@Manual{Rstat,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Development Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2011},
    note = {{ISBN} 3-900051-07-0},
    url = {http://www.R-project.org/},
  }


@Article{Gentleman2004,
        Abstract = {The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.},
        Doi = {10.1186/gb-2004-5-10-r80},
        File = {Gentleman_et_al_GenomeBiology_2004.pdf:/home/lgatto/Biblio/Gentleman_et_al_GenomeBiology_2004.pdf:PDF},
        Keywords = {Computational Biology; Internet; Repro; Software; ducibility of Results},
        Owner = {lgatto},
        Pii = {gb-2004-5-10-r80},
        Pmid = {15461798},
        Timestamp = {2006.09.27},
        Url = {http://dx.doi.org/10.1186/gb-2004-5-10-r80},
        author = {Gentleman, Robert C. and Carey, Vincent J. and Bates, Douglas M. and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and Hornik, Kurt and Hothorn, Torsten and Huber, Wolfgang and Iacus, Stefano and Irizarry, Rafael and Leisch, Friedrich and Li, Cheng and Maechler, Martin and Rossini, Anthony J. and Sawitzki, Gunther and Smith, Colin and Smyth, Gordon and Tierney, Luke and Yang, Jean Y. H. and Zhang, Jianhua},
        title = {Bioconductor: open software development for computational biology and bioinformatics.},
        journal = {Genome Biol},
        volume = {5},
        number = {10},
        pages = {-80},
        year = {2004},
        tags = "reproducible research, software, R, Bioconductor, statistics"
}

@article{Pedrioli2004,
        pmid = {15529173},
        author = {Pedrioli, Patrick G A and Eng, Jimmy K and Hubley, Robert and Vogelzang, Mathijs and Deutsch, Eric W and Raught, Brian and Pratt, Brian and Nilsson, Erik and Angeletti, Ruth H and Apweiler, Rolf and Cheung, Kei and Costello, Catherine E and Hermjakob, Henning and Huang, Sequin and Julian, Randall K and Kapp, Eugene and McComb, Mark E and Oliver, Stephen G and Omenn, Gilbert and Paton, Norman W and Simpson, Richard and Smith, Richard and Taylor, Chris F and Zhu, Weimin and Aebersold, Ruedi},
        title = {A common open representation of mass spectrometry data and its application to proteomics research.},
        journal = {Nat. Biotechnol.},
        volume = {22},
        number = {11},
        pages = {1459-66},
        year = {2004},
        doi = {10.1038/nbt1031},
        tags = "bioinformatics, mass spectrometry, proteomics, standard"
}


@article{Martens2010,
        pmid = {20716697},
        author = {Martens, Lennart and Chambers, Matthew and Sturm, Marc and Kes
sner, Darren and Levander, Fredrik and Shofstahl, Jim and Tang, Wilfred H and Ro
mpp, Andreas and Neumann, Steffen and Pizarro, Angel D and Montecchi-Palazzi, Lu
isa and Tasman, Natalie and Coleman, Mike and Reisinger, Florian and Souda, Pune
et and Hermjakob, Henning and Binz, Pierre-Alain and Deutsch, Eric W},
        title = {mzML - a Community Standard for Mass Spectrometry Data.},
        journal = {Molecular \& Cellular Proteomics : MCP},
        year = {2010},
        doi = {10.1074/mcp.R110.000133},
        tags = "bioinformatics, mass spectrometry, proteomics, standard, formats"
}

@Article{Taylor2007,
        Abstract = {Both the generation and the analysis of proteomics data are now widespread, and high-throughput approaches are commonplace. Protocols continue to increase in complexity as methods and technologies evolve and diversify. To encourage the standardized collection, integration, storage and dissemination of proteomics data, the Human Proteome Organization’s Proteomics Standards Initiative develops guidance modules for reporting the use of techniques such as gel electrophoresis and mass spectrometry. This paper describes the processes and principles underpinning the development of these modules; discusses the ramifications for various interest groups such as experimentalists, funders, publishers and the private sector; addresses the issue of overlap with other reporting guidelines; and highlights the criticality of appropriate tools and resources in enabling ’MIAPE-compliant’ reporting.},
        Doi = {10.1038/nbt1329},
        File = {Taylor2007.pdf:Taylor2007.pdf:PDF},
        Institution = {The HUPO Proteomics Standards Initiative, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK. chris.taylor@ebi.ac.uk},
        Keywords = {Databases, Protein; Gene Expression Profiling; Genome, Human; Guidelines as Topic; Humans; Information Storage and Retrieval; Internationality; Proteomics; Research},
        Month = {Aug},
        Owner = {lgatto},
        Pii = {nbt1329},
        Pmid = {17687369},
        Timestamp = {2010.02.03},
        Url = {http://dx.doi.org/10.1038/nbt1329},
        author = {Taylor, Chris F. and Paton, Norman W. and Lilley, Kathryn S. and Binz, Pierre-Alain and Julian, Randall K. and Jones, Andrew R. and Zhu, Weimin and Apweiler, Rolf and Aebersold, Ruedi and Deutsch, Eric W. and Dunn, Michael J. and Heck, Albert J. R. and Leitner, Alexander and Macht, Marcus and Mann, Matthias and Martens, Lennart and Neubert, Thomas A. and Patterson, Scott D. and Ping, Peipei and Seymour, Sean L. and Souda, Puneet and Tsugita, Akira and Vandekerckhove, Joel and Vondriska, Thomas M. and Whitelegge, Julian P. and Wilkins, Marc R. and Xenarios, Ioannnis and Yates, John R. and Hermjakob, Henning},
        title = {The minimum information about a proteomics experiment (MIAPE).},
        journal = {Nat Biotechnol},
        volume = {25},
        number = {8},
        pages = {887-893},
        year = {2007},
        tags = "reproducibility, quality, proteomics, data management, mass spectrometry, standard"
}

