• J. A. Vizcaíno, G. Mayer, S. R. Perkins, H. Barsnes, M. Vaudel, Y. Perez-Riverol, T. Ternent, J. Uszkoreit, M. Eisenacher, L. Fischer, and others, “The mzIdentML data standard version 1.2, supporting advances in proteome informatics,” Molecular & Cellular Proteomics, p. mcp–M117, 2017.
    [Bibtex]
    @article{vizcaino2017mzidentml,
    title={The mzIdentML data standard version 1.2, supporting advances in proteome informatics},
    author={Vizca{\'i}no, Juan Antonio and Mayer, Gerhard and Perkins, Simon R and Barsnes, Harald and Vaudel, Marc and Perez-Riverol, Yasset and Ternent, Tobias and Uszkoreit, Julian and Eisenacher, Martin and Fischer, Lutz and others},
    journal={Molecular \& Cellular Proteomics},
    pages={mcp--M117},
    year={2017},
    publisher={ASBMB}
    }
  • E. Audain, J. Uszkoreit, T. Sachsenberg, J. Pfeuffer, X. Liang, H. Hermjakob, A. Sanchez, M. Eisenacher, K. Reinert, D. L. Tabb, and others, “In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics,” Journal of proteomics, vol. 150, pp. 170-182, 2017.
    [Bibtex]
    @article{audain2017depth,
    title={In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics},
    author={Audain, Enrique and Uszkoreit, Julian and Sachsenberg, Timo and Pfeuffer, Julianus and Liang, Xiao and Hermjakob, Henning and Sanchez, Aniel and Eisenacher, Martin and Reinert, Knut and Tabb, David L and others},
    journal={Journal of proteomics},
    volume={150},
    pages={170--182},
    year={2017},
    publisher={Elsevier}
    }
  • H. L. Röst, R. Aebersold, and O. T. Schubert, “Automated SWATH data analysis using targeted extraction of ion chromatograms,” Proteomics: Methods and Protocols, pp. 289-307, 2017.
    [Bibtex]
    @article{rost2017automated,
    title={Automated SWATH data analysis using targeted extraction of ion chromatograms},
    author={R{\"o}st, Hannes L and Aebersold, Ruedi and Schubert, Olga T},
    journal={Proteomics: Methods and Protocols},
    pages={289--307},
    year={2017},
    publisher={Springer New York}
    }
  • F. da Veiga Leprevost, B. A. Grüning, S. Alves Aflitos, H. L. Röst, J. Uszkoreit, H. Barsnes, M. Vaudel, P. Moreno, L. Gatto, J. Weber, and others, “BioContainers: an open-source and community-driven framework for software standardization,” Bioinformatics, p. btx192, 2017.
    [Bibtex]
    @article{da2017biocontainers,
    title={BioContainers: an open-source and community-driven framework for software standardization},
    author={da Veiga Leprevost, Felipe and Gr{\"u}ning, Bj{\"o}rn A and Alves Aflitos, Saulo and R{\"o}st, Hannes L and Uszkoreit, Julian and Barsnes, Harald and Vaudel, Marc and Moreno, Pablo and Gatto, Laurent and Weber, Jonas and others},
    journal={Bioinformatics},
    pages={btx192},
    year={2017},
    publisher={Oxford University Press}
    }
  • [DOI] H. Weisser and J. S. Choudhary, “Targeted feature detection for data-dependent shotgun proteomics,” Journal of Proteome Research, 2017.
    [Bibtex]
    @article{weisser2017targeted,
    title={Targeted feature detection for data-dependent shotgun proteomics},
    author={Weisser, Hendrik and Choudhary, Jyoti S},
    journal={Journal of Proteome Research},
    year={2017},
    publisher={ACS Publications},
    doi={10.1021/acs.jproteome.7b00248}
    }
  • [DOI] J. Pfeuffer, T. Sachsenberg, O. Alka, M. Walzer, A. Fillbrunn, L. Nilse, O. Schilling, K. Reinert, and O. Kohlbacher, “OpenMS – A platform for reproducible analysis of mass spectrometry data,” Journal of Biotechnology, 2017.
