11 October 2023
Update to transfer to organization KujawinskiLaboratory. All prior edits as user KujawinskiLaboratory were Krista Longnecker, whose GitHub name is now @redbluewater
22 February 2023
repository for code to process CMP017 samples for C-CoMP
Krista Longnecker \
Samples received at WHOI and analyzed with Lumos using semi-targeted method (set of known m/z values to fragment and then fragment other features if the MS does not find a m/z on the list). See the KujawinskiLaboratory/UntargCode/ for a full description of all the steps used here and the resulting datafiles.
The final set of files generated by this analysis can be analyzed in R/MATLAB/Python, and/or submitted to GNPS for molecular networking analysis. The final set of files will in the /output_dir/xcms2/ folder and are described as follows:
- 'SargPatch_untarg_{neg/pos}_aligned.csv'
- This is the aligned set of mzRT features from the analysis, with one row per mzRT feature. In addition to information about mz value and retention time, there is one column for each sample with the peak areafor the sample
- 'SargPatch_untarg_{neg/pos}_picked.csv'
- This is an unaligned list of mzRT features, these are not grouped into peaks by samples but can be useful for troubleshooting
- 'camera_{neg/pos}.csv'
- This is the aligned set of mzRT features, with the adducts and isotopes determined from CAMERA. This is the best file to use in R/MATLAB/Python for downstream analysis
- 'edgelist_{neg/pos}.csv'
- This is a list of edges that is needed for the GNPS analysis.
- 'fName_featureQuant_afterCAMERA_{neg/pos}.txt'
- This is the aligned list of mzRT features, with CAMERA information, in a format that can be submitted to GNPS.
- 'fName_featureQuant_all_{neg/pos}.txt'
- This is a feature table, mzRT information and peak areas for samples, in a format that can be submitted to GNPS. This version includes all mzRT features.
- 'fName_featureQuant_combined_{neg/pos}.txt'
- This is feature table, mzRT information and peak areas for samples, in a format that can be submitted to GNPS. In this datafile, only features with MS2 information are included
- 'ms2spectra_all_{neg/pos}.mgf'
- This is an mgf file, which can be submitted to GNPS; this version contains every MS2 spectra
- 'ms2spectra_combined_{neg/pos}.mgf'
- This is an mgf file, which can be submitted to GNPS; this version combines MS2 spectra based on the metric set at step 4.
Note that the {neg/pos} in the file name indicates that two files are produced - one for negative ion mode and one for positive ion mode.