@Article{Perez-Riverol,
  author =       {Perez-Riverol, Yasset and Wang, Rui and Hermjakob, Henning and Vesada, Vladimir and Vizca\'ino, Juan Antonio},
  title =        {Software libraries for Mass Spectrometry based Proteomics: A developer’s perspective},
  journal =      {BBA -- Proteins and Proteomics},
  year =         {Current issue}
}

@Article{Orchard,
  author = {Orchard, Sandra},
  title  = {{PSI} community},
  journal = {BBA -- Proteins and Proteomics},
  year =  {Current issue}
}

@Article{Jones,
  author = {Jones, Andrew},
  title  = {Standard formats},
  journal = {BBA -- Proteins and Proteomics},
  year =  {Current issue}
}



@article{IhakaGentleman1996,
  author = {Ross Ihaka and Robert Gentleman},
  title = {{R}: A Language for Data Analysis and Graphics},
  journal = {Journal of Computational and Graphical Statistics},
  year = 1996,
  volume = 5,
  number = 3,
  pages = {299--314},
  url = {http://www.amstat.org/publications/jcgs/}
}

@Manual{R2012,
    title = {{R}: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2012},
    note = {{ISBN} 3-900051-07-0},
    url = {http://www.R-project.org/},
}

@article{Gentleman2004,
        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},
        year = {2004},
        volume = {5},
        pages = {-80},
        number = {10},
        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},
        tags = {reproducible research, software, R, Bioconductor, statistics},
        timestamp = {2006.09.27},
        url = {http://dx.doi.org/10.1186/gb-2004-5-10-r80}
}

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


@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{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, Jérôme 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{Kessner2008,
        pmid = {18606607},
        author = {Kessner, Darren and Chambers, Matt and Burke, Robert and Agus, David and Mallick, Parag},
        title = {{ProteoWizard}: open source software for rapid proteomics tools development.},
        journal = {Bioinformatics},
        volume = {24},
        number = {21},
        pages = {2534-6},
        year = {2008},
        doi = {10.1093/bioinformatics/btn323},
        tags = "mass spectrometry, bioinformatics, data analysis, proteomics, software"
}

@Article{Rcpp2011,
    title = {{Rcpp}: Seamless {R} and {C++} Integration},
    author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
    journal = {Journal of Statistical Software},
    year = {2011},
    volume = {40},
    number = {8},
    pages = {1--18},
    url = {http://www.jstatsoft.org/v40/i08/},
  }

@Manual{mzR2012,
    title = {{mzR}: parser for {netCDF}, {mzXML}, {mzData} and {mzML} files (mass
spectrometry data)},
    author = {Bernd Fischer and Steffen Neumann and Laurent Gatto},
    note = {R package version 1.3.9},
    year = {2012},
    URL = {http://www.bioconductor.org/packages/release/bioc/html/mzR.html},
  }

@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 =      {Anal Chem},
  year =         {2006},
  month =        {Feb},
  number =       {3},
  volume =       {78},
  pages =        {779-87},
  doi =          {10.1021/ac051437y},
  PMID =         {16448051}}

@Article{Gatto2012,
  author =       {Gatto, L and Lilley, K S},
  title =        {{MSnbase} -- an {R/Bioconductor} 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}}


@Article{TargetSearch2009,
    title = {{TargetSearch} - a {Bioconductor} package for the efficient pre-processing of {GC-MS} metabolite profiling data},
    author = {Cuadros-Inostroza, Alvaro  and Caldana, Camila and Redestig, Henning and Lisec, Jan and Pena-Cortes, Hugo and Willmitzer, Lothar and  Hannah, Matthew A},
    journal = {BMC Bioinformatics},
    year = {2009},
    volume = {10},
    pages = {428},
    doi = {10.1186/1471-2105-10-428},
  }

@article{Ross2004,
        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},
        year = {2004},
        volume = {3},
        pages = {1154-1169},
        number = {12},
        month = {Dec},
        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},
        owner = {lgatto},
        pii = {M400129-MCP200},
        pmid = {15385600},
        tags = {iTRAQ, labelled, mass spectrometry, proteomics},
        timestamp = {2010.01.27},
        url = {http://dx.doi.org/10.1074/mcp.M400129-MCP200}
}