    [Bibtex]
    @article{pfeuffer2017denbi,
    title = "OpenMS – A platform for reproducible analysis of mass spectrometry data",
    journal = "Journal of Biotechnology",
    volume = "",
    number = "",
    pages = "",
    year = "2017",
    note = "",
    issn = "0168-1656",
    doi = "10.1016/j.jbiotec.2017.05.016",
    url = "http://www.sciencedirect.com/science/article/pii/S0168165617302511",
    author = "Julianus Pfeuffer and Timo Sachsenberg and Oliver Alka and Mathias Walzer and Alexander Fillbrunn and Lars Nilse and Oliver Schilling and Knut Reinert and Oliver Kohlbacher"
    }
  • H. L. Rost, T. Sachsenberg, S. Aiche, C. Bielow, H. Weisser, F. Aicheler, S. Andreotti, H. Ehrlich, P. Gutenbrunner, E. Kenar, X. Liang, S. Nahnsen, L. Nilse, J. Pfeuffer, G. Rosenberger, M. Rurik, U. Schmitt, J. Veit, M. Walzer, D. Wojnar, W. E. Wolski, O. Schilling, J. S. Choudhary, L. Malmstrom, R. Aebersold, K. Reinert, and O. Kohlbacher, “OpenMS: a flexible open-source software platform for mass spectrometry data analysis,” Nat Meth, vol. 13, iss. 9, pp. 741-748, 2016.
    [Bibtex]
    @article{Rost2016,
    author = {Rost, Hannes L and Sachsenberg, Timo and Aiche, Stephan and Bielow, Chris and Weisser, Hendrik and Aicheler, Fabian and Andreotti, Sandro and Ehrlich, Hans-Christian and Gutenbrunner, Petra and Kenar, Erhan and Liang, Xiao and Nahnsen, Sven and Nilse, Lars and Pfeuffer, Julianus and Rosenberger, George and Rurik, Marc and Schmitt, Uwe and Veit, Johannes and Walzer, Mathias and Wojnar, David and Wolski, Witold E and Schilling, Oliver and Choudhary, Jyoti S and Malmstrom, Lars and Aebersold, Ruedi and Reinert, Knut and Kohlbacher, Oliver},
    title = {OpenMS: a flexible open-source software platform for mass spectrometry data analysis},
    year = {2016},
    URL = {http://dx.doi.org/10.1038/nmeth.3959},
    abstract = {High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.},
    journal = {Nat Meth},
    volume = {13},
    number = {9},
    pages = {741-748},
    note = {Perspective}
    }
  • J. Veit, T. Sachsenberg, A. Chernev, F. Aicheler, H. Urlaub, and O. Kohlbacher, “LFQProfiler and RNPxl: Open-Source Tools for Label-Free Quantification and Protein–RNA Cross-Linking Integrated into Proteome Discoverer,” Journal of Proteome Research, vol. 15, iss. 9, pp. 3441-3448, 2016.
    [Bibtex]
    @article{veit2016lfqprofiler,
    title={LFQProfiler and RNPxl: Open-Source Tools for Label-Free Quantification and Protein--RNA Cross-Linking Integrated into Proteome Discoverer},
    author={Veit, Johannes and Sachsenberg, Timo and Chernev, Aleksandar and Aicheler, Fabian and Urlaub, Henning and Kohlbacher, Oliver},
    journal={Journal of Proteome Research},
    volume={15},
    number={9},
    pages={3441--3448},
    year={2016},
    publisher={ACS Publications}
    }
  • P. Navarro, J. Kuharev, L. C. Gillet, O. M. Bernhardt, B. MacLean, H. L. Röst, S. A. Tate, C. Tsou, L. Reiter, U. Distler, and others, “A multi-center study benchmarks software tools for label-free proteome quantification,” Nature biotechnology, vol. 34, iss. 11, p. 1130, 2016.
    [Bibtex]
    @article{navarro2016multi,
    title={A multi-center study benchmarks software tools for label-free proteome quantification},
    author={Navarro, Pedro and Kuharev, J{\"o}rg and Gillet, Ludovic C and Bernhardt, Oliver M and MacLean, Brendan and R{\"o}st, Hannes L and Tate, Stephen A and Tsou, Chih-Chiang and Reiter, Lukas and Distler, Ute and others},
    journal={Nature biotechnology},
    volume={34},
    number={11},
    pages={1130},
    year={2016},
    publisher={Europe PMC Funders}
    }
  • [DOI] H. Weisser, J. C. Wright, J. M. Mudge, P. Gutenbrunner, and J. S. Choudhary, “Flexible Data Analysis Pipeline for High-Confidence Proteogenomics,” Journal of Proteome Research, vol. 15, iss. 12, pp. 4686-4695, 2016.
