If you use mzR, please cite You may want to cite the formats and
libraries used in mzR:

  A cross-platform toolkit for mass spectrometry and proteomics
  Chambers, Matthew C. and Maclean, Brendan and Burke, Robert and
  Amodei, Dario and Ruderman, Daniel L. and Neumann, Steffen and Gatto,
  Laurent and Fischer, Bernd and Pratt, Brian and Egertson, Jarrett and
  Hoff, Katherine and Kessner, Darren and Tasman, Natalie and Shulman,
  Nicholas and Frewen, Barbara and Baker, Tahmina A. and Brusniak,
  Mi-Youn and Paulse, Christopher and Creasy, David and Flashner, Lisa
  and Kani, Kian and Moulding, Chris and Seymour, Sean L. and Nuwaysir,
  Lydia M. and Lefebvre, Brent and Kuhlmann, Frank and Roark, Joe and
  Rainer, Paape and Detlev, Suckau and Hemenway, Tina and Huhmer,
  Andreas and Langridge, James and Connolly, Brian and Chadick, Trey
  and Holly, Krisztina and Eckels, Josh and Deutsch, Eric W. and
  Moritz, Robert L. and Katz, Jonathan E. and Agus, David B. and
  MacCoss, Michael and Tabb, David L. and Mallick, Parag Nat
  Biotechnol. 2012 NOct;30(10):918-920.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {{Chambers} and Matthew C. and {Maclean} and {Brendan} and {Burke} and {Robert} and {Amodei} and {Dario} and {Ruderman} and Daniel L. and {Neumann} and {Steffen} and {Gatto} and {Laurent} and {Fischer} and {Bernd} and {Pratt} and {Brian} and {Egertson} and {Jarrett} and {Hoff} and {Katherine} and {Kessner} and {Darren} and {Tasman} and {Natalie} and {Shulman} and {Nicholas} and {Frewen} and {Barbara} and {Baker} and Tahmina A. and {Brusniak} and {Mi-Youn} and {Paulse} and {Christopher} and {Creasy} and {David} and {Flashner} and {Lisa} and {Kani} and {Kian} and {Moulding} and {Chris} and {Seymour} and Sean L. and {Nuwaysir} and Lydia M. and {Lefebvre} and {Brent} and {Kuhlmann} and {Frank} and {Roark} and {Joe} and {Rainer} and {Paape} and {Detlev} and {Suckau} and {Hemenway} and {Tina} and {Huhmer} and {Andreas} and {Langridge} and {James} and {Connolly} and {Brian} and {Chadick} and {Trey} and {Holly} and {Krisztina} and {Eckels} and {Josh} and {Deutsch} and Eric W. and {Moritz} and Robert L. and {Katz} and Jonathan E. and {Agus} and David B. and {MacCoss} and {Michael} and {Tabb} and David L. and {Mallick} and {Parag}},
    year = {2012},
    journal = {Nat Biotech},
    title = {{A cross-platform toolkit for mass spectrometry and proteomics}},
    doi = {10.1038/nbt.2377},
    pmid = {23051804},
    month = {oct},
    number = {10},
    volume = {30},
    pages = {918--920},
    url = {http://dx.doi.org/10.1038/nbt.2377},
  }

  Mol Cell Proteomics. 2010 Aug 17. mzML - a Community Standard for
  Mass Spectrometry Data. Martens L, Chambers M, Sturm M, Kessner D,
  Levander F, Shofstahl J, Tang WH, Rompp A, Neumann S, Pizarro AD,
  Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P,
  Hermjakob H, Binz PA, Deutsch EW.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Lennart Martens and Matthew Chambers and Marc Sturm and Darren Kessner and Fredrik Levander and Jim Shofstahl and Wilfred H Tang and Andreas Rompp and Steffen Neumann and Angel D Pizarro and Luisa Montecchi-Palazzi and Natalie Tasman and Mike Coleman and Florian Reisinger and Puneet Souda and Henning Hermjakob and Pierre-Alain Binz and Eric W Deutsch},
    title = {mz{ML} - a {C}ommunity {S}tandard for {M}ass {S}pectrometry {D}ata.},
    journal = {{Mol Cell Proteomics}},
    year = {2010},
    pmid = {20716697},
    doi = {10.1074/mcp.R110.000133},
  }

  Nat Biotechnol. 2004 Nov;22(11):1459-66. A common open representation
  of mass spectrometry data and its application to proteomics research.
  Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B,
  Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE,
  Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn
  G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Patrick G A Pedrioli and Jimmy K Eng and Robert Hubley and Mathijs Vogelzang and Eric W Deutsch and Brian Raught and Brian Pratt and Erik Nilsson and Ruth H Angeletti and Rolf Apweiler and Kei Cheung and Catherine E Costello and Henning Hermjakob and Sequin Huang and Randall K Julian and Eugene Kapp and Mark E McComb and Stephen G Oliver and Gilbert Omenn and Norman W Paton and Richard Simpson and Richard Smith and Chris F Taylor and Weimin Zhu and Ruedi Aebersold},
    title = {{A} common open representation of mass spectrometry data and its
	application to proteomics research.},
    journal = {Nat Biotechnol},
    year = {2004},
    volume = {22},
    number = {11},
    pages = {{1459--1466}},
    pmid = {15529173},
    doi = {10.1038/nbt1031},
  }

  Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2. A uniform
  proteomics MS/MS analysis platform utilizing open XML file formats.
  Keller A, Eng J, Zhang N, Li XJ, Aebersold R.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Andrew Keller and Jimmy Eng and Ning Zhang and Xiao-jun Li and Ruedi Aebersold},
    title = {{A} uniform proteomics {MS}/{MS} analysis platform utilizing open {XML} file formats.},
    journal = {Mol Syst Biol},
    year = {2005},
  }

  Bioinformatics. 2008 Nov 1;24(21):2534-6. Epub 2008 Jul 7.
  ProteoWizard: open source software for rapid proteomics tools
  development. Kessner D, Chambers M, Burke R, Agus D, Mallick P.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Darren Kessner and Matt Chambers and Robert Burke and David Agus and Parag Mallick},
    title = {{P}roteo{W}izard: open source software for rapid proteomics tools
	development.},
    journal = {Bioinformatics},
    year = {2008},
    volume = {24},
    number = {21},
    pages = {2534--2536},
    doi = {10.1093/bioinformatics/btn323},
    pmid = {18606607},
  }