Accurate Mass Database Search

accurate-mass-database-search

Summary

Annotate detected molecular features by searching their accurate m/z values against a curated metabolite database (HMDB) using configurable mass error tolerance and ion adduct rules. This skill produces compound identifiers, molecular formulas, and structural metadata linked to each MS1 peak.

When to use

After peak detection and MS1 feature extraction from FIA-MS, GC-MS, LC-MS(/MS), or CE-MS data, when you need to identify unknown metabolites by matching observed m/z values to a reference database and want to recover HMDB identifiers, molecular formulas, and structural annotations for downstream quantification or pathway analysis.

When NOT to use

• If the input data contain only MS/MS fragmentation spectra without MS1 m/z values (library matching or spectral similarity methods are more appropriate).
• If ion adduct modes are unknown or highly variable and cannot be specified in advance (ion mode determination must precede this skill).
• If the reference database is incomplete, outdated, or not curated for your biological system of interest (limiting annotation sensitivity and specificity).

Inputs

• Detected MS1 features (m/z, retention time, peak intensity, feature ID)
• Reference metabolite database (HMDB) with mapping files (HMDBMappingFile.tsv, HMDB2StructMapping.tsv)
• Ion adduct configuration files (positive_adducts.tsv, negative_adducts.tsv)
• Mass error tolerance threshold (ppm)

Outputs

• Annotated feature list with HMDB identifiers and compound metadata
• mzTab annotation summary file (containing feature list and mass search results)
• Match quality metrics (mass error in ppm, rank, match confidence)

How to apply

Load detected MS1 features (m/z, retention time, intensity) and configure the accurate mass search with: (1) a reference metabolite database (HMDB with HMDBMappingFile.tsv and HMDB2StructMapping.tsv files), (2) expected ion adducts (positive_adducts.tsv, negative_adducts.tsv specifying [M+H]+, [M-H]−, [M+Na]+, etc.), and (3) mass error tolerance (typically in ppm, e.g., 5 ppm for high-resolution Orbitrap). Execute the search against the database index, matching each feature's observed m/z to theoretical m/z values of known metabolites after applying adduct mass shifts. Rank candidate matches by mass error and, optionally, by database cross-references or structural similarity. Store matched annotations (HMDB ID, compound name, molecular formula, InChI, neutral mass) as feature metadata.

Related tools

• SmartPeak (Orchestrates peak detection, calibration, accurate mass search, and mzTab assembly in a unified workflow) — https://github.com/AutoFlowResearch/SmartPeak
• SmartPeakCLI (Command-line interface for executing accurate mass search and annotation workflows without GUI) — https://github.com/AutoFlowResearch/SmartPeak
• OpenMS (Underlying toolkit providing accurate mass search algorithms and m/z calibration)
• pyOpenMS (Python bindings for parsing and processing annotated feature files and database search results)

Examples

docker run --rm -ti -v C:/data:/sample-data autoflowresearch/smartpeak-cli:latest bash -c "SmartPeakCLI --config workflow.ini --data FIAMS_FullScan_Unknowns.mzML --database HMDB_mapping --adducts positive_adducts.tsv --mz_tolerance 5 --output results.mzTab"

Evaluation signals

• All detected MS1 features have a best-match HMDB entry or are explicitly marked as unannotated (no orphaned features).
• Mass errors for matched features are ≤ the specified tolerance threshold (e.g., ≤ 5 ppm for high-resolution instruments).
• Ion adduct assignments are consistent with the acquisition mode and fragmentation patterns (e.g., [M+H]+ in positive mode, [M-H]− in negative mode).
• mzTab output conforms to the mzTab specification and includes mandatory columns (feature m/z, formula, accession) and optional metadata (InChI, compound name, neutral mass).
• Reproducibility: re-running the search on the same data with the same parameters and database version yields identical annotations.

Limitations

• Mass error tolerance must be manually configured and is instrument-dependent; misconfigration leads to false positives or missed identifications.
• HMDB is primarily human-centric; coverage of non-mammalian, environmental, or drug metabolites may be incomplete.
• Multiple structural isomers can have identical m/z values; accurate mass search alone cannot distinguish them without orthogonal data (retention time, MS/MS fragmentation, or ion mobility).
• Isotope patterns and adduct ratios are not considered in the annotation step; results may include artefactual matches for low-intensity features or co-eluting unknowns.

Evidence

• [methods] Execute accurate mass search against the HMDB database using the mapping files (HMDBMappingFile.tsv, HMDB2StructMapping.tsv) and specified ion adducts (positive_adducts.tsv, negative_adducts.tsv) with the configured mass error tolerance.: "Execute accurate mass search against the HMDB database using the mapping files (HMDBMappingFile.tsv, HMDB2StructMapping.tsv) and specified ion adducts (positive_adducts.tsv, negative_adducts.tsv)"
• [methods] Annotate detected peaks with HMDB compound identifiers, molecular formulas, and structural metadata.: "Annotate detected peaks with HMDB compound identifiers, molecular formulas, and structural metadata."
• [methods] Assemble results into mzTab format containing the feature list and mass search annotations, then store the mzTab output file.: "Assemble results into mzTab format containing the feature list and mass search annotations, then store the mzTab output file."
• [readme] SmartPeak is an application that encapsulates advanced algorithms to enable fast, accurate, and automated processing of CE-, GC- and LC-MS(/MS) data, and HPLC data for targeted and semi-targeted metabolomics, lipidomics, and fluxomics experiments.: "SmartPeak is an application that encapsulates advanced algorithms to enable fast, accurate, and automated processing of CE-, GC- and LC-MS(/MS) data, and HPLC data for targeted and semi-targeted"