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