To cite patRoon in publications use:

  Helmus, R., ter Laak, T.L., van Wezel, A.P., de Voogt, P.,
  Schymanski, E.L. patRoon: open source software platform for
  environmental mass spectrometry based non-target screening. J
  Cheminform 13, 1 (2021). https://doi.org/10.1186/s13321-020-00477-w

A BibTeX entry for LaTeX users is

  @Article{,
    title = {patRoon: open source software platform for environmental mass spectrometry based non-target screening},
    author = {Rick Helmus and Thomas L. {ter Laak} and Annemarie P. {van Wezel} and Pim {de Voogt} and Emma L. Schymanski},
    journal = {Journal of Cheminformatics},
    year = {2021},
    volume = {13},
    number = {1},
    url = {https://doi.org/10.1186/s13321-020-00477-w},
    doi = {10.1186/s13321-020-00477-w},
  }

  Helmus, R., van de Velde, Bas, Brunner, Andrea M., ter Laak, T.L.,
  van Wezel, A.P., de Voogt, P., Schymanski, E.L. patRoon 2.0: Improved
  non-target analysis workflows including automated transformation
  product screening. Journal of Open Source Software, 7(71), 4029,
  https://doi.org/10.21105/joss.04029

A BibTeX entry for LaTeX users is

  @Article{,
    title = {patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening},
    author = {Rick Helmus and Bas {van de Velde} and Andrea M. Brunner and Thomas L. {ter Laak} and Annemarie P. {van Wezel} and Emma L. Schymanski},
    journal = {Journal of Open Source Software},
    publisher = {The Open Journal},
    year = {2022},
    volume = {7},
    number = {71},
    pages = {4029},
    url = {https://doi.org/10.21105/joss.04029},
    doi = {10.21105/joss.04029},
  }