Overview
NP3 MS Workflow combines preprocessing, spectral clustering, quantification, library annotation and molecular-network generation. Sample bioactivity metadata can support prioritization.
Also known as: NP3, NP³ MS Workflow
What can this tool do?
Common uses
- Process LC-MS/MS data for natural-product profiling and molecular-network exploration.
Scientific fit
Primary function
Preprocessing and feature extraction
Analysis types
Untargeted metabolomics
Data compatibility
Inputs
Mass spectra, Sample metadata
Outputs
Feature or peak table, Mass spectra, Human-readable report
Input formats
LC-MS/MS mzML or mzXML files and sample metadata
Output formats
MGF spectra, CSV count/peak-area tables and network/report files
Scope and considerations
Designed for
- NP3 MS Workflow combines preprocessing, spectral clustering, quantification, library annotation and molecular-network generation. Sample bioactivity metadata can support prioritization.
Not designed for
- Demonstrating biological activity or establishing a structure solely from a network or library match.
Important requirements
- Compatible LC-MS/MS acquisition and prepared sample metadata.
- Local dependencies for the full CLI; a GNPS2 interface exposes a subset of the workflow.
Considerations
- Bioactivity prioritization requires measured bioactivity metadata.
- Check ion-mode support against the selected version: the manual cautions that some negative-mode steps are less tested.
Access and documentation
License checked against official repository/package metadata. Installation and execution were not tested.
License: GPL-3.0-or-later
Evidence and review
Enveda intake candidate checked against official documentation, license information and primary publication on 2026-10-21. Editorial review only; no execution or independent benchmark.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- NP3 MS Workflow: An Open-Source Software System to Empower Natural Product-Based Drug Discovery Using Untargeted Metabolomics. Analytical Chemistry (2024). doi:10.1021/acs.analchem.3c05829
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-10-21 · First committed entry
Add nine reviewed Enveda tools and reconcile intake coverage
View change · Entry at this revision