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Overview

This repository accompanies the manuscript “Comprehensive mass spectrometry workflows to systematically elucidate transformation processes of organic micropollutants: a case study on photodegradation of four pharmaceuticals” and contains the R and patRoon based data processing scripts and algorithms that were used to elucidate transformation products from photodegradation experiments.

The repository layout is as follows:

  • workflow.R: the main processing script
  • workflow/ directory: script files that implement the main workflow
  • utils/ directory: scripts with utility functions used throughout the workflow
  • report_pd directory: all support files needed for automatic report generation
  • misc/ directory: miscellaneous workflow input files (suspect lists, sample info etc)
  • output/ directory: output files generated throughout the workflow
    • specifically: suspects_TPs-compounds.csv and suspects_TPs-formulas.csv: suspect lists generated during TP suspect screening workflows
  • renv.lock: an renv lockfile to recreate a reproducible R environment

Used software

General

Software Version URL
R 4.2.2 https://www.r-project.org/
DataAnalysis 4.4 https://www.bruker.com/
OpenMS 2.7 https://openms.de/
GenForm embededded in patRoon https://sourceforge.net/projects/genform/
MetFrag 2.5 http://ipb-halle.github.io/MetFrag/
BioTransformer 3.0.0 http://biotransformer.ca/
Chemical Transformation Simulator Accessed online July 19th 2024 https://qed.epa.gov/cts/
MolView 2.4 https://molview.org/
CDK Depict – https://www.simolecule.com/cdkdepict/depict.html
OpenBabel 3.1.1 https://github.com/openbabel/openbabel
Inkscape 1.2.2 https://inkscape.org/

Used R packages

package version url
ChemmineR 3.48.0 https://github.com/girke-lab/ChemmineR
RColorBrewer 1.1.3 https://cran.r-project.org/web/packages/RColorBrewer
callr 3.7.6 https://callr.r-lib.org
cliqueMS 1.7.1 http://cliquems.seeslab.net
data.table 1.15.4 https://r-datatable.com
depict 0.4.0 https://github.com/CDK-R/depict
fastcluster 1.2.6 https://danifold.net/fastcluster.html
fmcsR 1.38.0 https://github.com/girke-lab/fmcsR
future 1.33.2 https://future.futureverse.org
future.apply 1.11.2 https://future.apply.futureverse.org
kableExtra 1.4.0.4 http://haozhu233.github.io/kableExtra/
knitr 1.48 https://yihui.org/knitr/
magick 2.7.3 https://docs.ropensci.org/magick/
mzR 2.30.0 https://github.com/sneumann/mzR/
pagedown 0.20.1 https://github.com/rstudio/pagedown
patRoon 2.3.3 https://github.com/rickhelmus/patRoon
processx 3.8.4 https://processx.r-lib.org
rcdk 3.8.1 https://cdk-r.github.io/cdkr/
reactable 0.4.4 https://glin.github.io/reactable/
renv 1.0.7 https://rstudio.github.io/renv/
rmarkdown 2.27 https://github.com/rstudio/rmarkdown
svglite 2.1.3 https://svglite.r-lib.org
withr 3.0.0 https://withr.r-lib.org