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Metabolite annotation and identification

LipiDex 2

A standalone LC-MS lipidomics suite for in-silico library generation, MS/MS and MSn spectral searching, lipid feature annotation, peak-table integration, and automated identification quality control.

LC-MSLipidomicsDesktop graphical interfaceSource available with restrictions
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Overview

LipiDex 2 provides lipid spectral-library generation, spectral matching, peak annotation and quality-control modules. It extends lipidomics analysis to MSn fragmentation trees and includes Degreaser checks based on retention behavior, dilution response, spectral evidence and QC variability.

What can this tool do?

In-silico spectrum predictionSpectral-library matchingIdentification-confidence assessmentMS/MS processing

Common uses

  • Generate or search lipid spectral libraries and annotate LC-MS lipid features.
  • Apply retention-time, spectral-match, linearity, QC-RSD, and other evidence to filter lipid identifications.

Scientific fit

Primary function

Metabolite annotation and identification

Other functions

Spectral processing and comparison, Quality control and filtering, Quantification and targeted analysis

Analysis types

Lipidomics

MS level

MS/MS, MSⁿ

Acquisition

Data-dependent acquisition (DDA), Targeted MS/MS, General or unspecified acquisition

Ion mobility

Not specified

Data compatibility

Inputs

Raw instrument data, Mass spectra, Feature or peak table, Spectral library

Outputs

Compound list or annotations, Feature or peak table, Human-readable report

Input formats

Thermo raw, spectral libraries and Compound Discoverer cdResult by module

Output formats

CSV or TSV

Scope and considerations

Designed for

  • LC-MS lipid identification and quality-controlled lipidomics workflows.

Not designed for

  • A universal raw-data peak detector or unqualified assignment of lipid structural detail beyond the acquired fragmentation evidence.

Important requirements

  • Windows with .NET 7 and appropriate lipid spectra/libraries. Peak Finder specifically requires Compound Discoverer 3.3 cdResult input; other modules can run separately.

Considerations

  • Input requirements differ by module. Quality-control criteria need the relevant dilution series, replicate QCs or other evidence and do not confer experimental confirmation by themselves.

Access and documentation

Primary accessDocumentationDownload

Public source and executable releases are available, but no explicit repository-wide software license was identified. Compound Discoverer is a separate commercial dependency for Peak Finder.

Evidence and review

Enveda intake rechecked against official README/documentation, repository access terms and primary publication metadata on 2026-10-27. Editorial source review only; no software execution or independent benchmarking. See docs/enveda-expansion-review-2026-10-27.md.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. LipiDex 2 Integrates MSn Tree-Based Fragmentation Methods and Quality Control Modules to Improve Discovery Lipidomics. Analytical Chemistry (2024). doi:10.1021/acs.analchem.4c00359

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Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-10-27 · First committed entry

    Add 27 source-reviewed tools from Enveda intake

    View change · Entry at this revision

Full GitHub history