
@book{newS,
  author = {Richard A. Becker and John M. Chambers and Allan
                  R. Wilks},
  title = {The New {S} Language},
  publisher = {Chapman \& Hall},
  year = 1988,
  address = {London},
  abstract = {This book is often called the ``\emph{Blue Book}'',
                  and introduced what is now known as S version 3, or S3.}
} 

%% use https://www.doi2bib.org/ to generate bib entries
@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},
  }

@ONLINE{tartare,
  doi = {10.18129/B9.BIOC.TARTARE},
  url = {https://bioconductor.org/packages/tartare},
  author = {Christian Panse and  Tobias Kockmann},
  title = {tartare},
  publisher = {Bioconductor},
  year = {2019}
}


@article{Trachsel2018,
  doi = {10.1021/acs.jproteome.8b00173},
  url = {https://doi.org/10.1021/acs.jproteome.8b00173},
  year  = {2018},
  month = {jul},
  publisher = {American Chemical Society ({ACS})},
  volume = {17},
  number = {8},
  pages = {2908--2914},
  author = {Christian Trachsel and Christian Panse and Tobias Kockmann and Witold E. Wolski and Jonas Grossmann and Ralph Schlapbach},
  title = {{\href{https://github.com/fgcz/rawDiag}{{rawDiag}}}: {An R Package Supporting Rational {LC}{\textendash}{MS} Method Optimization for Bottom-up Proteomics}},
  journal = {Journal of Proteome Research}
}


@ONLINE{RFR,
        author = {Jim Shofstahl},
        title = {{New RawFileReader from Thermo Fisher Scientific},
        \url{http://planetorbitrap.com/rawfilereader}},
        year = {2018},
        URL = {http://planetorbitrap.com/rawfilereader#.WvWESK3QPmE},
        note = {version 4.0.22},
}






@book{newS,
  author = {Richard A. Becker and John M. Chambers and Allan
                  R. Wilks},
  title = {The New {S} Language},
  publisher = {Chapman \& Hall},
  year = 1988,
  address = {London},
  abstract = {This book is often called the ``\emph{Blue Book}'',
                  and introduced what is now known as S version 3, or S3.}
}

@article{Cox2008,
  doi = {10.1038/nbt.1511},
  url = {https://doi.org/10.1038/nbt.1511},
  year = {2008},
  month = nov,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {26},
  number = {12},
  pages = {1367--1372},
  author = {J\"{u}rgen Cox and Matthias Mann},
  title = {{MaxQuant} enables high peptide identification rates,  individualized p.p.b.-range mass accuracies and proteome-wide protein quantification},
  journal = {Nature Biotechnology}
}
@article{Cox2011,
  title = {Quantitative,  High-Resolution Proteomics for Data-Driven Systems Biology},
  volume = {80},
  ISSN = {1545-4509},
  url = {http://dx.doi.org/10.1146/annurev-biochem-061308-093216},
  DOI = {10.1146/annurev-biochem-061308-093216},
  number = {1},
  journal = {Annual Review of Biochemistry},
  publisher = {Annual Reviews},
  author = {Cox,  J\"{u}rgen and Mann,  Matthias},
  year = {2011},
  month = jul,
  pages = {273–299}
}
@article{MacLean2010,
  doi = {10.1093/bioinformatics/btq054},
  url = {https://doi.org/10.1093/bioinformatics/btq054},
  year = {2010},
  month = feb,
  publisher = {Oxford University Press ({OUP})},
  volume = {26},
  number = {7},
  pages = {966--968},
  author = {Brendan MacLean and Daniela M. Tomazela and Nicholas Shulman and Matthew Chambers and Gregory L. Finney and Barbara Frewen and Randall Kern and David L. Tabb and Daniel C. Liebler and Michael J. MacCoss},
  title = {Skyline: an open source document editor for creating and analyzing targeted proteomics experiments},
  journal = {Bioinformatics}
}

