Articles
Get started
- MSdev untargeted workflow
End-to-end untargeted LC-MS (lipidomics-style) pipeline: convert, xcms processing, spectra extraction, CompoundDb annotation, stats, export, and differential figures by sample.type.
- Get started with MSdev
Overview of the MSdev S4 project object, core slots, preferred accessors, and a minimal untargeted LC-MS pipeline.
Technical notes
- Rdisop mass decomposition (`decomposeMass`)
Quick reference for how Rdisop turns an exact mass (or isotope pattern) into candidate sum formulas, and how that fits a formula-calculator workflow.
- Spectra backends (`MsBackend*`)
Quick reference for choosing and using Spectra backends in MSdev / Bioconductor LC-MS workflows.
- Fast chromatogram extraction (xcms vs MSdev triad)
How xcms::chromatogram / featureChromatograms / chromPeakChromatograms extract EICs, why that path is slow at scale, and how MSdev’s get_xcms_*_chromatogram triad speeds up the same work.
- Feature grouping with `EicSimilarityParam`
xcms / MsFeatures feature compounding (RT → abundance → EIC shape), focusing on EIC extraction and the similarity matrix, and how MSdev’s stock path compares to custom MSdev_group_feature_EIC().
- Visualizing xcms data
ggplot2 / patchwork helpers for TICs, peaks, features, chromatograms, and XICs from XcmsExperiment, XCMSnExp, and XChromatogram objects.