% to: sb,jg if you want to add something use this tool here:
% http://www.bioinformatics.org/texmed/
@article{Gehrig2020,
  doi = {10.1021/jasms.0c00040},
  url = {https://doi.org/10.1021/jasms.0c00040},
  year = {2020},
  month = nov,
  publisher = {American Chemical Society ({ACS})},
  volume = {32},
  number = {1},
  pages = {157--168},
  author = {Peter M. Gehrig and Kathrin Nowak and Christian Panse and Mario Leutert and Jonas Grossmann and Ralph Schlapbach and Michael O. Hottiger},
  title = {Gas-Phase Fragmentation of {ADP}-Ribosylated Peptides: Arginine-Specific Side-Chain Losses and Their Implication in Database Searches},
  journal = {Journal of the American Society for Mass Spectrometry}
}

@Article{Kockmann2021,
    title = {The {rawrr R} Package: Direct Access to Orbitrap Data and Beyond},
    author = {Tobias Kockmann and Christian Panse},
    journal = {Journal of Proteome Research},
    year = {2021},
    doi = {10.1021/acs.jproteome.0c00866},
    url = {https://doi.org/10.1021/acs.jproteome.0c00866},
  }

@Article{pmid28035797,
   Author="Bilan, V. and Leutert, M.  and Nanni, P.  and Panse, C.  and Hottiger, M. O. ",
   Title="{{C}ombining {H}igher-{E}nergy {C}ollision {D}issociation and {E}lectron-{T}ransfer/{H}igher-{E}nergy {C}ollision {D}issociation {F}ragmentation in a {P}roduct-{D}ependent {M}anner {C}onfidently {A}ssigns {P}roteomewide {A}{D}{P}-{R}ibose {A}cceptor {S}ites}",
   Journal="Anal. Chem.",
   Year="2017",
   Volume="89",
   Number="3",
   Pages="1523--1530",
   Month="Feb",
   doi={10.1021/acs.analchem.6b03365}
}


@Manual{readMzXmlData,
    title = {readMzXmlData: Reads mass spectrometry data in mzXML format},
    author = {Sebastian Gibb},
    year = {2013},
    note = {R package version 2.6},
    url = {http://CRAN.R-project.org/package=readMzXmlData}
}
 

@Article{pmid22113085,
   Author="Gatto, L.  and Lilley, K. S. ",
   Title="{{M}{S}nbase-an {R}/{B}ioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation}",
   Journal="Bioinformatics",
   Year="2012",
   Volume="28",
   Number="2",
   Pages="288--289",
   Month="Jan"
}


@Article{pmid21374817,
   Author="Martens, L.  and Vizcaino, J. A.  and Banks, R. ",
   Title="{{Q}uality control in proteomics}",
   Journal="Proteomics",
   Year="2011",
   Volume="11",
   Number="6",
   Pages="1015--1016",
   Month="Mar"
}


@Article{pmid23657399,
    Author="{nbt.2588}",
    Title="{Raising standards}",
    Journal="Nat. Biotechnol.",
    Year="2013",
    Volume="31",
    Number="5",
    Pages="366",
    Month="May",
    Note={[doi:10.1038/nbt.2588], \url{http://www.nature.com/nbt/journal/v31/n5/pdf/nbt.2588.pdf} }
}



@Article{pmid17940529,
   Author="Bodenmiller, B.  and Malmstrom, J.  and Gerrits, B.  and Campbell, D.  and Lam, H.  and Schmidt, A.  and Rinner, O.  and Mueller, L. N.  and Shannon, P. T.  and Pedrioli, P. G.  and Panse, C.  and Lee, H. K.  and Schlapbach, R.  and Aebersold, R. ",
   Title="{{P}hospho{P}ep--a phosphoproteome resource for systems biology research in {D}rosophila {K}c167 cells}",
   Journal="Mol. Syst. Biol.",
   Year="2007",
   Volume="3",
   Pages="139"
}

@Article{pmid22693562,
   Author="Tweedie-Cullen, R. Y.  and Brunner, A. M.  and Grossmann, J.  and Mohanna, S.  and Sichau, D.  and Nanni, P.  and Panse, C.  and Mansuy, I. M. ",
   Title="{{I}dentification of combinatorial patterns of post-translational modifications on individual histones in the mouse brain}",
   Journal="PLoS ONE",
   Year="2012",
   Volume="7",
   Number="5",
   Pages="e36980",
   DOI={10.1371/journal.pone.0036980}
}

@Article{pPTM,
	Author="Nanni, P. and Panse, C. and Gehrig, P. and Mueller, S. and Grossmann, J. and Schlapbach, R. ",
	Title="{{P}{T}{M} {M}arker{F}inder, a software tool to detect and validate spectra from peptides carrying post-translational modifications}",
	Journal="Proteomics",
	Year="2013",
	Volume="13",
	Number="15",
	Pages="2251--2255",
	Month="Aug",
	doi = {10.1002/pmic.201300036}
}


