MET-IDEA: Data Extraction Tool for Mass Spectrometry-Based Metabolomics

A current and significant limitation to metabolomics is the
large-scale, high-throughput conversion of raw chromatographically coupled mass spectrometry datasets into
organized data matrices necessary for further statistical
processing and data visualization. This article describes
a new data extraction tool, MET-IDEA (Metabolomics Ion-based Data Extraction Algorithm) which surmounts this
void. MET-IDEA is compatible with a diversity of chromatographically coupled mass spectrometry systems,
generates an output similar to traditional quantification
methods, utilizes the sensitivity and selectivity associated
with selected ion quantification, and greatly reduces the
time and effort necessary to obtain large-scale organized
datasets by several orders of magnitude. The functionality
of MET-IDEA is illustrated using metabolomics data
obtained for elicited cell culture exudates from the model
legume, Medicago truncatula. The results indicate that
MET-IDEA is capable of rapidly extracting semiquantitative data from raw data files, which allows for more rapid
biological insight. MET-IDEA is freely available to academic users upon request.