To cite the MSstatsTMT package in publications use:

  Huang, T., Choi, M., Tzouros, M., Golling, S., Pandya, N.J., Banfai,
  B., Dunkley, T. and Vitek, O. MSstatsTMT: Statistical detection of
  differentially abundant proteins in experiments with isobaric
  labeling and multiple mixtures. Molecular & Cellular Proteomics
  (2020), 19(10), 1706-1723.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {MSstatsTMT: Statistical detection of differentially abundant proteins in experiments with isobaric labeling and multiple mixtures},
    author = {Ting Huang and Meena Choi and Manuel Tzouros and Sabrina Golling and Nikhil Janak Pandya and Balazs Banfai and Tom Dunkley and Olga Vitek},
    journal = {Molecular & Cellular Proteomics},
    volume = {19},
    number = {10},
    pages = {1706-1723},
    year = {2020},
  }