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xcms-preprocessing

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Programmatic untargeted LC-MS feature extraction in R with the modern xcms 4.x MsExperiment/XcmsExperiment API, taking raw mzML to a feature table via CentWave peak detection, retention-time alignment, peak-density correspondence, gap-filling, CAMERA redundancy collapse, and built-in QC feature filtering. Use when converting centroided LC-MS runs into a features-by-samples matrix and deciding centWave/grouping/alignment parameters. For drift correction and QC/CV filtering execution see metabolomics/normalization-qc; for metabolite identification see metabolomics/metabolite-annotation; for the MS-DIAL GUI alternative with MS2Dec deconvolution see metabolomics/msdial-preprocessing; for downstream statistics see metabolomics/statistical-analysis.

When to use

• converting centroided LC-MS runs into a features-by-samples matrix
• deciding centWave/grouping/alignment parameters
• detecting chromatographic peaks per file
• aligning retention times across runs
• grouping corresponding peaks into features
• filling gaps in feature tables
• collapsing adduct/isotope redundancy

When not to use

• drift correction and QC/CV filtering execution
• metabolite identification
• MS-DIAL GUI alternative with MS2Dec deconvolution
• downstream statistics
• GC-EI data preprocessing

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