@Article{Ross2004,
        Abstract = {We describe here a multiplexed protein quantitation strategy that provides relative and absolute measurements of proteins in complex mixtures. At the core of this methodology is a multiplexed set of isobaric reagents that yield amine-derivatized peptides. The derivatized peptides are indistinguishable in MS, but exhibit intense low-mass MS/MS signature ions that support quantitation. In this study, we have examined the global protein expression of a wild-type yeast strain and the isogenic upf1Delta and xrn1Delta mutant strains that are defective in the nonsense-mediated mRNA decay and the general 5’ to 3’ decay pathways, respectively. We also demonstrate the use of 4-fold multiplexing to enable relative protein measurements simultaneously with determination of absolute levels of a target protein using synthetic isobaric peptide standards. We find that inactivation of Upf1p and Xrn1p causes common as well as unique effects on protein expression.},
        Doi = {10.1074/mcp.M400129-MCP200},
        File = {:home/lgatto/Biblio/Ross2004.pdf:PDF},
        Institution = {Applied Biosystems, Framingham, MA 01701, USA.},
        Keywords = {Cations; Chromatography, Ion Exchange; Chromatography, Liquid; Down-Regulation; Exoribonucleases; Fungal Proteins; Indicators and Reagents; Ions; Mass Spectrometry; Models, Chemical; Peptides; Phenotype; Proteomics; RNA Helicases; RNA, Messenger; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Succinimides},
        Month = {Dec},
        Owner = {lgatto},
        Pii = {M400129-MCP200},
        Pmid = {15385600},
        Timestamp = {2010.01.27},
        Url = {http://dx.doi.org/10.1074/mcp.M400129-MCP200},
        author = {Ross, Philip L. and Huang, Yulin N. and Marchese, Jason N. and Williamson, Brian and Parker, Kenneth and Hattan, Stephen and Khainovski, Nikita and Pillai, Sasi and Dey, Subhakar and Daniels, Scott and Purkayastha, Subhasish and Juhasz, Peter and Martin, Stephen and Bartlet-Jones, Michael and He, Feng and Jacobson, Allan and Pappin, Darryl J.},
        title = {Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents.},
        journal = {Mol Cell Proteomics},
        volume = {3},
        number = {12},
        pages = {1154-1169},
        year = {2004},
        tags = "iTRAQ, labelled, mass spectrometry, proteomics"
}

@article{Thompson2003,
        pmid = {12713048},
        author = {Thompson, Andrew and Sch\"afer, J\"urgen and Kuhn, Karsten and Kienle, Stefan and Schwarz, Josef and Schmidt, G\"unter and Neumann, Thomas and Johnstone, R and Mohammed, A Karim A and Hamon, Christian},
        title = {Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by {MS/MS}.},
        journal = {Anal. Chem.},
        volume = {75},
        number = {8},
        pages = {1895-904},
        year = {2003},
        tags = "mass spectrometry, labelled, quantitative, TMT"
}

@article{Smith2006,
   author="Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.",
   title="XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification",
   journal="Analytical Chemistry",
   year="2006",
   volume="78",
   pages="779-787"
}

@Article{Huber2002,
    title = {Variance Stabilization Applied to Microarray Data Calibration and to the Quantification of Differential Expression},
    author = {Wolfgang Huber and Anja von Heydebreck and Holger Sueltmann and Annemarie Poustka and Martin Vingron},
    journal = {Bioinformatics},
    year = {2002},
    volume = {18 Suppl. 1},
    pages = {S96-S104},
}


