This repository contains the codes for general data processing of LC-MS untargeted metabolomics experiments using XCMS.
Data collected in an experiment in which different white and red wines from different varieties were injected in the HPLC-LTQ-Orbitrap instrument.
The dataset comprises 88 mzML files, with 10 samples each from white and red wines, 14 quality control (QC) samples, representing a pool of all wines, 7 blanks and additional 7 injections of blanks and QCs to equilibrate the system before starting the sequence.
- 1_Sequence.R: Defines who the injection sequence has been generated
- 2_Artefact_filter_FT.Rmd: Removes the fast fourier artifact peaks from spectra, typically contained in data generated by Orbitrap instruments.
- 3_Parameters_setup.Rmd: Different checks to determine the values to indicate in different parameters used in the XCMS functions.
- 4_XCMS_processing.Rmd: Data processing including chromatographic peak detection, retention time alignment, correspondance (peak grouping) and gap filling (initial general inspection).
- 5 - Annotation: 6a CompoundDB, 6b Feature annotation
- 6 - Postprocessing of annotated features
- 7 - Statistical analysis: overview with PCA, tests to select bk of color/variety