gcProfileMakeR

gcProfileMakeR classifies metabolites into constitutive and non-constitutive categories from Agilent Chemstation GC‑MS Excel output to distinguish physiological, genetic, or environmental contributions to metabolite variation.

Key Features:

• Data Preprocessing Filters: Removes contaminants and low-quality peaks from standard Excel output files generated by Agilent Chemstation GC‑MS systems.
• NormalizeWithinFiles: Assigns retention times to CAS numbers within individual samples for accurate within-file identification.
• NormalizeBetweenFiles: Groups compounds with similar retention times across multiple files to produce consensus compound identities between samples.
• getGroups: Categorizes metabolites into Constitutive Profile, Non-constitutive by Frequency (metabolites not present in all samples), and Non-constitutive by Quality.
• plotGroup: Plots grouped results to visualize classification outcomes.

Scientific Applications:

• Floral scent analysis in snapdragon genotypes: Applied to compare scent emissions across a wild type, Deficiens nicotianoides, compacta, and RNAi:AmLHY (circadian clock gene) genotypes to identify differences in constitutive versus non-constitutive compounds and timing of emission.
• Metabolomic profiling of complex samples: Enables classification of metabolite presence and quality within large GC‑MS datasets.
• Comparative genotype analysis: Supports comparative analysis of metabolic outputs between genotypes.
• Circadian rhythm studies: Facilitates investigation of circadian effects on metabolite production, as exemplified by RNAi:AmLHY analysis.

Methodology:

Uses standard Excel output files from GC‑MS; applies preprocessing filters to remove contaminants and low-quality peaks; normalizes retention times within and between files and assigns CAS numbers; groups compounds and classifies them into Constitutive Profile, Non-constitutive by Frequency, or Non-constitutive by Quality; optionally visualizes group results with plotGroup.