Introduction:

This workflow takes multiple LC-MS raw data files in netCDF or mzXML format as inputs and outputs peak table. It performs LC-MS data preprocessing and peak table operation, including peak detection, spectrum aligning, metabolites annotation and peak table pretreatment.

Input files:

Multiple GC-MS raw data files in netCDF, mzXML or mzML format.

Output files:

'lcms_raw_pkTable.txt', a peak table is generated with one line per "compound" and one column per sample.

'lcms_isotopes_removed_pkTable.txt', isotopes removed peak table.

'lcms_isotopes_removed_pkTable.txt', isotopes removed peak table.

'raw_tics.pdf', raw total ion chromatograms.

'raw_bpcs.pdf', raw base peak chromatograms.

'rtcorrected_tics.pdf', RT corrected total ion chromatograms.

'rtcorrected_bpcs.pdf', RT corrected base peak chromatograms.

'rt_deviation_plot.pdf', plot about RT deviation.

'EICs', Extracted Ion Chromatograms.

'identified_pkTable.txt', identified peak table file in Tab-delimited text format.

'identified_uniq_pkTable.txt', identified unique peak table file in Tab-delimited text format. When row names are duplication, the row with the maximum intensity will be retained.

'detailed_information.txt', detailed information about query and database relationship in library searching.

'outliers_processed_pkTable.txt', outliers processed peak table file in Tab-delimited txt format.

'zero_filled_pkTable.txt', zero filled peak table file in Tab-delimited text format.

'total_area_1000norm_pkTable.txt', total area normalized peak table file in Tab-delimited text format.

Parameter:

Please refer to the corresponding modules for specific parameters.