    [Bibtex]
    @article{weisser2016flexible,
    title={Flexible Data Analysis Pipeline for High-Confidence Proteogenomics},
    author={Weisser, Hendrik and Wright, James C and Mudge, Jonathan M and Gutenbrunner, Petra and Choudhary, Jyoti S},
    journal={Journal of Proteome Research},
    volume={15},
    number={12},
    pages={4686--4695},
    year={2016},
    publisher={ACS Publications},
    doi={10.1021/acs.jproteome.6b00765}
    }
  • S. Aiche, T. Sachsenberg, E. Kenar, M. Walzer, B. Wiswedel, T. Kristl, M. Boyles, A. Duschl, C. G. Huber, M. R. Berthold, and others, “Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry,” Proteomics, vol. 15, iss. 8, pp. 1443-1447, 2015.
    [Bibtex]
    @article{aiche2015workflows,
    title={Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry},
    author={Aiche, Stephan and Sachsenberg, Timo and Kenar, Erhan and Walzer, Mathias and Wiswedel, Bernd and Kristl, Theresa and Boyles, Matthew and Duschl, Albert and Huber, Christian G and Berthold, Michael R and others},
    journal={Proteomics},
    volume={15},
    number={8},
    pages={1443--1447},
    year={2015}
    }
  • F. Aicheler, J. Li, M. Hoene, R. Lehmann, G. Xu, and O. Kohlbacher, “Retention Time Prediction Improves Identification in Nontargeted Lipidomics Approaches,” Analytical chemistry, vol. 87, iss. 15, pp. 7698-7704, 2015.
    [Bibtex]
    @article{aicheler2015retention,
    title={Retention Time Prediction Improves Identification in Nontargeted Lipidomics Approaches},
    author={Aicheler, Fabian and Li, Jia and Hoene, Miriam and Lehmann, Rainer and Xu, Guowang and Kohlbacher, Oliver},
    journal={Analytical chemistry},
    volume={87},
    number={15},
    pages={7698--7704},
    year={2015},
    publisher={American Chemical Society}
    }
  • C. Ranninger, M. Rurik, A. Limonciel, S. Ruzek, R. Reischl, A. Wilmes, P. Jennings, P. Hewitt, W. Dekant, O. Kohlbacher, and others, “Nephron Toxicity Profiling via Untargeted Metabolome Analysis Employing a High Performance Liquid Chromatography-Mass Spectrometry-based Experimental and Computational Pipeline,” Journal of Biological Chemistry, vol. 290, iss. 31, pp. 19121-19132, 2015.
    [Bibtex]
    @article{ranninger2015nephron,
    title={Nephron Toxicity Profiling via Untargeted Metabolome Analysis Employing a High Performance Liquid Chromatography-Mass Spectrometry-based Experimental and Computational Pipeline},
    author={Ranninger, Christina and Rurik, Marc and Limonciel, Alice and Ruzek, Silke and Reischl, Roland and Wilmes, Anja and Jennings, Paul and Hewitt, Philip and Dekant, Wolfgang and Kohlbacher, Oliver and others},
    journal={Journal of Biological Chemistry},
    volume={290},
    number={31},
    pages={19121--19132},
    year={2015},
    publisher={ASBMB}
    }
  • H. L. Röst, U. Schmitt, R. Aebersold, and L. Malmström, “Fast and efficient XML data access for next-generation mass spectrometry,” PloS one, vol. 10, iss. 4, p. e0125108, 2015.
    [Bibtex]
    @article{rost2015fast,
    title={Fast and efficient XML data access for next-generation mass spectrometry},
    author={R{\"o}st, Hannes L and Schmitt, Uwe and Aebersold, Ruedi and Malmstr{\"o}m, Lars},
    journal={PloS one},
    volume={10},
    number={4},
    pages={e0125108},
    year={2015},
    publisher={Public Library of Science}
    }
  • H. L. Röst, G. Rosenberger, R. Aebersold, and L. Malmström, “Efficient visualization of high-throughput targeted proteomics experiments: TAPIR,” Bioinformatics, p. btv152, 2015.
