High-Throughput Data Analysis for Detecting and Identifying Differences between Samples in GC/MS-Based Metabolomic Analyses

TLDR

Metabolomics seeks to detect differences in metabolite profiles, and GC/MS is a common tool that can identify over 400 compounds per run, but peak deconvolution is time‑consuming, difficult to automate, and requires extra processing to compare samples. This study aims to develop an automated data‑processing strategy for GC/MS‑based metabolomics to eliminate the bottleneck in high‑throughput analyses. The authors present a semi‑automated approach that applies hierarchical multivariate curve resolution to all samples simultaneously. The method produces tables of metabolites with differential relative concentrations, processes 70 samples in a time comparable to GC/TOFMS, and has been validated on a standard mixture and Arabidopsis samples.

Abstract

In metabolomics, the objective is to identify differences in metabolite profiles between samples. A widely used tool in metabolomics investigations is gas chromatography−mass spectrometry (GC/MS). More than 400 compounds can be detected in a single analysis, if overlapping GC/MS peaks are deconvoluted. However, the deconvolution process is time-consuming and difficult to automate, and additional processing is needed in order to compare samples. Therefore, there is a need to improve and automate the data processing strategy for data generated in GC/MS-based metabolomics; if not, the processing step will be a major bottleneck for high-throughput analyses. Here we describe a new semiautomated strategy using a hierarchical multivariate curve resolution approach that processes all samples simultaneously. The presented strategy generates (after appropriate treatment, e.g., multivariate analysis) tables of all the detected metabolites that differ in relative concentrations between samples. The processing of 70 samples took similar time to that of the GC/TOFMS analyses of the samples. The strategy has been validated using two different sets of samples: a complex mixture of standard compounds and Arabidopsis samples.