@article{Thompson2003,
        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.},
        year = {2003},
        volume = {75},
        pages = {1895-904},
        number = {8},
        pmid = {12713048},
        tags = {mass spectrometry, labelled, quantitative, TMT}
}


@Manual{xml2012,
    title = {{XML}: Tools for parsing and generating {XML} within {R} and {S-Plus}.},
    author = {Lang, Duncan Temple},
    year = {2012},
    note = {R package version 3.9-4},
    url = {http://CRAN.R-project.org/package=XML},
}

@Manual{orgmassspecr2012,
    title = {{OrgMassSpecR}: Organic Mass Spectrometry},
    author = {Nathan G. Dodder and with code contributions from Katharine M. Mullen.},
    year = {2012},
    note = {R package version 0.3-12},
    url = {http://CRAN.R-project.org/package=OrgMassSpecR},
}

@Article{Gibb2012,
  author =       {Gibb, S and Strimmer, K},
  title =        {{MALDIquant}: a versatile {R} package for the analysis
                 of mass spectrometry data.},
  journal =      {Bioinformatics},
  year =         {2012},
  month =        {Sep},
  number =       {17},
  volume =       {28},
  pages =        {2270-1},
  doi =          {10.1093/bioinformatics/bts447},
  PMID =         {22796955}
}

@Article{Tautenhahn2008,
  author =       {Tautenhahn, R and B\"ottcher, C and Neumann, S},
  title =        {Highly sensitive feature detection for high
                 resolution {LC/MS}.},
  journal =      {BMC Bioinformatics},
  year =         {2008},
  month =        {},
  number =       {},
  volume =       {9},
  pages =        {504},
  doi =          {10.1186/1471-2105-9-504},
  PMID =         {19040729}
}

@Article{Benton2010,
  author =       {Benton, H P and Want, E J and Ebbels, T M},
  title =        {Correction of mass calibration gaps in liquid
                 chromatography-mass spectrometry metabolomics
                 data.},
  journal =      {Bioinformatics},
  year =         {2010},
  month =        {Oct},
  number =       {19},
  volume =       {26},
  pages =        {2488-9},
  doi =          {10.1093/bioinformatics/btq441},
  PMID =         {20671148}
}

@Article{Benton2008,
  author =       {Benton, H P and Wong, D M and Trauger, S A and
                 Siuzdak, G},
  title =        {{XCMS2}: processing tandem mass spectrometry data
                 for metabolite identification and structural
                 characterization.},
  journal =      {Anal Chem},
  year =         {2008},
  month =        {Aug},
  number =       {16},
  volume =       {80},
  pages =        {6382-9},
  doi =          {10.1021/ac800795f},
  PMID =         {18627180}
}

@Manual{synapter2012,
    title = {synapter: Label-free data analysis pipeline for optimal identification and quantitation},
    author = {Laurent Gatto, Nick J. Bond and Pavel V. Shliaha},
    note = {R package version 1.0.0},
    year = {2013},
    url = {http://lgatto.github.com/synapter/},
}


@Article{synapter,
  author  = {Bond, Nicholas J. and Shliaha, Pavel V. and  Lilley, Kathryn S. and Gatto, Laurent},
  title   = {Improving qualitative and quantitative performance for label free proteomics},
  journal = {J. Proteome Res.},
  year    = {2013},
  doi     = {10.1021/pr300776t},
  PMID    = {23510225}
}


@Article{Breitwieser2011,
  author =       {Breitwieser, F P and M\"uller, A and Dayon, L and
                 K\"ocher, T and Hainard, A and Pichler, P and
                 Schmidt-Erfurth, U and Superti-Furga, G and
                 Sanchez, J C and Mechtler, K and Bennett, K L and
                 Colinge, J},
  title =        {General statistical modeling of data from protein
                 relative expression isobaric tags.},
  journal =      {J Proteome Res},
  year =         {2011},
  month =        {Jun},
  number =       {6},
  volume =       {10},
  pages =        {2758-66},
  doi =          {10.1021/pr1012784},
  PMID =         {21526793}
}