    [Bibtex]
    @article{rost2015efficient,
    title={Efficient visualization of high-throughput targeted proteomics experiments: TAPIR},
    author={R{\"o}st, Hannes L and Rosenberger, George and Aebersold, Ruedi and Malmstr{\"o}m, Lars},
    journal={Bioinformatics},
    pages={btv152},
    year={2015},
    publisher={Oxford Univ Press}
    }
  • L. Nilse, F. C. Sigloch, M. L. Biniossek, and O. Schilling, “Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling,” PROTEOMICS-Clinical Applications, vol. 9, iss. 7-8, pp. 706-714, 2015.
    [Bibtex]
    @article{nilse2015toward,
    title={Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling},
    author={Nilse, Lars and Sigloch, Florian Christoph and Biniossek, Martin L and Schilling, Oliver},
    journal={PROTEOMICS-Clinical Applications},
    volume={9},
    number={7-8},
    pages={706--714},
    year={2015}
    }
  • H. L. Röst, G. Rosenberger, P. Navarro, L. Gillet, S. M. Miladinović, O. T. Schubert, W. Wolski, B. C. Collins, J. Malmström, L. Malmström, and others, “OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data,” Nature biotechnology, vol. 32, iss. 3, pp. 219-223, 2014.
    [Bibtex]
    @article{rost2014openswath,
    title={OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data},
    author={R{\"o}st, Hannes L and Rosenberger, George and Navarro, Pedro and Gillet, Ludovic and Miladinovi{\'c}, Sa{\v{s}}a M and Schubert, Olga T and Wolski, Witold and Collins, Ben C and Malmstr{\"o}m, Johan and Malmstr{\"o}m, Lars and others},
    journal={Nature biotechnology},
    volume={32},
    number={3},
    pages={219--223},
    year={2014},
    publisher={Nature Publishing Group}
    }
  • H. L. Röst, U. Schmitt, R. Aebersold, and L. Malmström, “pyOpenMS: A Python-based interface to the OpenMS mass-spectrometry algorithm library,” Proteomics, vol. 14, iss. 1, pp. 74-77, 2014.
    [Bibtex]
    @article{rost2014pyopenms,
    title={pyOpenMS: A Python-based interface to the OpenMS mass-spectrometry algorithm library},
    author={R{\"o}st, Hannes L and Schmitt, Uwe and Aebersold, Ruedi and Malmstr{\"o}m, Lars},
    journal={Proteomics},
    volume={14},
    number={1},
    pages={74--77},
    year={2014},
    publisher={Wiley Online Library}
    }
  • E. Kenar, H. Franken, S. Forcisi, K. Wörmann, H. Häring, R. Lehmann, P. Schmitt-Kopplin, A. Zell, and O. Kohlbacher, “Automated Label-free Quantification of Metabolites from Liquid Chromatography–Mass Spectrometry Data,” Molecular & Cellular Proteomics, vol. 13, iss. 1, pp. 348-359, 2014.
    [Bibtex]
    @article{kenar2014automated,
    title={Automated Label-free Quantification of Metabolites from Liquid Chromatography--Mass Spectrometry Data},
    author={Kenar, Erhan and Franken, Holger and Forcisi, Sara and W{\"o}rmann, Kilian and H{\"a}ring, Hans-Ulrich and Lehmann, Rainer and Schmitt-Kopplin, Philippe and Zell, Andreas and Kohlbacher, Oliver},
    journal={Molecular \& Cellular Proteomics},
    volume={13},
    number={1},
    pages={348--359},
    year={2014},
    publisher={ASBMB}
    }
  • T. Sachsenberg, F. Herbst, M. Taubert, R. Kermer, N. Jehmlich, M. von Bergen, J. Seifert, and O. Kohlbacher, “MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics,” Journal of proteome research, vol. 14, iss. 2, pp. 619-627, 2014.
    [Bibtex]
    @article{sachsenberg2014metaprosip,
    title={MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics},
    author={Sachsenberg, Timo and Herbst, Florian-Alexander and Taubert, Martin and Kermer, Ren{\'e} and Jehmlich, Nico and von Bergen, Martin and Seifert, Jana and Kohlbacher, Oliver},
    journal={Journal of proteome research},
    volume={14},
    number={2},
    pages={619--627},
    year={2014},
    publisher={American Chemical Society}
    }
  • K. Kramer, T. Sachsenberg, B. M. Beckmann, S. Qamar, K. Boon, M. W. Hentze, O. Kohlbacher, and H. Urlaub, “Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins,” Nature methods, vol. 11, iss. 10, pp. 1064-1070, 2014.
