Changelog

Source: NEWS.md

mrmhub 1.0.1

• Drift correction and correct_batch_serrf() no longer require the optional packages mirai and carrier. They run sequentially unless parallel workers are set up with mirai::daemons().
• Plot axes with large values, such as intensities, show compact scientific labels with one exponent per axis (e.g. 0.5E6, 1.0E6, 1.5E6) instead of a superscript exponent on each label, leaving more room for the panels.
• INTEGRATOR: reading mzML files and peak detection are faster. The batch column of the sample list and the uniform_width and baseline columns of the transition list are optional, and the valley-drop baseline is computed correctly when several features share one transition. Step 4 (chromatogram PDFs) finds R on the PATH and, on Windows, otherwise uses the newest installed R.
• MRMhub-viz now caches loaded data and draws chromatograms only as they scroll into view, resulting in smoother scrolling and faster, automatic updates when plot settings are changed. A new status line reports progress and errors.

mrmhub 1.0.0

First stable release of the MRMhub software framework.

Changes

• New function set_lipid_class() derives lipid classes from lipid feature names using the rgoslin package.
• Calibration curves support 1/sqrt(x) weighting.
• External calibration works with only one or two calibrator levels too.
• QC metrics report the number of replicates per QC type (new columns n_bqc, n_tqc, n_spl).
• New release v1.0.0 with INTEGRATOR binaries and the QUANT R package, with and without a complete demo project.
• Various bug fixes and improvements in robustness, performance and usability.

mrmhub 0.9.9

Peer-reviewed version of Burla, Teo et al., Nature Metabolism (2026), doi:10.1038/s42255-026-01629-2. The version initially submitted for review was 0.9.2.

Changes

• New isotope interference correction for precursor (MS1) and transition-level (MRM) interferences, based on the LICAR method (Gao et al., Anal. Chem. 2021).
• New batch-correction methods (experimental): empirical Bayes ComBat (correct_batch_combat(); Johnson et al., Biostatistics 2007) and SERRF random-forest normalization (correct_batch_serrf(); Fan et al., Anal. Chem. 2019), complementing correct_batch_centering().
• New import from and export to the community format mzTab-M (import_data_mztab(), save_dataset_mztab(); Hoffmann et al., Anal. Chem. 2019).
• New export to Bioconductor SummarizedExperiment (Morgan et al.) and lipidr LipidomicsExperiment objects (Mohamed et al., J. Proteome Res. 2020) via save_dataset_summarizedexperiment().
• More consistent plotting, with plot settings such as point size, colours, legend placement and dimensions definable globally via mrmhub_set_plot_defaults().
• New save_plot() writes any plot_*() figure to a file at a defined physical size and format, including multi-page PDFs.
• New save_dataset_rds() and read_dataset_rds() save and load a complete MRMhubExperiment, making it easy to share and archive datasets with all data, metadata and processing status.
• Improved console output, processing summaries and more actionable error messages.
• Enhanced up-front validation of function arguments.
• Improved data and metadata import, with more robust sample and feature ID matching, deduplication and stronger schema validation.
• Various bug fixes and improvements in performance, robustness and usability, partly based on user feedback.