Introduction:

This workflow takes multiple GC-MS raw data files in netCDF or mzXML format as inputs and outputs peak table. It performs GC-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:

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

'gcms_mass_spectra.msp', corresponding pseudospectrum(compound) mass spectrum information in MSP format, the identifier is same in peak table file.

'gcms_mass_spectra_999norm.msp', intensities normalized mass spectrum information in MSP format, intensities sum=999.

'TICs.pdf', Total Ion Chromatograms.

'BPCs.pdf', Base Peak Chromatograms.

'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.