To cite package ‘MSstats’ in publications use:

  M. Choi, C. Chang, T. Clough, D. Broudy, T. Killeen, B. MacLean, O.
  Vitek, MSstats: an R package for statistical analysis of quantitative
  mass spectrometry-based proteomic experiments, Bioinformatics.
  30:2524-2536, 2014.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments},
    author = {Meena Choi},
    journal = {Bioinformatics},
    volume = {30},
    page = {2524-2536},
    year = {2014},
  }