• J. Junker, C. Bielow, A. Bertsch, M. Sturm, K. Reinert, and O. Kohlbacher, “TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data,” Journal of proteome research, vol. 11, iss. 7, p. 3914–3920, 2012.
    [Bibtex]
    @article{junker2012toppas,
    title={TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data},
    author={Junker, Johannes and Bielow, Chris and Bertsch, Andreas and Sturm, Marc and Reinert, Knut and Kohlbacher, Oliver},
    journal={Journal of proteome research},
    volume={11},
    number={7},
    pages={3914--3920},
    year={2012},
    publisher={ACS Publications}
    }
  • S. Nahnsen and O. Kohlbacher, “In silico design of targeted SRM-based experiments,” BMC bioinformatics, vol. 13, iss. Suppl 16, p. S8, 2012.
    [Bibtex]
    @article{nahnsen2012silico,
    title={In silico design of targeted SRM-based experiments},
    author={Nahnsen, Sven and Kohlbacher, Oliver},
    journal={BMC bioinformatics},
    volume={13},
    number={Suppl 16},
    pages={S8},
    year={2012},
    publisher={BioMed Central Ltd}
    }
  • A. Bertsch, C. Gröpl, K. Reinert, and O. Kohlbacher, “OpenMS and TOPP: open source software for LC-MS data analysis,” Data Mining in Proteomics: From Standards to Applications, p. 353–367, 2011.
    [Bibtex]
    @article{bertsch2011openms,
    title={OpenMS and TOPP: open source software for LC-MS data analysis},
    author={Bertsch, Andreas and Gr{\"o}pl, Clemens and Reinert, Knut and Kohlbacher, Oliver},
    journal={Data Mining in Proteomics: From Standards to Applications},
    pages={353--367},
    year={2011},
    publisher={Humana Press}
    }
  • S. Nahnsen, A. Bertsch, J. Rahnenführer, A. Nordheim, and O. Kohlbacher, “Probabilistic consensus scoring improves tandem mass spectrometry peptide identification,” Journal of proteome research, vol. 10, iss. 8, p. 3332–3343, 2011.
    [Bibtex]
    @article{nahnsen2011probabilistic,
    title={Probabilistic consensus scoring improves tandem mass spectrometry peptide identification},
    author={Nahnsen, Sven and Bertsch, Andreas and Rahnenführer, Jörg and Nordheim, Alfred and Kohlbacher, Oliver},
    journal={Journal of proteome research},
    volume={10},
    number={8},
    pages={3332--3343},
    year={2011},
    publisher={ACS Publications}
    }
  • C. Bielow, S. Aiche, S. Andreotti, and K. Reinert, “MSSimulator: Simulation of mass spectrometry data,” Journal of proteome research, vol. 10, iss. 7, p. 2922–2929, 2011.
    [Bibtex]
    @article{bielow2011mssimulator,
    title={MSSimulator: Simulation of mass spectrometry data},
    author={Bielow, Chris and Aiche, Stephan and Andreotti, Sandro and Reinert, Knut},
    journal={Journal of proteome research},
    volume={10},
    number={7},
    pages={2922--2929},
    year={2011},
    publisher={ACS Publications}
    }
  • K. Reinert and O. Kohlbacher, “OpenMS and TOPP: open source software for LC-MS data analysis,” in Proteome Bioinformatics, Springer, 2010, p. 201–211.
    [Bibtex]
    @incollection{reinert2010openms,
    title={OpenMS and TOPP: open source software for LC-MS data analysis},
    author={Reinert, Knut and Kohlbacher, Oliver},
    booktitle={Proteome Bioinformatics},
    pages={201--211},
    year={2010},
    publisher={Springer}
    }
  • M. Sturm and others, “OpenMS-A framework for computational mass spectrometry,” PhD Thesis, 2010.
