Code used to analyse LC-HRMS data described in marine oligosaccharide paper can be found in the script 'LC-HRMS_data_analysis.R'
The paper: insert link and citation
LC-HRMS data (mzML) format is available on the MassIVE data base: insert DOI.
Data objects:
- my_own_model_10000-lowlr_016.h5 = NeatMS denoising model trained for the study
- R data objects from pre-processing (sequential)
- data.peaks.RData = R data object with picked peaks (output of findChromPeaks)
- data.peaks.ref.RData = R data object with refined peaks (output of refineChromPeaks)
- data.peaks.ref.gsub.RData = R data object with initial peak grouping for subset based retention time alignment
- data.peaks.ref.gsub.rt.RData = R data object with aligned peaks (output of adjustRtime)
- data.peaks.ref.gsub.rt.grp.RData = R data object with grouped peaks (output of groupChromPeaks)
- data.peaks.ref.gsub.rt.grp.fill.RData = R data object with filled peaks (output of fillChromPeaks)
- tables
- aligned_feature_table_deiso.csv = feature table in NeatMS input format after deisotoping - used as input for NeatMS denoising
- neatms_export_with_extra_properties.csv = OUTPUT of NeatMS denoising
- peaks_manually_checked.csv = list of retained peaks after manual review stage