@Article{tpp,
   Author="Deutsch, E. W.  and Mendoza, L.  and Shteynberg, D.  and Farrah, T.  and Lam, H.  and Tasman, N.  and Sun, Z.  and Nilsson, E.  and Pratt, B.  and Prazen, B.  and Eng, J. K.  and Martin, D. B.  and Nesvizhskii, A. I.  and Aebersold, R. ",
   Title="{{A} guided tour of the {T}rans-{P}roteomic {P}ipeline}",
   Journal="Proteomics",
   Year="2010",
   Volume="10",
   Number="6",
   Pages="1150--1159",
   Month="Mar"
}

@Article{openms,
   Author="Sturm, M.  and Bertsch, A.  and Gropl, C.  and Hildebrandt, A.  and Hussong, R.  and Lange, E.  and Pfeifer, N.  and Schulz-Trieglaff, O.  and Zerck, A.  and Reinert, K.  and Kohlbacher, O. ",
   Title="{{O}pen{M}{S} - an open-source software framework for mass spectrometry}",
   Journal="BMC Bioinformatics",
   Year="2008",
   Volume="9",
   Pages="163"
}

@Article{pmid17164402,
   Author="Zubarev, R.  and Mann, M. ",
   Title="{{O}n the proper use of mass accuracy in proteomics}",
   Journal="Mol. Cell Proteomics",
   Year="2007",
   Volume="6",
   Number="3",
   Pages="377--381",
   Month="Mar"
}


@Article{pmid20576481,
   Author="Grossmann, J.  and Roschitzki, B.  and Panse, C.  and Fortes, C.  and Barkow-Oesterreicher, S.  and Rutishauser, D.  and Schlapbach, R. ",
   Title="{{I}mplementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods}",
   Journal="J Proteomics",
   Year="2010",
   Volume="73",
   Number="9",
   Pages="1740--1746",
   Month="Aug",
   DOI={10.1016/j.jprot.2010.05.011}
}

@Article{pmid17114649,
   Author="Munton, R. P.  and Tweedie-Cullen, R.  and Livingstone-Zatchej, M.  and Weinandy, F.  and Waidelich, M.  and Longo, D.  and Gehrig, P.  and Potthast, F.  and Rutishauser, D.  and Gerrits, B.  and Panse, C.  and Schlapbach, R.  and Mansuy, I. M. ",
   Title="{{Q}ualitative and quantitative analyses of protein phosphorylation in naive and stimulated mouse synaptosomal preparations}",
   Journal="Mol. Cell Proteomics",
   Year="2007",
   Volume="6",
   Number="2",
   Pages="283--293",
   Month="Feb",
}

@Article{pmid23000593,
   Author="Ortea, I.  and Roschitzki, B.  and Ovalles, J. G.  and Longo, J. L.  and de la Torre, I.  and Gonzalez, I.  and Gomez-Reino, J. J.  and Gonzalez, A. ",
   Title="{{D}iscovery of serum proteomic biomarkers for prediction of response to infliximab (a monoclonal anti-{T}{N}{F} antibody) treatment in rheumatoid arthritis: an exploratory analysis}",
   Journal="J Proteomics",
   Year="2012",
   Volume="77",
   Pages="372--382",
   Month="Dec"
}

@Article{pmid6525415,
   Author="Roepstorff, P.  and Fohlman, J. ",
   Title="{{P}roposal for a common nomenclature for sequence ions in mass spectra of peptides}",
   Journal="Biomed. Mass Spectrom.",
   Year="1984",
   Volume="11",
   Number="11",
   Pages="601",
   Month="Nov",
   DOI={10.1002/bms.1200111109}
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@BOOK{visualizing,
AUTHOR={W. S. Cleveland},
TITLE={Visualizing Data},
PUBLISHER={Hobart Press},
ADDRESS={Summit, New Jersey, U.S.A.},
YEAR={1993}
}

@book{venables2002modern,
  title={Modern Applied Statistics with S},
  author={Venables, W.N. and Ripley, B.D.},
  isbn={9780387954578},
  lccn={2002022925},
  series={Statistics and Computing},
  url={http://books.google.ch/books?id=974c4vKurNkC},
  year={2002},
  publisher={Springer}
}

@book{gonick1991cartoon,
  title={Cartoon Guide to Genetics},
  author={Gonick, L.},
  isbn={9780062730992},
  lccn={82048252},
  url={http://books.google.ch/books?id=TR2zzV77DCMC},
  year={1991},
  publisher={HarperCollins}
}
@book{knuth1992literate,
  title={"Literate Programming"},
  author={Knuth, D.E.},
  isbn={9780937073810},
  lccn={lc91039510},
  series={CSLI lectures notes number},
  url={http://books.google.ch/books?id=vovpQgAACAAJ},
  year={1992},
  publisher={Center for the Study of Language and Information, Leland Stanford Junior University}
}

% 22262971 
@Article{pmid22262971,
   Author="Yuan, Z. and Shi, J. and Lin, W. and Chen, B. and Wu, F. X. ",
   Title="{{F}eatures-based deisotoping method for tandem mass spectra}",
   Journal="Adv Bioinformatics",
   Year="2011",
   Volume="2011",
   Pages="210805"
}
% 22772140 

