To cite package ‘MSstatsPTM’ in publications use:

  D. Kohler, T.H. Tsai, E. Verschueren, T. Huang, T. Hinkle, L. Phu, M.
  Choi, O. Vitek, MSstatsPTM: Statistical relative quantification of
  post-translational modifications in bottom-up mass spectrometry-based
  proteomics, Molecular and Cellular Proteomics. 100477, 2022.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {MSstatsPTM: Statistical relative quantification of 
         post-translational modifications in bottom-up mass spectrometry-based 
         proteomics},
    author = {Devon Kohler and Tsung-Heng Tsai and Erik Verschueren and Ting Huang and Trent Hinkle and Lilian Phu and Meena Choi and Olga Vitek},
    journal = {Molecular and Cellular Proteomics},
    volume = {100477},
    year = {2022},
  }