@Book{Wickham2009,
    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{Foster2011,
        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},
        year = {2011},
        volume = {11},
        pages = {2182-94},
        number = {11},
        doi = {10.1002/pmic.201000602},
        pmid = {21538885},
        tags = {bioinformatics, mass spectrometry, proteomics, quality}
}

@Article{Beasley-Green2012,
  author =       {Beasley-Green, A and Bunk, D and Rudnick, P and
                 Kilpatrick, L and Phinney, K},
  title =        {A proteomics performance standard to support
                 measurement quality in proteomics.},
  journal =      {Proteomics},
  year =         {2012},
  month =        {Apr},
  number =       {7},
  volume =       {12},
  pages =        {923-31},
  doi =          {10.1002/pmic.201100522},
  PMID =         {22522798}
}


@Article{Ma2012,
  author =       {Ma, Z Q and Polzin, K O and Dasari, S and
                 Chambers, M C and Schilling, B and Gibson, B W and
                 Tran, B Q and Vega-Montoto, L and Liebler, D C and
                 Tabb, D L},
  title =        {{QuaMeter}: Multivendor Performance Metrics for
                 {LC-MS/MS} Proteomics Instrumentation.},
  journal =      {Anal Chem},
  year =         {2012},
  month =        {Jul},
  number =       {14},
  volume =       {84},
  pages =        {5845-50},
  doi =          {10.1021/ac300629p},
  PMID =         {22697456}}


@article{Ishihama2005,
        author = {Ishihama, Yasushi and Oda, Yoshiya and Tabata, Tsuyoshi and Sato,
        Toshitaka and Nagasu, Takeshi and Rappsilber, Juri and Mann, Matthias},
        title = {Exponentially modified protein abundance index ({emPAI}) for estimation
        of absolute protein amount in proteomics by the number of sequenced
        peptides per protein.},
        journal = {Mol Cell Proteomics},
        year = {2005},
        volume = {4},
        pages = {1265-1272},
        number = {9},
        month = {Sep},
        abstract = {To estimate absolute protein contents in complex mixtures, we previously
        defined a protein abundance index (PAI) as the number of observed
        peptides divided by the number of observable peptides per protein
        (Rappsilber, J., Ryder, U., Lamond, A. I., and Mann, M. (2002) Large-scale
        proteomic analysis of the human spliceosome. Genome. Res. 12, 1231-1245).
        Here we report that PAI values obtained at different concentrations
        of serum albumin show a linear relationship with the logarithm of
        protein concentration in LC-MS/MS experiments. This was also the
        case for 46 proteins in a mouse whole cell lysate. For absolute quantitation,
        PAI was converted to exponentially modified PAI (emPAI), equal to
        10PAI minus one, which is proportional to protein content in a protein
        mixture. For the 46 proteins in the whole lysate, the deviation percentages
        of the emPAI-based abundances from the actual values were within
        63\% on average, similar or better than determination of abundance
        by protein staining. emPAI was applied to comprehensive protein expression
        analysis and to a comparison study between gene and protein expression
        in a human cancer cell line, HCT116. The values of emPAI are easily
        calculated and add important quantitation information to proteomic
        experiments; therefore we suggest that they should be reported in
        large scale proteomic identification projects.},
        doi = {10.1074/mcp.M500061-MCP200},
        file = {:./Ishihama2005.pdf:PDF},
        institution = {Laboratory of Seeds Finding Technology (LSFT), Eisai Co., Ltd., 5-1-3
        Tokodai, Tsukuba, Ibaraki 300-2635, Japan. y-ishihama@hhc.eisai.co.jp},
        keywords = {Animals; Cell Extracts; Cell Line, Tumor; Chromatography, Liquid;
        Clone Cells; Colonic Neoplasms, pathology; Gene Expression; Humans;
        Mass Spectrometry; Mice; Neuroblastoma, pathology; Peptides, chemistry;
        Proteins, analysis/genetics; Proteomics; Sequence Analysis, Protein;
        Serum Albumin, analysis},
        language = {eng},
        medline-pst = {ppublish},
        owner = {Administrator},
        pii = {M500061-MCP200},
        pmid = {15958392},
        timestamp = {2010.01.13},
        url = {http://dx.doi.org/10.1074/mcp.M500061-MCP200}
}

