To cite the DEP package in publications use:

  Xiaofei Zhang, Arne H. Smits, Gabrielle B.A. van Tilburg, Huib Ovaa,
  Wolfgang Huber and Michiel Vermeulen. Proteome-wide identification of
  ubiquitin interactions using UbIA-MS. Nature Protocols (2018).

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Proteome-wide identification of ubiquitin interactions using UbIA-MS},
    author = {Xiaofei Zhang and Arne H Smits and Gabrielle BA {van Tilburg} and Huib Ovaa and Wolfgang Huber and Michiel Vermeulen},
    journal = {Nature Protocols},
    year = {2018},
    volume = {13},
    pages = {530–550},
  }