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feat(mztab-m): add an mzTab-M data source and query layer #62

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Merged
oss6 merged 1 commit into from
Oct 25, 2026
Merged

feat(mztab-m): add an mzTab-M data source and query layer #62

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3 changes: 2 additions & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: lcmsPlot
Type: Package
Title: Comprehensive Liquid Chromatography-Mass Spectrometry (LC-MS) data visualisation package
Version: 1.1.18
Version: 1.1.19
Authors@R: c(
person(
"Ossama",
Expand Down Expand Up @@ -81,6 +81,7 @@ Collate:
'data-source-ms-dial.R'
'data-source-compound-discoverer-node.R'
'data-source-lipid-search.R'
'data-source-mztab.R'
'data-validation.R'
'data-adapters.R'
'lcmsPlotDataContainer-class.R'
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3 changes: 3 additions & 0 deletions NAMESPACE
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Expand Up @@ -37,6 +37,7 @@ export(CompoundDiscovererNodeSource)
export(LipidSearchSource)
export(MZmineFeatureListsSource)
export(MsDialPeaksSource)
export(MzTabMSource)
export(XcmsRawList)
export(create_xcms_raw_list)
export(detectedPeaks)
Expand All @@ -59,6 +60,7 @@ export(lp_layout)
export(lp_legend)
export(lp_lipid_search)
export(lp_mass_trace)
export(lp_mztab)
export(lp_peak_count_image)
export(lp_peak_density)
export(lp_purity_distribution)
Expand All @@ -75,6 +77,7 @@ export(summaries)
exportClasses(CompoundDiscovererNodeSource)
exportClasses(ExternalDataSource)
exportClasses(LipidSearchSource)
exportClasses(MzTabMSource)
exportClasses(XcmsRawList)
exportClasses(lcmsPlotClass)
exportClasses(lcmsPlotDataContainer)
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14 changes: 14 additions & 0 deletions NEWS.md
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@@ -1,3 +1,17 @@
# lcmsPlot 1.1.19

- New `MzTabMSource()` reads mzTab-M 2.0 files (as exported by MS-DIAL,
MZmine, OpenMS, ...) alongside their raw files (#51). Small molecule
features (SMF) become peaks with their `feature_id`, `adduct_ion` and
`charge`, annotated with the `name`, `formula`, `database_identifier` and
`reliability` of the summary (SML) rows that reference them. The new
`lp_mztab()` layer selects the features to plot, e.g.
`lp_mztab(features_query = "reliability <= 2")`.
- The vignette plots a real mzTab-M example: the HUPO-PSI MTBLS263 file
(Progenesis QI) with the MetaboLights raw files it describes, cut down to
eight features. Both ship in `inst/extdata` (`MTBLS263.mztab`,
`mtbls263-mzml.zip`); `tools/mztab/make-mtbls263-example.R` rebuilds them.

# lcmsPlot 1.1.18

- **Breaking: `lcmsPlotDataContainer` now holds RforMassSpectrometry data
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