@article{Karp2010,
	pmid = {20382981},
	author = {Karp, Natasha A and Huber, Wolfgang and Sadowski, Pawel G and Charles, Philip D and Hester, Svenja V and Lilley, Kathryn S},
	title = {Addressing accuracy and precision issues in iTRAQ quantitation.},
	journal = {Mol. Cell Proteomics},
	volume = {9},
	number = {9},
	pages = {1885-97},
	year = {2010},
	doi = {10.1074/mcp.M900628-MCP200},
	tags = "Bioconductor, bioinformatics, iTRAQ, labelled, mass spectrometry, normalisation/preprocessing, proteomics, R, quantitative, statistics"
}

@article{Taylor2008,
        pmid = {18688232},
        author = {Taylor, Chris F and Binz, Pierre-Alain and Aebersold, Ruedi and Affolter, Michel and Barkovich, Robert and Deutsch, Eric W and Horn, David M and Hühmer, Andreas and Kussmann, Martin and Lilley, Kathryn and Macht, Marcus and Mann, Matthias and Müller, Dieter and Neubert, Thomas A and Nickson, Janice and Patterson, Scott D and Raso, Roberto and Resing, Kathryn and Seymour, Sean L and Tsugita, Akira and Xenarios, Ioannis and Zeng, Rong and Julian, Randall K},
        title = {Guidelines for reporting the use of mass spectrometry in proteomics.},
        journal = {Nat. Biotechnol.},
        volume = {26},
        number = {8},
        pages = {860-1},
        year = {2008},
        doi = {10.1038/nbt0808-860},
        tags = "data management, mass spectrometry, proteomics, quality, reproducibility, standard"
}

@article{Shadforth05,
        pmid = {16242023},
        author = {Shadforth, Ian P and Dunkley, Tom P J and Lilley, Kathryn S and Bessant, Conrad},
        title = {i-Tracker: for quantitative proteomics using iTRAQ.},
        journal = {BMC Genomics},
        volume = {6},
        pages = {145},
        year = {2005},
        doi = {10.1186/1471-2164-6-145},
        tags = "iTRAQ, proteomics, mass spectrometry, quantitative, software, statistics, labelled, bioinformatics"
}

@article{Bolstad03,
	pmid = {12538238},
	author = {Bolstad, B M and Irizarry, R A and Astrand, M and Speed, T P},
	title = {A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.},
	journal = {Bioinformatics},
	volume = {19},
	number = {2},
	pages = {185-93},
	year = {2003},
	tags = "Bioconductor, bioinformatics, normalisation/preprocessing, microarray"
}

@Book{ggplot2,
    author = {Hadley Wickham},
    title = {ggplot2: elegant graphics for data analysis},
    publisher = {Springer New York},
    year = {2009},
    isbn = {978-0-387-98140-6},
    url = {http://had.co.nz/ggplot2/book},
  }

@article{Foster11,
	pmid = {21538885},
	author = {Foster, Joseph M and Degroeve, Sven and Gatto, Laurent and Visser, Matthieu and Wang, Rui and Griss, Johannes and Apweiler, Rolf and Martens, Lennart},
	title = {A posteriori quality control for the curation and reuse of public proteomics data.},
	journal = {Proteomics},
	volume = {11},
	number = {11},
	pages = {2182-94},
	year = {2011},
	doi = {10.1002/pmic.201000602},
	tags = "bioinformatics, mass spectrometry, proteomics, quality"
}

@article{Orchard2007,
        pmid = {17907277},
        author = {Orchard, Sandra and Montechi-Palazzi, Luisa and Deutsch, Eric W and Binz, Pierre-Alain and Jones, Andrew R and Paton, Norman and Pizarro, Angel and Creasy, David M and Wojcik, J\'er\^ome and Hermjakob, Henning},
        title = {Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Sup\'erieure (ENS), Lyon, France.},
        journal = {Proteomics},
        volume = {7},
        number = {19},
        pages = {3436-40},
        year = {2007},
        doi = {10.1002/pmic.200700658},
        tags = "mass spectrometry, bioinformatics, formats, proteomics, standard"
}

@Article{Gatto2012,
  author =       {Gatto, L and Lilley, K S},
  title =        {{MS}nbase -- an {R}/{B}ioconductor package for isobaric
                 tagged mass spectrometry data visualization,
                 processing and quantitation.},
  journal =      {Bioinformatics},
  year =         {2012},
  month =        {Jan},
  number =       {2},
  volume =       {28},
  pages =        {288-9},
  doi =          {10.1093/bioinformatics/btr645},
  PMID =         {22113085}}

@Manual{synapter,
    title = {synapter: Label-free data analysis pipeline for optimal identification and
quantitation},
    author = {Laurent Gatto and Pavel V. Shliaha and Nick J. Bond},
    note = {R package version 1.1.2},
    url = {http://lgatto.github.com/synapter/},
  }
