NMR AND LC-MS SCRIPTS AND PROCESSING STEPS FOR META-ANALYSIS MANUSCRIPT:
Navigate to the LC-MS or NMR folder for processing steps on that instrument.
In the NMR folder, here on Github, you will find the MATLAB functions for referencing alignment, baseline correction, and peak picking.
All NMR and LC-MS datasets and acquisition parameters can be found in Metabolomics Workbench (https://www.metabolomicsworkbench.org):
LC-MS Study ID: ST002092
NMR polar Study ID: ST002095
NMR non-polar Study ID: ST002096
The data can be accessed directly via its Project DOI: http://dx.doi.org/10.21228/M82978.
QUALITY CONTROL SCRIPTS:
The scripts for feature filtering and elemental formula comparisons between SIRIUS and the LC-MS meta-analysis results are available on GitHub (https://github.com/McIntyre-Lab/papers/tree/master/shaver_metaanalysis_2022 ).
Python code for quality control (QC) is available at: (https://github.com/secimTools/SECIMTools) and can be run via Galaxy tools at (https://docs.galaxyproject.org/en/master/) or from a command line interface.
The meta-analysis (meta_analysis.py) and rank transformation (add_group_rank.py) python code is available on the SECIMtools GitHub page, version 22.3.23 or higher.
Shell scripts for running QC are available in (https://github.com/McIntyre-Lab/papers/tree/master/shaver_metaanalysis_2022).