@Article{Zhang2010,
  author =       {Zhang, Y and Wen, Z and Washburn, M P and Florens,
                 L},
  title =        {Refinements to label free proteome quantitation:
                 how to deal with peptides shared by multiple
                 proteins.},
  journal =      {Anal Chem},
  year =         {2010},
  month =        {Mar},
  number =       {6},
  volume =       {82},
  pages =        {2272-81},
  doi =          {10.1021/ac9023999},
  PMID =         {20166708}}

@Article{Mohammed2012,
  author =       {Mohammed, Y and Mostovenko, E and Henneman, A A
                 and Marissen, R J and Deelder, A M and Palmblad, M},
  title =        {Cloud Parallel Processing of Tandem Mass
                 Spectrometry Based Proteomics Data.},
  journal =      {J Proteome Res},
  year =         {2012},
  month =        {Sep},
  number =       {},
  volume =       {},
  pages =        {},
  doi =          {10.1021/pr300561q},
  PMID =         {22916831}}


@book{Gentleman2008,
  author = {Robert Gentleman},
  title = {{R} Programming for Bioinformatics},
  publisher = {Chapman \& Hall/CRC},
  year = {2008},
  note = {ISBN 978-1-420-06367-7},
  url = {http://www.bioconductor.org/pub/RBioinf/}
}

@inproceedings{Leisch2002,
    address = {Heidelberg, Germany},
    author = {Leisch, Friedrich},
    booktitle = {Compstat 2002, Proceedings in Computational Statistics},
    citeulike-article-id = {10930765},
    citeulike-linkout-0 = {http://www.stat.uni-muenchen.de/\~{}leisch/Sweave},
    comment = {ISBN 3-7908-1517-9},
    editor = {H{\"{a}}rdle, Wolfgang and R{\"{o}}nz, Bernd},
    keywords = {latex, r, sweave},
    publisher = {Physica Verlag},
    title = {{Sweave: Dynamic Generation of Statistical Reports Using Literate Data Analysis}},
    url = {http://www.stat.uni-muenchen.de/\~{}leisch/Sweave},
    year = {2002}
}

@article{Aebersold2011,
        author = {Aebersold, Ruedi},
        title = {Editorial: From Data to Results},
        journal = {Molecular \& Cellular Proteomics},
        year = {2011},
        volume = {10},
        number = {11},
        doi = {10.1074/mcp.E111.014787},
        eprint = {http://www.mcponline.org/content/10/11/E111.014787.full.pdf+html},
        file = {:/home/lgatto/Biblio/Aebersold2011.pdf:PDF},
        url = {http://www.mcponline.org/content/10/11/E111.014787.short}
}


@Book{Chambers2008,
  author       = {John M. Chambers},
  title	       = {Software for Data Analysis: Programming with {R}},
  publisher    = {Springer},
  year	       = 2008,
  address      = {New York},
  isbn	       = {978-0-387-75935-7},
  url	       = {http://stat.stanford.edu/~jmc4/Rbook/},
  publisherurl = {http://www.springer.com/statistics/computational/book/978-0-387-75935-7},
  abstract     = {The R version of S4 and other R techniques.  This book
                  guides the reader in programming with R, from
                  interactive use and writing simple functions to the
                  design of R packages and intersystem interfaces.},
  orderinfo    = {springer.txt},
}

@Article{Gonzalez-Galarza2012,
  author =       {Gonzalez-Galarza, F F and Lawless, C and Hubbard,
                 S J and Fan, J and Bessant, C and Hermjakob, H and
                 Jones, A R},
  title =        {A critical appraisal of techniques, software
                 packages, and standards for quantitative proteomic
                 analysis.},
  journal =      {OMICS},
  year =         {2012},
  month =        {Sep},
  number =       {9},
  volume =       {16},
  pages =        {431-42},
  doi =          {10.1089/omi.2012.0022},
  PMID =         {22804616}
}

