title: iMS2Flux--a high-throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis.
abstract: BACKGROUND
  Metabolic flux analysis has become an established method in systems biology and functional genomics. The most common approach for determining intracellular metabolic fluxes is to utilize mass spectrometry in combination with stable isotope labeling experiments. However, before the mass spectrometric data can be used it has to be corrected for biases caused by naturally occurring stable isotopes, by the analytical technique(s) employed, or by the biological sample itself. Finally the MS data and the labeling information it contains have to be assembled into a data format usable by flux analysis software (of which several dedicated packages exist). Currently the processing of mass spectrometric data is time-consuming and error-prone requiring peak by peak cut-and-paste analysis and manual curation. In order to facilitate high-throughput metabolic flux analysis, the automation of multiple steps in the analytical workflow is necessary.
  
  
  RESULTS
  Here we describe iMS2Flux, software developed to automate, standardize and connect the data flow between mass spectrometric measurements and flux analysis programs. This tool streamlines the transfer of data from extraction via correction tools to ¹³C-Flux software by processing MS data from stable isotope labeling experiments. It allows the correction of large and heterogeneous MS datasets for the presence of naturally occurring stable isotopes, initial biomass and several mass spectrometry effects. Before and after data correction, several checks can be performed to ensure accurate data. The corrected data may be returned in a variety of formats including those used by metabolic flux analysis software such as 13CFLUX, OpenFLUX and 13CFLUX2.
  
  
  CONCLUSIONS
  iMS2Flux is a versatile, easy to use tool for the automated processing of mass spectrometric data containing isotope labeling information. It represents the core framework for a standardized workflow and data processing. Due to its flexibility it facilitates the inclusion of different experimental datasets and thus can contribute to the expansion of flux analysis applications.
authors.affiliation: Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research-IPK, 06466 Gatersleben, Germany.
authors.forename: C Hart
authors.initials: CH
authors.lastname: Poskar
authors.forename: Jan
authors.initials: J
authors.lastname: Huege
authors.forename: Christian
authors.initials: C
authors.lastname: Krach
authors.forename: Mathias
authors.initials: M
authors.lastname: Franke
authors.forename: Yair
authors.initials: Y
authors.lastname: Shachar-Hill
authors.forename: Björn H
authors.initials: BH
authors.lastname: Junker
mesh_terms: D007553:Isotope Labeling / Q000706:statistics & numerical data*; D013058:Mass Spectrometry / Q000706:statistics & numerical data*; D053858:Metabolic Networks and Pathways; D012984:Software; D049490:Systems Biology / Q000379:methods*