To cite the package, please use one of the appropriate publications listed below.

Nanni P, Panse C, Gehrig P, Mueller S, Grossmann J, Schlapbach R. (2013) PTM MarkerFinder, a software tool to detect and validate spectra from peptides carrying post-translational modifications. PROTEOMECS. 2013 Aug;13(15):2251-5.<doi:10.1002/pmic.201300036>. Epub 2013 Jul 1.

Panse C, Trachsel C, Grossmann J and Schlapbach R. (2015). specL - An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics. Bioinformatics.<doi:10.1093/bioinformatics/btv105>.

Grossmann J, Roschitzki B, Panse C, Fortes C, Barkow-Oesterreicher S, Rutishauser D, Schlapbach R. (2010). Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods. J Proteomics. 2010 Aug 5;73(9):1740-6.<doi:10.1016/j.jprot.2010.05.011>. Epub 2010 May 31.

Corresponding BibTeX entries:

  @Article{,
    title = {{PTM MarkerFinder}, a software tool to detect and validate
      spectra from peptides carrying post-translational
      modifications.},
    author = {Paolo Nanni and Christian Panse and Peter Gehrig and
      Susanne Mueller and Jonas Grossmann and Ralph Schlapbach},
    journal = {PROTEOMICS},
    year = {2013},
    volume = {13},
    number = {15},
    pages = {2251-2255},
    doi = {10.1002/pmic.201300036 },
    url = {http://dx.doi.org/10.1002/pmic.201300036},
  }
  @Article{,
    title = {{spec{L} - {A}n {R}/{B}ioconductor package to prepare
      peptide spectrum matches for use in targeted proteomics}},
    author = {Christian Panse and Christian Trachsel and Jonas
      Grossmann and Ralph Schlapbach},
    journal = {Bioinformatics},
    pages = {2228-2231},
    month = {Feb},
    year = {2015},
    doi = {10.1093/bioinformatics/btv105},
    url = {http://dx.doi.org/10.1093/bioinformatics/btv105},
  }
  @Article{,
    title = {Implementation and evaluation of relative and absolute
      quantification in shotgun proteomics with label-free methods },
    author = {Jonas Grossmann and Bernd Roschitzki and Christian Panse
      and Claudia Fortes and Simon Barkow-Oesterreicher and Dorothea
      Rutishauser and Ralph Schlapbach},
    journal = {Journal of Proteomics},
    volume = {73},
    number = {9},
    pages = {1740 - 1746},
    year = {2010},
    issn = {1874-3919},
    doi = {10.1016/j.jprot.2010.05.011},
    url =
      {http://www.sciencedirect.com/science/article/pii/S1874391910001703},
  }