@Article{Mueller2008,
  author =       {Mueller, L N and Brusniak, M Y and Mani, D R and
                 Aebersold, R},
  title =        {An assessment of software solutions for the
                 analysis of mass spectrometry based quantitative
                 proteomics data.},
  journal =      {J Proteome Res},
  year =         {2008},
  month =        {Jan},
  number =       {1},
  volume =       {7},
  pages =        {51-61},
  doi =          {10.1021/pr700758r},
  PMID =         {18173218}}


@article{Gentleman2004a,
        author = {Gentleman, Robert and Lang, Duncan Temple},
        title = {Statistical Analyses and Reproducible Research},
        journal = {Bioconductor Project Working Papers. Working Paper 2},
        year = {2004},
        month = {May},
        file = {:Gentleman_and_Lang_COBRA_2003.pdf:PDF},
        owner = {lgatto},
        tags = {statistics, reproducible research},
        timestamp = {2009.08.03},
        url = {http://www.bepress.com/bioconductor/paper2}
}

@article{Gentleman2005,
        author = {Gentleman, Robert},
        title = {Reproducible Research: A Bioinformatics Case Study},
        journal = {Statistical Applications in Genetics and Molecular Biology},
        year = {2005},
        volume = {4},
        number = {1},
        doi = {10.2202/1544-6115.1034},
        file = {Gentleman2005.pdf:Gentleman2005.pdf:PDF},
        owner = {lgatto},
        tags = {reproducible research, Bioconductor},
        timestamp = {2009.08.03},
        url = {http://www.bepress.com/sagmb/vol4/iss1/art2}
}

@article{Knuth1984,
        author = {Knuth, Donald E.},
        title = {Literate Programming},
        journal = {The Computer Journal (British Computer Society)},
        year = {1984},
        volume = {27},
        pages = {91-111},
        number = {2},
        doi = {10.1093/comjnl/27.2.97},
        file = {Knuth1984.pdf:Knuth1984.pdf:PDF},
        owner = {lgatto},
        tags = {reproducible research},
        timestamp = {2009.08.03}
}

@article{Peng2009,
        author = {Peng, Roger D.},
        title = {Reproducible research and Biostatistics.},
        journal = {Biostatistics},
        year = {2009},
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        number = {3},
        month = {Jul},
        doi = {10.1093/biostatistics/kxp014},
        file = {Peng2009.pdf:Peng2009.pdf:PDF},
        keywords = {Biometry; Peer Review, Research; Publishing; Reproducibility of Results;
        Research},
        pmid = {19535325},
        tags = {reproducible research},
        timestamp = {2010.02.03},
        url = {http://dx.doi.org/10.1093/biostatistics/kxp014}
}

@article{Peng2011,
        author = {Roger D Peng},
        title = {Reproducible research in computational science.},
        journal = {Science},
        year = {2011},
        volume = {334},
        pages = {1226--1227},
        number = {6060},
        month = {Dec},
        abstract = {Computational science has led to exciting new developments, but the
        nature of the work has exposed limitations in our ability to evaluate
        published findings. Reproducibility has the potential to serve as
        a minimum standard for judging scientific claims when full independent
        replication of a study is not possible.},
        doi = {10.1126/science.1213847},
        file = {:/home/lgatto/Biblio/Peng2011.pdf:PDF},
        institution = {Department of Biostatistics, Johns Hopkins Bloomberg School of Public
        Health, Baltimore, MD 21205, USA. rpeng@jhsph.edu},
        keywords = {reproducible research},
        language = {eng},
        medline-pst = {ppublish},
        owner = {lgatto},
        pii = {334/6060/1226},
        pmid = {22144613},
        timestamp = {2011.12.16},
        url = {http://dx.doi.org/10.1126/science.1213847}
}


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        author = {Donoho, David L},
        title = {An invitation to reproducible computational research.},
        journal = {Biostatistics},
        year = {2010},
        volume = {11},
        pages = {385-8},
        number = {3},
        doi = {10.1093/biostatistics/kxq028},
        pmid = {20538873},
        tags = {reproducible research}
}

@article{Nilsson10,
        pmid = {20805795},
        author = {Nilsson, Tommy and Mann, Matthias and Aebersold, Ruedi and Yates, John R and Bairoch, Amos and Bergeron, John J M},
        title = {Mass spectrometry in high-throughput proteomics: ready for the big time.},
        journal = {Nat. Methods},
        volume = {7},
        number = {9},
        pages = {681-5},
        year = {2010},
        doi = {10.1038/nmeth0910-681},
        tags = "mass spectrometry, proteomics"
}

@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"
}

@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"
}

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@INPROCEEDINGS{Kubczak2006,
   author={Kubczak, C. and Margaria, T. and Fritsch, A. and Steffen, B.},
   booktitle={Leveraging Applications of Formal Methods, Verification and Validation, 2006. ISoLA 2006. Second International Symposium on},
   title={Biological {LC/MS} Preprocessing and Analysis with {jABC}, {jETI} and {xcms}},
   year={2006},
   month={nov.},
   volume={},
   number={},
   pages={303-308},
   keywords={biological LC/MS preprocessing;domain-specific statistics language;jABC service definition environment;jETI;remote service integration;service-oriented fashion;statistical analysis;xcms;Web services;biology computing;software engineering;statistical analysis;workflow management software;},
   doi={10.1109/ISoLA.2006.48},
   ISSN={},
}

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  author =       {B\"{o}cker, S and Lipt\'{a}k, Z and Martin, M and Pervukhin, A and Sudek, H},
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@ARTICLE{texshade2000,
   AUTHOR = "Eric Beitz",
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@article{Uhlen2005,
    address = {Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden. mathias.uhlen@biotech.kth.se},
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    doi = {10.1074/mcp.M500279-MCP200},
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    journal = {Molecular \& cellular proteomics : MCP},
    keywords = {human\_proteome, proteomics},
    month = dec,
    number = {12},
    pages = {1920--1932},
    pmid = {16127175},
    posted-at = {2012-03-21 13:53:22},
    priority = {2},
    title = {{A human protein atlas for normal and cancer tissues based on antibody proteomics.}},
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    year = {2005}
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@article{Uhlen2010,
    author = {Uhlen, Mathias and Oksvold, Per and Fagerberg, Linn and Lundberg, Emma and Jonasson, Kalle and Forsberg, Mattias and Zwahlen, Martin and Kampf, Caroline and Wester, Kenneth and Hober, Sophia and Wernerus, Henrik and Bj\"{o}rling, Lisa and Ponten, Fredrik},
    citeulike-article-id = {8380545},
    citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt1210-1248},
    citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt1210-1248},
    citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/21139605},
    citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=21139605},
    comment = {Update of Protein Atlas. About 50\% of proteins are claimed to be assessed by immunostaining in various human tissues and neoplasms},
    doi = {10.1038/nbt1210-1248},
    issn = {1546-1696},
    journal = {Nature biotechnology},
    keywords = {proteomics, tissue},
    month = dec,
    number = {12},
    pages = {1248--1250},
    pmid = {21139605},
    posted-at = {2010-12-08 22:24:39},
    priority = {0},
    publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
    title = {{Towards a knowledge-based Human Protein Atlas.}},
    url = {http://dx.doi.org/10.1038/nbt1210-1248},
    volume = {28},
    year = {2010}
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@ARTICLE{Cote06,
  author = {C\^ot\'e, Richard G and Jones, Philip and Apweiler, Rolf and Hermjakob,
        Henning},
  title = {The Ontology Lookup Service, a lightweight cross-platform tool for
        controlled vocabulary queries.},
  journal = {BMC Bioinformatics},
  year = {2006},
  volume = {7},
  pages = {97},
  doi = {10.1186/1471-2105-7-97},
  pmid = {16507094},
  tags = {ontology, software}
}

@ARTICLE{Cote08,
  author = {C\^ot\'e, Richard G and Jones, Philip and Martens, Lennart and Apweiler,
        Rolf and Hermjakob, Henning},
  title = {The Ontology Lookup Service: more data and better tools for controlled
        vocabulary queries.},
  journal = {Nucleic Acids Res.},
  year = {2008},
  volume = {36},
  pages = {372-376},
  number = {Web Server issue},
  doi = {10.1093/nar/gkn252},
  pmid = {18467421},
  tags = {ontology, software}
}

