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).

Corresponding BibTeX entry:

  @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},
    doi = {10.1038/nprot.2017.179},
  }