References

Packages used as part of this project are listed as well as in-text references.

Adusumilli, Ravali and Mallick, Parag. 2017. “Data Conversion with ProteoWizard msConvert.” Methods in Molecular Biology (Clifton, N.J.) 1550: 339–68. https://doi.org/10.1007/978-1-4939-6747-6_23.

Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2022. Rmarkdown: Dynamic Documents for r. https://CRAN.R-project.org/package=rmarkdown.

Bache, Stefan Milton, and Hadley Wickham. 2022. Magrittr: A Forward-Pipe Operator for r. https://CRAN.R-project.org/package=magrittr.

Barthelme, Simon. 2022. Imager: Image Processing Library Based on CImg. https://CRAN.R-project.org/package=imager.

Chambers, Matthew C., Brendan Maclean, Robert Burke, Dario Amodei, Daniel L. Ruderman, Steffen Neumann, Laurent Gatto, et al. 2012. “A Cross-Platform Toolkit for Mass Spectrometry and Proteomics.” Nature Biotechnology 30 (10): 918–20. https://doi.org/10.1038/nbt.2377.

Chang, Winston, Joe Cheng, JJ Allaire, Carson Sievert, Barret Schloerke, Yihui Xie, Jeff Allen, Jonathan McPherson, Alan Dipert, and Barbara Borges. 2022. Shiny: Web Application Framework for r. https://shiny.rstudio.com/.

Daróczi, Gergely. 2021. Logger: A Lightweight, Modern and Flexible Logging Utility. https://daroczig.github.io/logger/.

Deutsch, Eric W. 2010. “Mass Spectrometer Output File Format mzML.” In Proteome Bioinformatics, edited by Simon J. Hubbard and Andrew R. Jones, 319–31. Methods in Molecular Biology™. Totowa, NJ: Humana Press. https://doi.org/10.1007/978-1-60761-444-9_22.

Grolemund, Garrett, and Hadley Wickham. 2011. “Dates and Times Made Easy with lubridate.” Journal of Statistical Software 40 (3): 1–25. https://www.jstatsoft.org/v40/i03/.

Hester, Jim, and Jennifer Bryan. 2022. Glue: Interpreted String Literals. https://CRAN.R-project.org/package=glue.

Müller, Kirill. 2020. Here: A Simpler Way to Find Your Files. https://CRAN.R-project.org/package=here.

Müller, Kirill, and Hadley Wickham. 2022. Tibble: Simple Data Frames. https://CRAN.R-project.org/package=tibble.

Müller, Kirill, Hadley Wickham, David A. James, and Seth Falcon. 2022. RSQLite: SQLite Interface for r. https://CRAN.R-project.org/package=RSQLite.

Ooms, Jeroen. 2014. “The Jsonlite Package: A Practical and Consistent Mapping Between JSON Data and r Objects.” arXiv:1403.2805 [Stat.CO]. https://arxiv.org/abs/1403.2805.

———. 2022. Jsonlite: A Simple and Robust JSON Parser and Generator for r. https://CRAN.R-project.org/package=jsonlite.

Place, Benjamin J. 2021a. “Development of a Data Analysis Tool to Determine the Measurement Variability of Consensus Mass Spectra.” Journal of the American Society for Mass Spectrometry 32 (3): 707–15. https://doi.org/10.1021/jasms.0c00423.

———. 2021b. “Suspect List of Possible Per- and Polyfluoroalkyl Substances (PFAS).” National Institute of Standards; Technology. https://doi.org/10.18434/MDS2-2387.

R Core Team. 2021. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.

R Special Interest Group on Databases (R-SIG-DB), Hadley Wickham, and Kirill Müller. 2022. DBI: R Database Interface. https://CRAN.R-project.org/package=DBI.

RDKit: Open-Soure Cheminformatics (version 2021.09.4). n.d. https://doi.org/10.5281/zenodo.5835217.

RStudio Team. 2020. RStudio: Integrated Development Environment for r. Boston, MA: RStudio, PBC. http://www.rstudio.com/.

Schloerke, Barret, and Jeff Allen. 2022. Plumber: An API Generator for r. https://CRAN.R-project.org/package=plumber.

Spinu, Vitalie, Garrett Grolemund, and Hadley Wickham. 2021. Lubridate: Make Dealing with Dates a Little Easier. https://CRAN.R-project.org/package=lubridate.

Temple Lang, Duncan. 2022. XML: Tools for Parsing and Generating XML Within r and s-Plus. http://www.omegahat.net/RSXML/.

Urbanek, Simon. 2015. Base64enc: Tools for Base64 Encoding. http://www.rforge.net/base64enc.

Ushey, Kevin, JJ Allaire, and Yuan Tang. 2022. Reticulate: Interface to Python. https://CRAN.R-project.org/package=reticulate.

Wickham, Hadley. 2016. Ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org.

———. 2022a. Forcats: Tools for Working with Categorical Variables (Factors). https://CRAN.R-project.org/package=forcats.

———. 2022b. Stringr: Simple, Consistent Wrappers for Common String Operations. https://CRAN.R-project.org/package=stringr.

———. 2022c. Tidyverse: Easily Install and Load the Tidyverse. https://CRAN.R-project.org/package=tidyverse.

Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. “Welcome to the tidyverse.” Journal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.

Wickham, Hadley, Jennifer Bryan, and Malcolm Barrett. 2022. Usethis: Automate Package and Project Setup. https://CRAN.R-project.org/package=usethis.

Wickham, Hadley, Winston Chang, Lionel Henry, Thomas Lin Pedersen, Kohske Takahashi, Claus Wilke, Kara Woo, Hiroaki Yutani, and Dewey Dunnington. 2023. Ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics. https://CRAN.R-project.org/package=ggplot2.

Wickham, Hadley, Romain François, Lionel Henry, and Kirill Müller. 2022. Dplyr: A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr.

Wickham, Hadley, Maximilian Girlich, and Edgar Ruiz. 2022. Dbplyr: A Dplyr Back End for Databases. https://CRAN.R-project.org/package=dbplyr.

Wickham, Hadley, and Lionel Henry. 2023. Purrr: Functional Programming Tools. https://CRAN.R-project.org/package=purrr.

Wickham, Hadley, Jim Hester, and Jennifer Bryan. 2022. Readr: Read Rectangular Text Data. https://CRAN.R-project.org/package=readr.

Wickham, Hadley, Davis Vaughan, and Maximilian Girlich. 2023. Tidyr: Tidy Messy Data. https://CRAN.R-project.org/package=tidyr.

Xie, Yihui. 2014. “Knitr: A Comprehensive Tool for Reproducible Research in R.” In Implementing Reproducible Computational Research, edited by Victoria Stodden, Friedrich Leisch, and Roger D. Peng. Chapman; Hall/CRC. http://www.crcpress.com/product/isbn/9781466561595.

———. 2015. Dynamic Documents with R and Knitr. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. https://yihui.org/knitr/.

———. 2016. Bookdown: Authoring Books and Technical Documents with R Markdown. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/bookdown.

———. 2022a. Bookdown: Authoring Books and Technical Documents with r Markdown. https://CRAN.R-project.org/package=bookdown.

———. 2022b. Knitr: A General-Purpose Package for Dynamic Report Generation in r. https://yihui.org/knitr/.

Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.

Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook.