What does this strategy enable?
MS2Planner uses topological sorting on a feature graph to maximize scheduled coverage. Features selected for one path are excluded from the next planning iteration. This is computational scheduling of repeat acquisitions, rather than a requirement to measure fragmentation quality after every run.
Transferable workflow
Workflow
- 1
Acquire an MS1 survey
The published IODA experiment begins with a full-scan MS1 measurement.
- 2
Prepare features for scheduling
Provide precursor masses, retention times and signals for the acquisition model.
- 3
Optimize successive acquisition paths
Use topological sorting; exclude scheduled features before computing the next path.
- 4
Export instrument inclusion lists
The study provides companion scripts for inclusion-list generation.
- 5
Acquire and assess scheduled spectra
The paper tests inclusion-prioritized DDA and targeted-MS2 variants, with and without dynamic exclusion. Review coverage and spectral quality for the chosen mode.
Connected resources
Tools used in this strategy
Strategy profile
Related objectives
Molecular discovery, Unknown identification
Components
Data acquisition, Preprocessing and feature extraction, Annotation or identification
Biological context
Broadly applicable
Ion mobility
Not specified
Scope and considerations
Designed for
- Increasing MS/MS coverage in untargeted LC-MS experiments when repeat injections are practical.
- Building richer fragmentation coverage for annotation and discovery from representative or pooled samples.
Important requirements
- Full-scan survey features and instrument support for the selected inclusion-list acquisition mode.
- Sufficient sample for repeated injections and chromatography consistent with the planned retention-time windows.
Considerations
- Planning assumptions and acquisition timing must fit the instrument and chromatography.
- This is not equivalent to a simple exclusion list updated after each measured DDA run; no universal coverage gain is promised.
Reusable resources
Publication
Zuo Z, Cao L, et al. MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition. Bioinformatics 37(Suppl 1), i231-i236 (2021).