Phase I Phase Ii Transformation Rules

phase-i-phase-ii-transformation-rules

Summary

Systematically enumerate candidate metabolite molecular formulas by applying phase I (oxidation, reduction, hydrolysis) and phase II (conjugation) biotransformation rules to a parent drug's raw chemical formula. This skill is essential for constraining the chemical search space in metabolite identification workflows when only the parent drug formula is known.

When to use

When you have a parent drug's raw chemical formula and need to predict its likely metabolite formulas for subsequent mass spectrometry matching, especially in high-resolution MS workflows where exact mass matching requires known candidate formulas. Apply this skill upstream of spectral matching or when metabolite standards are unavailable.

When NOT to use

• The parent drug formula is unknown or ambiguous — formula-based prediction requires exact starting composition.
• You already have experimentally observed metabolite m/z values and only need to annotate them post-hoc; use metabolite identification matching instead.
• The drug undergoes phase I/II transformations not covered by the tool's built-in rule set (e.g. rare or non-standard metabolic pathways); manual curation or literature review would be more appropriate.

Inputs

• Parent drug raw chemical formula (string, e.g. C₂₁H₃₂N₂O₂)
• Configuration file specifying active transformation rules (R script, TEMPLATE_config.R)
• Optional: mzML mass spectrometry data file (for subsequent matching)

Outputs

• Structured metabolite formula table (TSV or CSV format)
• Predicted metabolite candidate formulas with transformation type annotations
• Mass values derived from predicted formulas (for MS matching)

How to apply

Load the parent drug's raw chemical formula into MetIDfyR as a TSV input file (see TEMPLATE_start_mlc.tsv). The tool systematically applies phase I biotransformation rules (oxidative and reductive modifications typical of cytochrome P450 metabolism) and phase II rules (glucuronidation, sulfation, acetylation, and other conjugations). Configure the prediction scope via a config file (TEMPLATE_config.R) specifying which transformation types to include. Execute the prediction module, which enumerates all combinatorially valid candidate formulas, then collect and format the output into a structured TSV table annotated with transformation type labels. Validate output formulas by checking they are chemically plausible (e.g., no negative atom counts, reasonable mass increments for the transformation type applied).

Related tools

• MetIDfyR (R script that implements phase I and phase II biotransformation rule enumeration and metabolite formula prediction from parent drug formula) — https://github.com/agnesbrnb/MetIDfyR
• MetApp (Shiny application for visualization and reporting of predicted and detected metabolites) — https://github.com/GIELCH/MetApp

Examples

Rscript MetIDfyR.R -i input/lgd_DIA_peak-picked.tsv -o LGD4033_results -c input/config_LGD.R

Evaluation signals

• Output formulas are chemically valid: all atom counts are non-negative, molecular weight is plausible for the parent drug mass plus transformation mass delta.
• Phase I predictions (oxidation, reduction, hydrolysis) show systematic mass shifts consistent with known P450 modifications (e.g., +16 for monooxygenation, -2 for dehydration).
• Phase II predictions include expected conjugation products (e.g., parent formula + 176 for glucuronidation, +80 for sulfation).
• Output TSV schema matches expected structure: columns for predicted_formula, transformation_type, mass_shift, and traceability to parent drug.
• Predicted formulas match subsequently observed m/z values in high-resolution MS data when matched using exact mass tolerance (typically <5 ppm).

Limitations

• MetIDfyR is tested and validated on R version 3.6.1 up to R 4.0; behavior on newer R versions may be unpredictable.
• The tool enumerates combinatorially — complex drugs with many potential transformation sites may generate very large candidate lists, requiring post-hoc filtering.
• Rule set is limited to common phase I and II pathways; drugs undergoing rare, non-standard, or species-specific metabolism may produce incomplete or inaccurate predictions.
• No changelog is available, limiting ability to track rule updates or bug fixes between versions.

Evidence

• [other] enumerate candidate metabolite formulas based on systematic phase I and phase II biotransformation rules: "enumerate candidate metabolite formulas based on systematic phase I and phase II biotransformation rules"
• [readme] predict and detect metabolites in mass spectrometry data (mzML) based on the raw formula of the drug of interest: "predict and detect metabolites in mass spectrometry data (mzML) based on the raw formula of the drug of interest"
• [readme] a configuration file with the parameter (see TEMPLATE_config.R): "a configuration file with the parameter (see TEMPLATE_config.R)"
• [readme] a tsv file containing the parent drug informations (see TEMPLATE_start_mlc.tsv): "a tsv file containing the parent drug informations (see TEMPLATE_start_mlc.tsv)"
• [other] Collect and format predicted metabolite formulas and associated transformation types into a structured output table (CSV or TSV): "Collect and format predicted metabolite formulas and associated transformation types into a structured output table (CSV or TSV)"