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