# Analyzing Plant Low-Molecular-Weight Polar Metabolites: A GC-MS Approach

## TL;DR

This review discusses how GC-MS is used to study small plant metabolites, covering methods from sample prep to data analysis.

## Contribution

The paper provides a comprehensive review of GC-MS workflows and solutions to challenges in plant metabolite analysis.

## Key findings

- GC-MS offers high-resolution separation of complex plant metabolomes, including isomeric compounds.
- Derivatization protocols enable reliable analysis of semi- and non-volatile plant metabolites.
- Artifacts during derivatization remain a challenge requiring careful validation and investigation.

## Abstract

Decades ago, the introduction of GC-MS marked a significant advancement in primary plant metabolite studies. Here, in our review, we will delve into critical aspects of the workflow, spanning the selection of an analytical platform, sample preparation, analytical acquisition, and data processing and interpretation. The exceptional separation capabilities of GC, characterized by remarkable chromatographic resolution, render it ideal for analysis of the complex plant metabolome, including the separation of isomeric compounds. The diversity of analytical platforms allows the investigation of plant metabolomes using targeted and non-targeted approaches. GC-MS, equipped with efficient extraction methods and reliable derivatization protocols for semi- and non-volatile compounds, enables qualitative and quantitative analysis of these molecules. The stability of derivatives forms the foundation for the robustness and reproducibility of GC-MS methods, and their mass spectra provide characteristic fragments for confident identification and sensitive quantification of individual metabolites. There has been key progress in the advancement of GC-MS approaches to studying plant metabolism. However, the presence of artifacts during GC-MS analysis, particularly during derivatization, is a challenge that requires careful validations, which frequently necessitate additional investigations. The feasible solutions that were achieved to overcome the limitations in GC-MS-based studies are a particular focus of the present discussion.