@Article{pmid22772140,
   Author="Bantscheff, M.  and Lemeer, S.  and Savitski, M. M.  and Kuster, B. ",
   Title="{{Q}uantitative mass spectrometry in proteomics: critical review update from 2007 to the present}",
   Journal="Anal Bioanal Chem",
   Year="2012",
   Volume="404",
   Number="4",
   Pages="939--965",
   Month="Sep",
   DOI={10.1007/s00216-012-6203-4}
}
% 22821268 
@Article{pmid22821268,
   Author="Cappadona, S.  and Baker, P. R.  and Cutillas, P. R.  and Heck, A. J.  and van Breukelen, B. ",
   Title="{{C}urrent challenges in software solutions for mass spectrometry-based quantitative proteomics}",
   Journal="Amino Acids",
   Year="2012",
   Volume="43",
   Number="3",
   Pages="1087--1108",
   Month="Sep",
   DOI={10.1007/s00726-012-1289-8}
}

@Manual{R,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Development Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2008},
note = {{ISBN} 3-900051-07-0},
url = {http://www.R-project.org},
}


@Article{specL,
   Author="Panse, C.  and Trachsel, C.  and Grossmann, J.  and Schlapbach, R. ",
   Title="{spec{L}--an {R}/{B}ioconductor package to prepare peptide spectrum matches for use in targeted proteomics}",
   Journal="Bioinformatics",
   Year="2015",
   Volume="31",
   Number="13",
   Pages="2228--2231",
   Month="Jul",
   doi = {10.1093/bioinformatics/btv105}
}


@Inbook{VM-MAD,
author="Aleksiev, Tyanko
and Barkow-Oesterreicher, Simon
and Kunszt, Peter
and Maffioletti, Sergio
and Murri, Riccardo
and Panse, Christian",
editor="Kunkel, Julian Martin
and Ludwig, Thomas
and Meuer, Hans Werner",
title="VM-MAD: A Cloud/Cluster Software for Service-Oriented Academic Environments",
bookTitle="Supercomputing: 28th International Supercomputing Conference, ISC 2013, Leipzig, Germany, June 16-20, 2013. Proceedings",
year="2013",
publisher="Springer Berlin Heidelberg",
address="Berlin, Heidelberg",
pages="447--461",
isbn="978-3-642-38750-0",
doi="10.1007/978-3-642-38750-0_34",
url="http://dx.doi.org/10.1007/978-3-642-38750-0_34"
}


% 27130639 
@Article{msqc1,
Author="Kockmann, T.  and Trachsel, C.  and Panse, C.  and Wahlander, A.  and Selevsek, N.  and Grossmann, J.  and Wolski, W. E.  and Schlapbach, R. ",
Title="{{T}argeted proteomics coming of age - {S}{R}{M}, {P}{R}{M} and {D}{I}{A} performance evaluated from a core facility perspective}",
Journal="Proteomics",
Year="2016",
Volume="16",
Number="15-16",
Pages="2183--2192",
Month="Aug",
DOI={10.1002/pmic.201500502}
}



@Article{pmid15238601,
Author="Krokhin, O. V.  and Craig, R.  and Spicer, V.  and Ens, W.  and Standing, K. G.  and Beavis, R. C.  and Wilkins, J. A. ",
Title="{{A}n improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase {H}{P}{L}{C}: its application to protein peptide mapping by off-line {H}{P}{L}{C}-{M}{A}{L}{D}{I} {M}{S}}",
Journal="Mol. Cell Proteomics",
Year="2004",
Volume="3",
Number="9",
Pages="908--919",
Month="Sep",
DOI={10.1074/mcp.M400031-MCP200}
}

@article{rawDiag,
  doi = {10.1101/304485},
  url = {https://doi.org/10.1101/304485},
  year  = {2018},
  month = {apr},
  publisher = {Cold Spring Harbor Laboratory},
  author = {Christian Trachsel and Christian Panse and Tobias Kockmann and Witold Eryk Wolski and Jonas Grossmann and Ralph Schlapbach},
  title = {{rawDiag} - an R package supporting rational {LC}-{MS} method optimization for bottom-up proteomics}
}

@article{Egloff2018,
  doi = {10.1101/287813},
  url = {https://doi.org/10.1101/287813},
  year  = {2018},
  month = {mar},
  publisher = {Cold Spring Harbor Laboratory},
  author = {Pascal Egloff and Iwan Zimmermann and Fabian M. Arnold and Cedric A.J. Hutter and Damien Morger and Lennart Opitz and Lucy Poveda and Hans-Anton Keserue and Christian Panse and Bernd Roschitzki and Markus Seeger},
  title = {Engineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles}
}

@misc{peakplot,
author = {Panse, Christian and Gerrits, Bertran and Schlapbach, Ralph },
title = {{PEAKPLOT}: {Visualizing Fragmented Peptide Mass Spectra in Proteomics}},
url = {https://www.r-project.org/conferences/useR-2009/abstracts/pdf/Panse+Gerrits+Schlapbach.pdf},
note = {useR!2009 conference, Rennes, F},
year = {2009},
}
