Overview
MeRgeION builds local spectral libraries by extracting and combining MS scans around user-specified compounds. Its R functions also support local spectral searching, analog analysis and network-oriented exploration without requiring public deposition of the library.
What can this tool do?
Common uses
- Build local LC-MS/MS spectral libraries without publishing confidential metadata.
- Search unknown spectra against local or public reference libraries.
Scientific fit
Primary function
Spectral processing and comparison
Other functions
Metabolite annotation and identification, Data management and sharing
Analysis types
Targeted metabolomics, Untargeted metabolomics
MS level
MS1, MS/MS
Acquisition
Data-dependent acquisition (DDA), Targeted MS/MS
Ion mobility
Not specified
Data compatibility
Inputs
Raw instrument data, Mass spectra, Sample metadata
Outputs
Spectral library, Compound list or annotations
Input formats
mzML/mzXML scans plus targets/metadata, or two-column query spectra
Output formats
R spectral-library objects, candidate match tables and mirror/network plots
Scope and considerations
Designed for
- A workflow for extracting and merging LC-MS/MS spectra into local GNPS-style spectral libraries with user metadata, plus local and public-library searching for annotation.
Not designed for
- Reference-free structure determination or permission to redistribute third-party spectra included in a local library.
Important requirements
- R/Bioconductor dependencies and Java/OpenBabel components as documented; compatible mzML/mzXML DDA or targeted-MS/MS data, target masses/optional retention times and library metadata.
Considerations
- Library quality depends on extraction/merging settings and metadata. The linked example library is positive-ion; assess polarity and acquisition compatibility before transferring search thresholds.
Access and documentation
Package DESCRIPTION says only GNU without a version or complete grant; no precise unrestricted license is inferred. Linked reference libraries have separate provenance and reuse terms.
Evidence and review
Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch2.md.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- MeRgeION: a Multifunctional R Pipeline for Small Molecule LC-MS/MS Data Processing, Searching, and Organizing. Analytical Chemistry (2023). doi:10.1021/acs.analchem.2c04343
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-10-27 · First committed entry
Add 24 reviewed Enveda tools in a separate second batch
View change · Entry at this revision