gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites

Area of Science:

• Metabolomics
• Bioinformatics
• Plant Science

Background:

• Metabolomes contain constitutive and non-constitutive metabolites, influenced by various factors.
• Identifying these metabolites in large datasets presents significant computational challenges.

Purpose of the Study:

• To develop an automated R package (gcProfileMakeR) for analyzing GC-MS metabolomics data.
• To facilitate the distinction between constitutive and non-constitutive metabolites.

Main Methods:

• gcProfileMakeR processes standard Excel output from Agilent Chemstation GC-MS using CAS numbers.
• Includes data preprocessing filters for contaminants and low-quality peaks.
• Functions normalize data within and between files, group compounds, and classify metabolite profiles (Constitutive, Non-constitutive by Frequency, Non-constitutive by Quality).

Main Results:

• The package was applied to analyze floral scent emissions in four snapdragon genotypes with genetic modifications.
• Differences in constitutive and non-constitutive scent profiles and emission timing were identified.
• gcProfileMakeR successfully defined scent profiles and identified differing metabolites across genotypes and circadian datasets.

Conclusions:

• gcProfileMakeR is an effective tool for defining constitutive and non-constitutive scent profiles.
• The package aids in analyzing genotype and circadian datasets to identify differential metabolites.