This respository contains all the files and scripts necessary to participate in the FTICR-MS data analysis demonstration at the SBR SFA Community Workshop 2019. Moreover, this repository will hopefully provide insight into FTICR-MS analysis more broadly. This will not outline all possible analysis types, but rather investigate only a few. If there are any questions, please refer them to [email protected].

Here is a brief outline of the included files:

Carbon_Efficiency.R: This script will calculate carbon-use efficiency for each carbon content in a dataset and will generate one figure.
FTICR Analysis Walkthrough.docx: This Word document has step-by-step instructions which will walk through how to analyze the provided FTICR data
FTMS_Analysis.R: This script is a necessary pre-processing step for a provided FTICR report in order for other scripts to function. This will remove isotopic peaks and limit the mass range of peaks to 200-900 m/z. This script is based upon the 'ftmsRanalysis' R package
HJ_Andrews_Tutorial_Report.csv: An example FTICR report generate from Watershed 1 within the HJ Andrews Experimental Forest, Oregon
SBR_SFA_ICR_Tutorial.pptx: The PowerPoint shown at the Watershed Workshop ICR Tutorial
Transformation_Analysis.R: This script will perform a "transformation analysis" which will identify putative biochemical reactions within a dataset given a transformation database. Such analyses are outlined in Breitling et al., 2006 - Metabolomics and Graham et al., 2017 - JGR: Biogeosciences. This script will generate two figures.
Transformation_List_Amino_Acid.csv: The transformation database for the transformation analysis; only identifies putative amino acid transformations.
install_packages_commands.txt: A file to allow copying-and-pasting of R install package commands.

The AGU CZO:Watershed Workshop 2019 folder contains the necessary files for the FTICR tutorial given at that workshop.
The EMSL Summer School 2020 folder contains all of the necessary files for the tutorial given during the summer school.