    [Bibtex]
    @phdthesis{sturm2010openms,
    title={OpenMS-A framework for computational mass spectrometry},
    author={Sturm, Marc and others},
    year={2010},
    school={Universit{\"a}t T{\"u}bingen}
    }
  • A. Bertsch, S. Jung, A. Zerck, N. Pfeifer, S. Nahnsen, C. Henneges, A. Nordheim, and O. Kohlbacher, “Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics,” Journal of proteome research, vol. 9, iss. 5, p. 2696–2704, 2010.
    [Bibtex]
    @article{bertsch2010optimal,
    title={Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics},
    author={Bertsch, Andreas and Jung, Stephan and Zerck, Alexandra and Pfeifer, Nico and Nahnsen, Sven and Henneges, Carsten and Nordheim, Alfred and Kohlbacher, Oliver},
    journal={Journal of proteome research},
    volume={9},
    number={5},
    pages={2696--2704},
    year={2010},
    publisher={ACS Publications}
    }
  • M. Sturm and O. Kohlbacher, “TOPPView: an open-source viewer for mass spectrometry data,” Journal of proteome research, vol. 8, iss. 7, p. 3760–3763, 2009.
    [Bibtex]
    @article{sturm2009toppview,
    title={TOPPView: an open-source viewer for mass spectrometry data},
    author={Sturm, Marc and Kohlbacher, Oliver},
    journal={Journal of proteome research},
    volume={8},
    number={7},
    pages={3760--3763},
    year={2009},
    publisher={ACS Publications}
    }
  • C. Bielow, S. Aiche, S. Andreotti, A. Bertsch, C. Gröpl, R. Hussong, N. Pfeifer, M. Sturm, A. Zerck, A. Hildebrandt, and others, “OpenMS—An Open Source Framework for Mass Spec-trometry Data,” German Conference on Bioinformatics 2009, p. 154.
    [Bibtex]
    @article{bielow2009openms,
    title={OpenMS—An Open Source Framework for Mass Spec-trometry Data},
    author={Bielow, Chris and Aiche, Stephan and Andreotti, Sandro and Bertsch, Andreas and Gr{\"o}pl, Clemens and Hussong, Rene and Pfeifer, Nico and Sturm, Marc and Zerck, Alexandra and Hildebrandt, Andreas and others},
    journal={German Conference on Bioinformatics 2009},
    pages={154}
    }
  • A. Bertsch, A. Leinenbach, A. Pervukhin, M. Lubeck, R. Hartmer, C. Baessmann, Y. A. Elnakady, R. Müller, S. Böcker, C. G. Huber, and others, “De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation,” Electrophoresis, vol. 30, iss. 21, p. 3736–3747, 2009.
    [Bibtex]
    @article{bertsch2009novo,
    title={De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation},
    author={Bertsch, Andreas and Leinenbach, Andreas and Pervukhin, Anton and Lubeck, Markus and Hartmer, Ralf and Baessmann, Carsten and Elnakady, Yasser Abbas and M{\"u}ller, Rolf and B{\"o}cker, Sebastian and Huber, Christian G and others},
    journal={Electrophoresis},
    volume={30},
    number={21},
    pages={3736--3747},
    year={2009},
    publisher={Wiley Online Library}
    }
  • N. Pfeifer, A. Leinenbach, C. G. Huber, and O. Kohlbacher, “Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach,” Journal of proteome research, vol. 8, iss. 8, p. 4109–4115, 2009.
    [Bibtex]
    @article{pfeifer2009improving,
    title={Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach},
    author={Pfeifer, Nico and Leinenbach, Andreas and Huber, Christian G and Kohlbacher, Oliver},
    journal={Journal of proteome research},
    volume={8},
    number={8},
    pages={4109--4115},
    year={2009},
    publisher={ACS Publications}
    }
  • L. Nilse, M. Sturm, D. Trudgian, M. Salek, P. F. Sims, K. M. Carroll, and S. J. Hubbard, “SILACAnalyzer-a tool for differential quantitation of stable isotope derived data,” in Computational Intelligence Methods for Bioinformatics and Biostatistics, Springer Berlin Heidelberg, 2009, p. 45–55.
    [Bibtex]
    @incollection{nilse2009silacanalyzer,
    title={SILACAnalyzer-a tool for differential quantitation of stable isotope derived data},
    author={Nilse, Lars and Sturm, Marc and Trudgian, David and Salek, Mogjiborahman and Sims, Paul FG and Carroll, Kathleen M and Hubbard, Simon J},
    booktitle={Computational Intelligence Methods for Bioinformatics and Biostatistics},
    pages={45--55},
    year={2009},
    publisher={Springer Berlin Heidelberg}
    }
  • O. Kohlbacher and K. Reinert, “OpenMS and TOPP: Open source software for lc-ms data analysis,” Proteome Bioinformatics, vol. 604, iss. 2, 2009.
    [Bibtex]
    @article{kohlbacher2009openms,
    title={OpenMS and TOPP: Open source software for lc-ms data analysis},
    author={Kohlbacher, O and Reinert, K},
    journal={Proteome Bioinformatics},
    volume={604},
    number={2},
    year={2009}
    }
  • M. Sturm, A. Bertsch, C. Gröpl, A. Hildebrandt, R. Hussong, E. Lange, N. Pfeifer, O. Schulz-Trieglaff, A. Zerck, K. Reinert, and others, “OpenMS–an open-source software framework for mass spectrometry,” BMC bioinformatics, vol. 9, iss. 1, p. 163, 2008.
    [Bibtex]
    @article{sturm2008openms,
    title={OpenMS--an open-source software framework for mass spectrometry},
    author={Sturm, Marc and Bertsch, Andreas and Gr{\"o}pl, Clemens and Hildebrandt, Andreas and Hussong, Rene and Lange, Eva and Pfeifer, Nico and Schulz-Trieglaff, Ole and Zerck, Alexandra and Reinert, Knut and others},
    journal={BMC bioinformatics},
    volume={9},
    number={1},
    pages={163},
    year={2008},
    publisher={BioMed Central Ltd}
    }
  • O. Schulz-Trieglaff, R. Hussong, C. Gröpl, A. Leinenbach, A. Hildebrandt, C. Huber, and K. Reinert, “Computational quantification of peptides from LC-MS data,” Journal of Computational Biology, vol. 15, iss. 7, p. 685–704, 2008.
    [Bibtex]
    @article{schulz2008computational,
    title={Computational quantification of peptides from LC-MS data},
    author={Schulz-Trieglaff, Ole and Hussong, Rene and Gr{\"o}pl, Clemens and Leinenbach, Andreas and Hildebrandt, Andreas and Huber, Christian and Reinert, Knut},
    journal={Journal of Computational Biology},
    volume={15},
    number={7},
    pages={685--704},
    year={2008},
    publisher={Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA}
    }
  • E. Lange, “Analysis of mass spectrometric data: peak picking and map alignment,” Freie Universtaet Berlin, 2008.
    [Bibtex]
    @article{lange2008analysis,
    title={Analysis of mass spectrometric data: peak picking and map alignment},
    author={Lange, Eva},
    journal={Freie Universtaet Berlin},
    year={2008}
    }
  • O. Schulz-Trieglaff, N. Pfeifer, C. Gröpl, O. Kohlbacher, and K. Reinert, “LC-MSsim–a simulation software for liquid chromatography mass spectrometry data,” BMC bioinformatics, vol. 9, iss. 1, p. 1, 2008.
    [Bibtex]
    @article{schulz2008lc,
    title={LC-MSsim--a simulation software for liquid chromatography mass spectrometry data},
    author={Schulz-Trieglaff, Ole and Pfeifer, Nico and Gr{\"o}pl, Clemens and Kohlbacher, Oliver and Reinert, Knut},
    journal={BMC bioinformatics},
    volume={9},
    number={1},
    pages={1},
    year={2008},
    publisher={BioMed Central}
    }
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