MScout is free for non-commercial use. Click here to download the Linux version (32 and 64-bit). You'll be asked to fill out a short form and agree to a license.
A Windows/Cygwin version is planned.
Usage
MScout is a command-line program. The general format for usage for the 64-bit version is
% mscout64 <options> <input MS1 file(s)>
For the 32-bit version, simply replace mscout64 with mscout32.