To cite the SWATH2stats package in publications use:

  Blattmann P, Heusel M, Aebersold R. SWATH2stats: An R/Bioconductor
  Package to Process and Convert Quantitative SWATH-MS Proteomics Data
  for Downstream Analysis Tools. PLoS ONE 11(4): e0153160 (2016).

A BibTeX entry for LaTeX users is

  @Article{,
    title = {SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools},
    author = {Peter Blattmann and Moritz Heusel and Ruedi Aebersold},
    journal = {PLoS ONE},
    year = {2016},
    volume = {11},
    issue = {4},
    pages = {e0153160},
    doi = {10.1371/journal.pone.0153160},
    url = {http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0153160},
  }