13C15N_abundance_correction

Correction method as described in https://doi.org/10.1021/acs.analchem.9b01788

This method relies on the Isotope correction Toolbox as described in this paper by Jungreuthmayer et al.

Preparation

• have perl and python installed an running
  • for perl setup we refer to ict
  • python version 3 with the modules argparse, numpy and csv is needed
• adjust the data in data_template.txt and save them as measured_data.txt (or any other name. Adjust accordingly in later steps)
• complete the model in notation.fml (can also be done afterwards)
  • In case of questions regarding the atom numbering refer to the images inside the InChI folder
• clone the repository recursively (to include ICT) git clone --recurse-submodules [email protected]:modsim/13C15N_abundance_correction.git

Correction Workflow

• run ICT on the data: ./externals/isotope_correction_toolbox/ict.pl -c chemdata.txt -m measured_data.txt -o corrected_data.txt
  • watch for errors and fix them
• Optional: in the ict2fluxml.py file adjust the default standard deviation. By default it is set to 0.01
• convert the ICT output to FluxML: ./ict2fluxml.py corrected_data.txt
• copy and past the output to the notation.fml file (inside the <data> tag)
• execute your regular flux estimation workflow