@article{Rst2016,
  doi = {10.1038/nmeth.3959},
  url = {https://doi.org/10.1038/nmeth.3959},
  year = {2016},
  month = aug,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {13},
  number = {9},
  pages = {741--748},
  author = {Hannes L R\"{o}st and Timo Sachsenberg and Stephan Aiche and Chris Bielow and Hendrik Weisser and Fabian Aicheler and Sandro Andreotti and Hans-Christian Ehrlich and Petra Gutenbrunner and Erhan Kenar and Xiao Liang and Sven Nahnsen and Lars Nilse and Julianus Pfeuffer and George Rosenberger and Marc Rurik and Uwe Schmitt and Johannes Veit and Mathias Walzer and David Wojnar and Witold E Wolski and Oliver Schilling and Jyoti S Choudhary and Lars Malmstr\"{o}m and Ruedi Aebersold and Knut Reinert and Oliver Kohlbacher},
  title = {{OpenMS}: a flexible open-source software platform for mass spectrometry data analysis},
  journal = {Nature Methods}
}

@article{Goloborodko2013,
  doi = {10.1007/s13361-012-0516-6},
  url = {https://doi.org/10.1007/s13361-012-0516-6},
  year = {2013},
  month = jan,
  publisher = {American Chemical Society ({ACS})},
  volume = {24},
  number = {2},
  pages = {301--304},
  author = {Anton A. Goloborodko and Lev I. Levitsky and Mark V. Ivanov and Mikhail V. Gorshkov},
  title = {Pyteomics{\textemdash}a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics},
  journal = {Journal of The American Society for Mass Spectrometry}
}

@ONLINE{https://doi.org/10.18129/b9.bioc.msstats,
  doi = {10.18129/B9.BIOC.MSSTATS},
  url = {https://bioconductor.org/packages/MSstats},
  author = {{Meena Choi [Aut,  Cre],  Cyril Galitzine [Aut],  Tsung-Heng Tsai[Aut],  Olga Vitek [Aut]}},
  title = {MSstats},
  publisher = {Bioconductor},
  year = {2017}
}

@article{Choi2014,
  doi = {10.1093/bioinformatics/btu305},
  url = {https://doi.org/10.1093/bioinformatics/btu305},
  year = {2014},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {30},
  number = {17},
  pages = {2524--2526},
  author = {Meena Choi and Ching-Yun Chang and Timothy Clough and Daniel Broudy and Trevor Killeen and Brendan MacLean and Olga Vitek},
  title = {{MSstats}: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments},
  journal = {Bioinformatics}
}

@article{Goeminne2015,
  doi = {10.1074/mcp.m115.055897},
  url = {https://doi.org/10.1074/mcp.m115.055897},
  year = {2015},
  month = nov,
  publisher = {American Society for Biochemistry {\&} Molecular Biology ({ASBMB})},
  volume = {15},
  number = {2},
  pages = {657--668},
  author = {Ludger J. E. Goeminne and Kris Gevaert and Lieven Clement},
  title = {Peptide-level Robust Ridge Regression Improves Estimation,  Sensitivity,  and Specificity in Data-dependent Quantitative Label-free Shotgun Proteomics},
  journal = {Molecular {\&} Cellular Proteomics}
}

@article{Gatto2011,
  doi = {10.1093/bioinformatics/btr645},
  url = {https://doi.org/10.1093/bioinformatics/btr645},
  year = {2011},
  month = nov,
  publisher = {Oxford University Press ({OUP})},
  volume = {28},
  number = {2},
  pages = {288--289},
  author = {Laurent Gatto and Kathryn S. Lilley},
  title = {{MSnbase}-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization,  processing and quantitation},
  journal = {Bioinformatics}
}

