be recalibrated and <list of calibrants> a list of calibrants in the same format used by rt (see this program). The <offset> is an optional offset between retention times in the calibration file and the peaklist.
magnus.palmblad@gmail.com