msRecal

Copyright Notice

msRecal is Copyright (C) 2001- Magnus Palmblad and Jeroen de Bruin

msRecal 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 msRecal

msRecal recalibrates LC-MS data using peptides identified by MS/MS as internal calibrants. These peptide identifications can be derived from the same dataset, as shown in Palmblad et al. 2006, or by aligning one or more LC-MS/MS datasets to the LC-MS dataset to be calibrated [Palmblad et al. 2009]. This version of msHybrid is primarily meant for inclusion and use with scientific workflow managers such as Taverna.


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

Compiling msRecal

Compile msRecal with: gcc -O3 -o msRecal msRecal.c -lm

Using msRecal

Usage: msRecal -m <FTICR dataset in mzXML> -p <calibrant dataset in pepXML> -o <output file> -s <max. scan difference for calibrant> -e <max. residual mass measurement error in ppm> -L <lower calibrant score bound> -U <upper calibrant bound> -t <threshold score variable (probability, E-value...)> -c <crop uncalibrated data (0/1)> -C <min. number of acceptable calibrants> -b <minimum intensity>



magnus.palmblad@gmail.com