@Manual{hpar2012,
    title = {hpar: Human Protein Atlas in R},
    author = {Laurent Gatto},
    year = {2012},
    note = {R package version 0.99.0},
}

@Manual{GO.db2012,
    title = {GO.db: A set of annotation maps describing the entire Gene Ontology},
    author = {Marc Carlson},
    year = {2012},
    note = {R package version 2.8.0},
}

@Manual{org.Hs.eg.db2012,
    title = {org.Hs.eg.db: Genome wide annotation for Human},
    author = {Marc Carlson},
    year = {2012},
    note = {R package version 2.8.0},
}

@Manual{reactome.db2012,
    title = {reactome.db: A set of annotation maps for reactome},
    author = {Willem Ligtenberg},
    year = {2012},
    note = {R package version 1.1.0},
}

@Article{DEustachio2011,
  author =       {D'Eustachio, P},
  title =        {Reactome knowledgebase of human biological
                 pathways and processes.},
  journal =      {Methods Mol Biol},
  year =         {2011},
  month =        {},
  number =       {},
  volume =       {694},
  pages =        {49-61},
  doi =          {10.1007/978-1-60761-977-2\_4},
  PMID =         {21082427}}

@Article{Haw2011,
  author =       {Haw, R and Hermjakob, H and D'Eustachio, P and
                 Stein, L},
  title =        {Reactome pathway analysis to enrich biological
                 discovery in proteomics data sets.},
  journal =      {Proteomics},
  year =         {2011},
  month =        {Sep},
  number =       {18},
  volume =       {11},
  pages =        {3598-613},
  doi =          {10.1002/pmic.201100066},
  PMID =         {21751369}}


@Article{Croft2011,
  author =       {Croft, D and O'Kelly, G and Wu, G and Haw, R and
                 Gillespie, M and Matthews, L and Caudy, M and
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                 Jupe, S and Kalatskaya, I and Mahajan, S and May,
                 B and Ndegwa, N and Schmidt, E and Shamovsky, V
                 and Yung, C and Birney, E and Hermjakob, H and
                 D'Eustachio, P and Stein, L},
  title =        {Reactome: a database of reactions, pathways and
                 biological processes.},
  journal =      {Nucleic Acids Res},
  year =         {2011},
  month =        {Jan},
  number =       {Database issue},
  volume =       {39},
  pages =        {D691-7},
  doi =          {10.1093/nar/gkq1018},
  PMID =         {21067998}}

@Article{Ashburner2000,
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                 Matese, J C and Richardson, J E and Ringwald, M
                 and Rubin, G M and Sherlock, G},
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                 biology. The Gene Ontology Consortium.},
  journal =      {Nat Genet},
  year =         {2000},
  month =        {May},
  number =       {1},
  volume =       {25},
  pages =        {25-9},
  doi =          {10.1038/75556},
  PMID =         {10802651}}


@Article{R4Prot2013,
  author =       {Gatto, Laurent and Christoforou, Andy},
  title =        {Using {R} and Bioconductor for proteomics data analysis},
  journal =      {BBA - Proteins and Proteomics},
  PMID =         {23692960},
  doi =          {10.1016/j.bbapap.2013.04.032},
  year =         {2013}
}

