Overview
OrbiFragsNets annotates Orbitrap data-dependent MS2 peaks with candidate fragment formulas using peak-specific uncertainty and chemical-consistency networks. Its workflow extracts profile-derived spectral information before selecting consistent fragment-annotation networks.
What can this tool do?
Common uses
- OrbiFragsNets annotates Orbitrap data-dependent MS2 peaks with candidate fragment formulas using peak-specific uncertainty and chemical-consistency networks.
Scientific fit
Primary function
Metabolite annotation and identification
Other functions
Molecular networking and chemical similarity, Spectral processing and comparison
Data compatibility
Inputs
Mass spectra
Outputs
Compound list or annotations, Statistical results
Input formats
Profile-mode Orbitrap mzML with precursor/formula constraints
Output formats
Annotated MS2 fragment-formula networks and spectral result tables
Scope and considerations
Designed for
- OrbiFragsNets annotates Orbitrap data-dependent MS2 peaks with candidate fragment formulas using peak-specific uncertainty and chemical-consistency networks.
Not designed for
- Universal centroid-spectrum annotation or full molecular-structure confirmation from a selected fragment network.
Important requirements
- Python dependencies and compatible profile-mode Orbitrap mzML data with precursor information and appropriate elemental/formula constraints.
Considerations
- Profile information used for uncertainty is lost after centroiding. Elemental bounds and precursor constraints determine the formula space and must match the experiment.
Access and documentation
MIT source distribution. External datasets, dependent packages and any hosted routes retain their own terms; software operation was not tested.
License: MIT
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-batch3.md.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- OrbiFragsNets. A tool for automatic annotation of orbitrap MS2 spectra using networks grade as selection criteria. MethodsX (2023). doi:10.1016/j.mex.2023.102257
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 45 source-reviewed Enveda tool entries in third expansion batch
View change · Entry at this revision