iMS2Flux– a high–throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis

Abstract

BackgroundMetabolic 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.ResultsHere 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.ConclusioniMS2Flux 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.

Interpretation and Integration of 13C-Fluxomics Data

“…FiatFlux [26] a software for metabolic flux analysis from labeled mass spectrometric data with flux ratio constraints Flux-P [24] an automate and standardized workflow of 13C-based metabolic flux analysis in the Bio-jETI workflow framework iMS2Flux [23] a high-throughput pipline for isotope labeled mass spectrometric data for metabolic flux analysis INCA [20] the first publicly available computational platform for isotopically non-stationary metabolic flux analysis limitation of current computer memory [27]. These are all issues that await more in-depth studies.…”

“…A recent progress was a whole-cell computational model including all of biomolecular components and their interactions [19]. In addition to development of stand-alone software systems (Table 1) [20][21][22][23][24][25][26], the building of open platform for public use should be emphasized considering that the huge demand of simulation or decomposition calculation of metabolism systems has exceeds the…”

High-Throughput Data Pipelines for Metabolic Flux Analysis in Plants

“…Adapted from ref. [41] where the stoichiometric matrix, S, multiplied by the vector of metabolic fluxes, v, is equal to the rate of change of the metabolite concentrations, X. MFA may then be classified based on whether the experiment is performed in metabolic and isotopic stationary or instationary states [30,31]. Equation 2 illustrates this classification through the general form of the isotopomer balance for the rate of change of metabolite concentrations X with fractional labeling x i for isotopomer i,…”

“…2 Illustration of the workflow of steady-state 13 C metabolic flux analysis in plants, adapted from ref. [66] There is only one software platform which attempts to combine these parts, FiatFlux [40], however in doing so it is severely restricted and not suitable for plants [41].…”

“…To support highthroughput MFA, it was critical to develop a piece of software that could oversee all of the processing tasks as well as remain generic and easily extendible. To this end the iMS2Flux software was developed [41] and is freely available (see Note 3). This project was executed in an interpreted language (PERL, the Practical Extraction and Reporting Language) so that the source code is immediately available and runs on all major computing platforms.…”