@Article{Chambers2012,
  author =       {Chambers, M C and Maclean, B and Burke, R and
                 Amodei, D and Ruderman, D L and Neumann, S and
                 Gatto, L and Fischer, B and Pratt, B and Egertson,
                 J and Hoff, K and Kessner, D and Tasman, N and
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                 Flashner, L and Kani, K and Moulding, C and
                 Seymour, S L and Nuwaysir, L M and Lefebvre, B and
                 Kuhlmann, F and Roark, J and Rainer, P and Detlev,
                 S and Hemenway, T and Huhmer, A and Langridge, J
                 and Connolly, B and Chadick, T and Holly, K and
                 Eckels, J and Deutsch, E W and Moritz, R L and
                 Katz, J E and Agus, D B and MacCoss, M and Tabb, D
                 L and Mallick, P},
  title =        {A cross-platform toolkit for mass spectrometry and
                 proteomics.},
  journal =      {Nat Biotechnol},
  year =         {2012},
  month =        {Oct},
  number =       {10},
  volume =       {30},
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@Article{Craig2004,
  author =       {Craig, R and Beavis, R C},
  title =        {TANDEM: matching proteins with tandem mass
                 spectra.},
  journal =      {Bioinformatics},
  year =         {2004},
  month =        {Jun},
  number =       {9},
  volume =       {20},
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@Article{Vizcaino2014,
  author =       {Vizcaino, Juan A and Deutsch, Eric W and Wang, Rui
                  and Csordas, Attila and Reisinger, Florian and Rios,
                  Daniel and Dianes, Jose A and Sun, Zhi and Farrah,
                  Terry and Bandeira, Nuno and Binz, Pierre-Alain and
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                  Gerhard and Gatto, Laurent and Campos, Alex and
                  Chalkley, Robert J and Kraus, Hans-Joachim and
                  Albar, Juan Pablo and Martinez-Bartolome, Salvador
                  and Apweiler, Rolf and Omenn, Gilbert S and Martens,
                  Lennart and Jones, Andrew R and Hermjakob, Henning},
  title =        {{ProteomeXchange} provides globally coordinated
                  proteomics data submission and dissemination},
  journal =      {Nat Biotech},
  year =         {2014},
  volume =       {32},
  issue =        {3},
  pages =        {223-226},
  doi =          {10.1038/nbt.2839}
}

@article{Kim:2008go,
  author =       {Kim, Sangtae and Gupta, Nitin and Pevzner, Pavel A},
  title =        {{Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases.}},
  journal =      {Journal of Proteome Research},
  year =         {2008},
  volume =       {7},
  number =       {8},
  pages =        {3354--3363},
  month =        aug
}

@article{Kim:2010ks,
  author =       {Kim, Sangtae and Mischerikow, Nikolai and Bandeira, Nuno and Navarro, J Daniel and Wich, Louis and Mohammed, Shabaz and Heck, Albert J R and Pevzner, Pavel A},
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  journal =      {Molecular {\&} Cellular Proteomics: MCP},
  year =         {2010},
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  month =        dec
}

@article{Piehowski2013a,
  Abstract = {For bottom-up proteomics, there are wide variety of database-searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid-search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection--referred to as STEPS--utilizes user-defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal "parameter set" for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true-positive identifications are demonstrated using datasets derived from immunoaffinity-depleted blood serum and a bacterial cell lysate, two common proteomics sample types.},
  Author = {Piehowski, Paul D. and Petyuk, Vladislav A. and Sandoval, John D. and Burnum, Kristin E. and Kiebel, Gary R. and Monroe, Matthew E. and Anderson, Gordon A. and Camp, 2nd, David G and Smith, Richard D.},
  Doi = {10.1002/pmic.201200096},
  Institution = {Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA99352, USA.},
  Journal = {Proteomics},
  Keywords = {Bacterial Proteins, analysis/chemistry; Blood Proteins, analysis/chemistry; Databases, Protein; Humans; Peptide Fragments, analysis/chemistry; Proteins, analysis/chemistry; Proteomics, methods; Shewanella; Tandem Mass Spectrometry, methods},
  Language = {eng},
  Medline-Pst = {ppublish},
  Month = {Mar},
  Number = {5},
  Owner = {D3M629},
  Pages = {766--770},
  Pmid = {23303698},
  Timestamp = {2014.03.24},
  Title = {STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results.},
  Url = {http://dx.doi.org/10.1002/pmic.201200096},
  Volume = {13},
  Year = {2013},
  Bdsk-Url-1 = {http://dx.doi.org/10.1002/pmic.201200096}}


@Article{Gatto:2015,
  author =       {Gatto, L and Breckels, L M and Naake, T and Gibb, S},
  title =        {{Visualisation of proteomics data using R and
                 Bioconductor}.},
  journal =      {Proteomics},
  year =         {2015},
  month =        {Feb},
  number =       {},
  volume =       {},
  pages =        {},
  doi =          {10.1002/pmic.201400392},
  PMID =         {25690415}}