    [Bibtex]
    @article{kramer2014photo,
    title={Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins},
    author={Kramer, Katharina and Sachsenberg, Timo and Beckmann, Benedikt M and Qamar, Saadia and Boon, Kum-Loong and Hentze, Matthias W and Kohlbacher, Oliver and Urlaub, Henning},
    journal={Nature methods},
    volume={11},
    number={10},
    pages={1064--1070},
    year={2014},
    publisher={Nature Publishing Group}
    }
  • J. Griss, A. R. Jones, T. Sachsenberg, M. Walzer, L. Gatto, J. Hartler, G. G. Thallinger, R. M. Salek, C. Steinbeck, N. Neuhauser, and others, “The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience,” Molecular & Cellular Proteomics, vol. 13, iss. 10, pp. 2765-2775, 2014.
    [Bibtex]
    @article{griss2014mztab,
    title={The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience},
    author={Griss, Johannes and Jones, Andrew R and Sachsenberg, Timo and Walzer, Mathias and Gatto, Laurent and Hartler, J{\"u}rgen and Thallinger, Gerhard G and Salek, Reza M and Steinbeck, Christoph and Neuhauser, Nadin and others},
    journal={Molecular \& Cellular Proteomics},
    volume={13},
    number={10},
    pages={2765--2775},
    year={2014},
    publisher={ASBMB}
    }
  • M. Walzer, L. E. Pernas, S. Nasso, W. Bittremieux, S. Nahnsen, P. Kelchtermans, P. Pichler, H. W. van den Toorn, A. Staes, J. Vandenbussche, and others, “qcML: an exchange format for quality control metrics from mass spectrometry experiments,” Molecular & Cellular Proteomics, vol. 13, iss. 8, pp. 1905-1913, 2014.
    [Bibtex]
    @article{walzer2014qcml,
    title={qcML: an exchange format for quality control metrics from mass spectrometry experiments},
    author={Walzer, Mathias and Pernas, Lucia Espona and Nasso, Sara and Bittremieux, Wout and Nahnsen, Sven and Kelchtermans, Pieter and Pichler, Peter and van den Toorn, Henk WP and Staes, An and Vandenbussche, Jonathan and others},
    journal={Molecular \& Cellular Proteomics},
    volume={13},
    number={8},
    pages={1905--1913},
    year={2014},
    publisher={American Society for Biochemistry and Molecular Biology}
    }
  • H. Weisser, S. Nahnsen, J. Grossmann, L. Nilse, A. Quandt, H. Brauer, M. Sturm, E. Kenar, O. Kohlbacher, R. Aebersold, and others, “An automated pipeline for high-throughput label-free quantitative proteomics,” Journal of proteome research, vol. 12, iss. 4, pp. 1628-1644, 2013.
    [Bibtex]
    @article{weisser2013automated,
    title={An automated pipeline for high-throughput label-free quantitative proteomics},
    author={Weisser, Hendrik and Nahnsen, Sven and Grossmann, Jonas and Nilse, Lars and Quandt, Andreas and Brauer, Hendrik and Sturm, Marc and Kenar, Erhan and Kohlbacher, Oliver and Aebersold, Ruedi and others},
    journal={Journal of proteome research},
    volume={12},
    number={4},
    pages={1628--1644},
    year={2013},
    publisher={ACS Publications}
    }
  • M. Walzer, D. Qi, G. Mayer, J. Uszkoreit, M. Eisenacher, T. Sachsenberg, F. F. Gonzalez-Galarza, J. Fan, C. Bessant, E. W. Deutsch, and others, “The mzQuantML Data Standard for Mass Spectrometry–based Quantitative Studies in Proteomics,” Molecular & Cellular Proteomics, vol. 12, iss. 8, pp. 2332-2340, 2013.
    [Bibtex]
    @article{walzer2013mzquantml,
    title={The mzQuantML Data Standard for Mass Spectrometry--based Quantitative Studies in Proteomics},
    author={Walzer, Mathias and Qi, Da and Mayer, Gerhard and Uszkoreit, Julian and Eisenacher, Martin and Sachsenberg, Timo and Gonzalez-Galarza, Faviel F and Fan, Jun and Bessant, Conrad and Deutsch, Eric W and others},
    journal={Molecular \& Cellular Proteomics},
    volume={12},
    number={8},
    pages={2332--2340},
    year={2013},
    publisher={ASBMB}
    }
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