citHeader("If you use mzR, please cite")

citEntry(entry="article",  
    author = "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",
    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",
    textVersion = paste("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.")
)

citHeader("You may want to cite the formats and libraries used in mzR:")

citEntry(entry="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",
   textVersion = paste("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."))

citEntry(entry="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",
   textVersion = paste("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."))


citEntry(entry="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",
   textVersion = paste("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."))

citEntry(entry="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",
   textVersion = paste("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."))

