Metabolite candidate matching

metabolite-candidate-matching

Summary

Match predicted candidate metabolites against observed mass spectrometry features in mzML data using mass accuracy and intensity thresholds to determine which candidates are present in a sample. This skill bridges in silico metabolite prediction with experimental MS detection.

When to use

Apply this skill when you have: (1) a set of predicted candidate metabolites with known mass-to-charge ratios and chemical properties derived from a parent drug formula; (2) raw mass spectrometry data in mzML format from a sample suspected to contain those metabolites; and (3) a need to determine which predicted candidates actually correspond to detected spectral features rather than false positives or noise.

When NOT to use

• Input is already a peak-picked feature table or aligned feature matrix — use this skill on raw or minimally processed mzML data.
• Metabolite candidates lack reliable mass-to-charge ratios or chemical formulas — the skill requires precise m/z values for matching.
• Mass spectrometry data is in NetCDF or other binary formats without mzML conversion — the workflow expects mzML format specifically.

Inputs

• mzML mass spectrometry data file (raw or peak-picked)
• TSV file containing parent drug information and predicted candidate metabolites with chemical formulas
• Configuration file (R script) specifying mass accuracy tolerance, intensity thresholds, and matching parameters

Outputs

• TSV detection report listing matched candidate metabolites and unmatched candidates
• Match quality metrics (mass error, intensity, confidence score) for each candidate
• Optional: visualization-ready data structures for MetApp (Shiny application) display and PDF report generation

How to apply

Load the mzML mass spectrometry file and extract observed spectral features (m/z values, intensities, and optional retention times). Parse the predicted candidate metabolites with their calculated mass-to-charge ratios. Match each candidate against observed features by computing mass error and comparing against a user-defined mass accuracy threshold (specified in a configuration file). Apply intensity thresholds to filter low-signal matches. Aggregate matches and assign confidence levels based on how many isotopic or fragmentation patterns align. Generate a detection report listing which candidates matched observed signals, with match quality metrics suitable for downstream interpretation or visualization.

Related tools

• MetIDfyR (Core R script that implements metabolite prediction, feature extraction from mzML, and candidate-feature matching via mass accuracy and intensity filtering) — https://github.com/agnesbrnb/MetIDfyR
• MSnbase (R/Bioconductor package for parsing and manipulating mzML mass spectrometry data and extracting spectral features)
• Rdisop (R package for computing molecular formulas and mass-to-charge ratios from chemical formulas)
• MetApp (Shiny application for interactive visualization and validation of matched metabolites and generation of PDF reports) — 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

• All predicted candidate metabolites are assigned either a match status (matched with m/z error, intensity, and quality score) or an explicit 'unmatched' label in the output TSV.
• Matched candidates have mass error values within the configured mass accuracy tolerance (e.g., typical pharmaceutical workflows use ±5 ppm or ±10 ppm); inspect the error distribution to verify no systematic bias.
• Matched candidates have intensity values above the configured threshold; verify that weak or noise-level matches are filtered and documented.
• Isotopic or retention-time patterns (if available) for top-ranked matches align with theoretical predictions; cross-check with MetApp visualizations or generated PDF reports.
• Output file schema matches the expected format (TSV columns include: candidate name, theoretical m/z, observed m/z, mass error, intensity, match score, retention time if applicable); validate against TEMPLATE output structure.

Limitations

• Matching relies on mass accuracy and intensity thresholds; if the instrument's mass resolution is poor (>10 ppm error) or sample concentration is very low, true metabolites may be missed or mismatched.
• mzML files must be peak-picked or processed to extract features; matching on raw, centroided spectra may inflate false positives.
• No changelog is maintained in the repository, limiting reproducibility across versions and clarity on algorithm updates or bug fixes.
• The skill does not perform automated retention-time prediction; retention-time matching is optional and relies on external standards or prior knowledge.
• MetIDfyR was developed and tested on R versions 3.6.1–4.0; compatibility with R versions >4.0 is not formally documented.

Evidence

• [readme] MetIDfyR predicts and detects metabolites in mass spectrometry data (mzML) based on the raw formula of the drug of interest: "an open-source, cross-platform and versatile R script to predict and detect metabolites in mass spectrometry data (mzML) based on the raw formula of the drug of interest"
• [other] Workflow includes parsing candidates, extracting spectral features, matching with mass and intensity thresholds, and generating a detection report: "1. Load the mzML mass spectrometry file using R. 2. Parse predicted candidate metabolites and their chemical properties (mass-to-charge ratios, retention times if available). 3. Extract spectral"
• [readme] Configuration file and template inputs are required to specify matching parameters: "Need - a configuration file with the parameter (see TEMPLATE_config.R). - a mzML file containing the sample informations - a tsv file containing the parent drug informations"
• [readme] Command-line invocation specifies input, output directory, and configuration file: "Rscript MetIDfyR.R -i path-to-input-file -o output-directory -c config-file"