@article{Chambers2012,
  doi = {10.1038/nbt.2377},
  url = {https://doi.org/10.1038/nbt.2377},
  year = {2012},
  month = oct,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {30},
  number = {10},
  pages = {918--920},
  author = {Matthew C Chambers and Brendan Maclean and Robert Burke and Dario Amodei and Daniel L Ruderman and Steffen Neumann and Laurent Gatto and Bernd Fischer and Brian Pratt and Jarrett Egertson and Katherine Hoff and Darren Kessner and Natalie Tasman and Nicholas Shulman and Barbara Frewen and Tahmina A Baker and Mi-Youn Brusniak and Christopher Paulse and David Creasy and Lisa Flashner and Kian Kani and Chris Moulding and Sean L Seymour and Lydia M Nuwaysir and Brent Lefebvre and Frank Kuhlmann and Joe Roark and Paape Rainer and Suckau Detlev and Tina Hemenway and Andreas Huhmer and James Langridge and Brian Connolly and Trey Chadick and Krisztina Holly and Josh Eckels and Eric W Deutsch and Robert L Moritz and Jonathan E Katz and David B Agus and Michael MacCoss and David L Tabb and Parag Mallick},
  title = {A cross-platform toolkit for mass spectrometry and proteomics},
  journal = {Nature Biotechnology}
}

@article{Mallick2010,
  title = {Proteomics: a pragmatic perspective},
  volume = {28},
  ISSN = {1546-1696},
  url = {http://dx.doi.org/10.1038/nbt.1658},
  DOI = {10.1038/nbt.1658},
  number = {7},
  journal = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  author = {Mallick,  Parag and Kuster,  Bernhard},
  year = {2010},
  month = jul,
  pages = {695–709}
}

@article{Savaryn2016,
  title = {A researcher’s guide to mass spectrometry‐based proteomics},
  volume = {16},
  ISSN = {1615-9861},
  url = {http://dx.doi.org/10.1002/pmic.201600113},
  DOI = {10.1002/pmic.201600113},
  number = {18},
  journal = {PROTEOMICS},
  publisher = {Wiley},
  author = {Savaryn,  John P. and Toby,  Timothy K. and Kelleher,  Neil L.},
  year = {2016},
  month = aug,
  pages = {2435–2443}
}

@article{Zubarev2013,
  title = {Orbitrap Mass Spectrometry},
  volume = {85},
  ISSN = {1520-6882},
  url = {http://dx.doi.org/10.1021/ac4001223},
  DOI = {10.1021/ac4001223},
  number = {11},
  journal = {Analytical Chemistry},
  publisher = {American Chemical Society (ACS)},
  author = {Zubarev,  Roman A. and Makarov,  Alexander},
  year = {2013},
  month = may,
  pages = {5288–5296}
}


@ONLINE{MSV000086542,
  doi = {10.25345/C5MZ14},
  url = {https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000086542},
  author = {Kockmann,  Tobias},
  language = {en},
  title = {MassIVE MSV000086542 - Automated quality control sample 1 (autoQC01) analyzed across different Thermo Scientific mass spectrometers},
  publisher = {MassIVE},
  year = {2020}
}

@article{Kelstrup2014,
  doi = {10.1021/pr500985w},
  url = {https://doi.org/10.1021/pr500985w},
  year = {2014},
  month = nov,
  publisher = {American Chemical Society ({ACS})},
  volume = {13},
  number = {12},
  pages = {6187--6195},
  author = {Christian D. Kelstrup and Rosa R. Jersie-Christensen and Tanveer S. Batth and Tabiwang N. Arrey and Andreas Kuehn and Markus Kellmann and Jesper V. Olsen},
  title = {Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer},
  journal = {Journal of Proteome Research}
}

@article{Gallien2012,
  doi = {10.1074/mcp.o112.019802},
  url = {https://doi.org/10.1074/mcp.o112.019802},
  year = {2012},
  month = sep,
  publisher = {American Society for Biochemistry {\&} Molecular Biology ({ASBMB})},
  volume = {11},
  number = {12},
  pages = {1709--1723},
  author = {Sebastien Gallien and Elodie Duriez and Catharina Crone and Markus Kellmann and Thomas Moehring and Bruno Domon},
  title = {Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer},
  journal = {Molecular {\&} Cellular Proteomics}
}

