Copyright Notice

recalibrate_using_MSMS is Copyright (C) 2005- Magnus Palmblad

recalibrate_using_MSMS 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 recalibrate_using_MSMS

recalibrate_using_MSMS 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 recalibrate_using_MSMS here.
recalibrate_using_MSMS also needs something like combine_masslist_and_Mascot_for_recalibration (available here) and a filter to format Mascot output (an example in AWK is availble here). Any search engine can be used though.

Compiling recalibrate_using_MSMS

Compile recalibrate_using_MSMS with: gcc -o recalibrate_using_MSMS recalibrate_using_MSMS.c -lm -lgsl -lgslcblas

Using recalibrate_using_MSMS

Usage: recalibrate_using_MSMS <2D peaklist> <calibration file> <offset> <modifications> <output> where <2D peaklist> is a combined peaklist file from a 2D dataset (e.g. from mipp2D_to_peaklist) and <calibration file> is the calibration file output form combine_masslist_and_Mascot_for_recalibration with retention as row numbers and <offset> is an offset between retention times in the calibration file and the peaklist.