HolobiomicsLab 
custom-database-searching
Summary
Search LC-MS/MS metabolomics spectra against custom compound databases prepared with CFM-id fragment predictions to identify compounds by spectral matching. This skill enables targeted compound identification when standard databases are insufficient or when organism-specific or metabolite-class-specific databases are needed.
When to use
When you have LC-MS/MS data in Mascot Generic Format (mgf) files and need to identify compounds against a curated custom database (e.g., prepared using CFM-id for a specific metabolite class or organism) rather than relying on in-built commercial spectral libraries alone.
When NOT to use
- Input query file is not in Mascot Generic Format (mgf)
- Custom database was not prepared using CFM-id or is in an incompatible format
- Only generic/in-built spectral databases are available and custom databases cannot be constructed
Inputs
- Custom compound database (prepared using CFM-id)
- Mascot Generic Format (mgf) query file containing LC-MS/MS spectra
Outputs
- Identified compounds with match scores and metadata
- Results file with ranked compound identifications
How to apply
Load a custom compound database prepared using CFM-id (a fragment prediction tool) into MS2Compound v1.0.2, import the mgf query file containing LC-MS/MS spectra, execute the matching algorithm to compare query spectra against database entries, and compute similarity scores for each match. The tool generates a results file with identified compounds ranked by match score and annotated with metadata. Success requires that the custom database was properly constructed using CFM-id in a compatible format and that the mgf file contains valid MS/MS spectra with appropriate precursor and fragment m/z values.
Related tools
- MS2Compound (Graphical user interface for spectral matching and compound identification against custom databases) — https://sourceforge.net/projects/ms2compound/
- CFM-id (Fragment prediction tool used to prepare and generate custom compound databases compatible with MS2Compound)
Evaluation signals
- Match scores are computed and returned for each spectrum-to-database comparison
- All query spectra from the mgf file are processed and assigned at least one match result
- Identified compounds are ranked by match score (highest confidence first)
- Results file contains structured metadata (e.g., compound name, database ID, similarity metric) for each match
- No errors or warnings related to database format compatibility or mgf parsing are reported during execution
Limitations
- MS2Compound v1.0.2 is Windows-only (Windows 7, 8, and 10) with no cross-platform support
- Requires minimum 2 GB RAM and Intel i3 64-bit CPU; performance with very large custom databases or mgf files on minimal hardware is not characterized
- Dependency on CFM-id-generated databases means accuracy is limited by the quality and completeness of fragment predictions from CFM-id
- No changelog or version history available; updates and bug fixes are not documented
- Installation directory path must not contain spaces, which may complicate deployment in certain environments
Evidence
- [readme] MS2Compound (v1.0.2) is a user friendly Graphical User Interface (GUI) for the identification of the compounds from LC-MS and MS/MS metabolomics data.: "MS2Compound (v1.0.2) is a user friendly Graphical User Interface (GUI) for the identification of the compounds from LC-MS and MS/MS metabolomics data."
- [readme] The current version of MS2Compound is compatible with the customized database prepared using CFM-id, the fragment prediction tool. Mascot Generic Format (mgf) files can be used as query input file: "The current version of MS2Compound is compatible with the customized database prepared using CFM-id, the fragment prediction tool. Mascot Generic Format (mgf) files can be used as query input file"
- [other] Execute the matching algorithm to compare query spectra against database entries and compute similarity scores.: "Execute the matching algorithm to compare query spectra against database entries and compute similarity scores."
- [readme] The tool is independent from all the pre-requisite dependencies.: "The tool is independent from all the pre-requisite dependencies."
- [readme] Windows 7, 8, and 10: "Windows 7, 8, and 10"