@article{Makarov2000,
  doi = {10.1021/ac991131p},
  url = {https://doi.org/10.1021/ac991131p},
  year = {2000},
  month = mar,
  publisher = {American Chemical Society ({ACS})},
  volume = {72},
  number = {6},
  pages = {1156--1162},
  author = {Alexander Makarov},
  title = {Electrostatic Axially Harmonic Orbital Trapping:~ A High-Performance Technique of Mass Analysis},
  journal = {Analytical Chemistry}
}
@article{Aebersold2003,
  title = {Mass spectrometry-based proteomics},
  volume = {422},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/nature01511},
  DOI = {10.1038/nature01511},
  number = {6928},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Aebersold,  Ruedi and Mann,  Matthias},
  year = {2003},
  month = mar,
  pages = {198–207}
}
@article {Deutsch2020.12.07.415539,
	author = {Deutsch, Eric W. and Perez-Riverol, Yasset and Carver, Jeremy and Kawano, Shin and Mendoza, Luis and Van Den Bossche, Tim and Gabriels, Ralf and Binz, Pierre-Alain and Pullman, Benjamin and Sun, Zhi and Shofstahl, Jim and Bittremieux, Wout and Mak, Tytus D. and Klein, Joshua and Zhu, Yunping and Lam, Henry and Vizca{\'\i}no, Juan Antonio and Bandeira, Nuno},
	title = {Universal Spectrum Identifier for mass spectra},
	elocation-id = {2020.12.07.415539},
	year = {2020},
	doi = {10.1101/2020.12.07.415539},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {The Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding a virtual path to any mass spectrum contained in datasets deposited to public proteomics repositories. USIs enable greater transparency for providing spectral evidence in support of key findings in publications, with more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2020/12/09/2020.12.07.415539},
	eprint = {https://www.biorxiv.org/content/early/2020/12/09/2020.12.07.415539.full.pdf},
	journal = {bioRxiv}
}

@article{ThermoRawFileParser,
  doi = {10.1021/acs.jproteome.9b00328},
  url = {https://doi.org/10.1021/acs.jproteome.9b00328},
  year = {2019},
  month = nov,
  publisher = {American Chemical Society ({ACS})},
  volume = {19},
  number = {1},
  pages = {537--542},
  author = {Niels Hulstaert and Jim Shofstahl and Timo Sachsenberg and Mathias Walzer and Harald Barsnes and Lennart Martens and Yasset Perez-Riverol},
  title = {{ThermoRawFileParser}: Modular,  Scalable,  and Cross-Platform {RAW} File Conversion},
  journal = {Journal of Proteome Research}
}

@book{Sarkar2008,
  title = {Lattice: Multivariate Data Visualization with R},
  ISBN = {9780387759692},
  url = {http://dx.doi.org/10.1007/978-0-387-75969-2},
  DOI = {10.1007/978-0-387-75969-2},
  publisher = {Springer New York},
  author = {Sarkar,  Deepayan},
  year = {2008}
}

@BOOK{Cleveland1993,
  Author={Cleveland, William S.},
  Title={Visualizing Data},
  Publisher={Hobart Press, Summit, New Jersey, U.S.A},
  YEAR={1993},
  Edition={1st}
}

@Book{Wickham2009,
  doi = {10.1007/978-0-387-98141-3},
    author = {Hadley Wickham},
    title = {ggplot2: Elegant Graphics for Data Analysis},
    publisher = {Springer-Verlag New York},
    year = {2009},
    isbn = {978-0-387-98140-6},
    url = {http://ggplot2.org},
}

@article{Bruderer2017,
  title = {Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results},
  volume = {16},
  ISSN = {1535-9476},
  url = {http://dx.doi.org/10.1074/mcp.RA117.000314},
  DOI = {10.1074/mcp.ra117.000314},
  number = {12},
  journal = {Molecular &amp; Cellular Proteomics},
  publisher = {Elsevier BV},
  author = {Bruderer,  Roland and Bernhardt,  Oliver M. and Gandhi,  Tejas and Xuan,  Yue and Sondermann,  Julia and Schmidt,  Manuela and Gomez-Varela,  David and Reiter,  Lukas},
  year = {2017},
  month = dec,
  pages = {2296–2309}
}