MetCirc: navigating mass spectral similarity in high-resolution MS/MS metabolomics data. - Thomas Naake; Emmanuel Gaquerel (Bioinform., 2017)

MatrixQCvis: shiny-based interactive data quality exploration for omics data. - Thomas Naake; Wolfgang Huber (Bioinform., 2022)

MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. - Thomas Naake; Johannes Rainer; Wolfgang Huber (Bioinform., 2023)

SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python. - Marilyn De Graeve; Wout Bittremieux; Thomas Naake; Carolin Huber; Matthias Anagho-Mattanovich; Nils Hoffmann; Pierre Marchal; Victor Chrone; Philippine Louail; Helge Hecht; Michael Witting; Johannes Rainer (J. Open Source Softw., 2025)