iMS2Flux is a command line based high-throughput processing tool set for stable isotope labelled mass spectral data targeting metabolic flux analysis. To get started simply download and unzip the iMS2Flux.zip file and follow the getting started document for your OS.
Current version 7.2.1 (last updated 9/30/2014) - Completes support and correction functionality for a new user specified generic data class. See the change log for full details.