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.
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.
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.
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.
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.
Corresponding BibTeX entries:
@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},
}
@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},
}
@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},
}
@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},
}
@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},
}