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Publications

Peer-reviewed papers, software citations, and community research built with OpenMS.

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Key publications

Please reference these papers when you publish work that uses OpenMS or pyOpenMS.

Archive

All publications

Browse peer-reviewed research from the OpenMS community, year by year.

  • A proteomics sample metadata representation for multiomics integration and big data analysis

    Nature Communications · 2021

    Dai, Chengxin; Füllgrabe, Anja; Pfeuffer, Julianus; Solovyeva, Elizaveta M; Deng, Jingwen; Moreno, Pablo; Kamatchinathan, Selvakumar; Kundu, Deepti Jaiswal; George, Nancy; Fexova, Silvie

  • DIAproteomics: A multifunctional data analysis pipeline for data-independent acquisition proteomics and peptidomics

    Journal of proteome research · 2021

    Bichmann, Leon; Gupta, Shubham; Rosenberger, George; Kuchenbecker, Leon; Sachsenberg, Timo; Ewels, Phil; Alka, Oliver; Pfeuffer, Julianus; Kohlbacher, Oliver; Rost, Hannes

  • HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy

    Journal for immunotherapy of cancer · 2021

    Marcu, Ana; Bichmann, Leon; Kuchenbecker, Leon; Kowalewski, Daniel Johannes; Freudenmann, Lena Katharina; Backert, Linus; Mühlenbruch, Lena; Szolek, András; Lübke, Maren; Wagner, Philipp

  • A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

    Nature communications · 2020

    Wein, Samuel; Andrews, Byron; Sachsenberg, Timo; Santos-Rosa, Helena; Kohlbacher, Oliver; Kouzarides, Tony; Garcia, Benjamin A; Weisser, Hendrik

  • Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry

    Nature communications · 2020

    Stützer, Alexandra; Welp, Luisa M; Raabe, Monika; Sachsenberg, Timo; Kappert, Christin; Wulf, Alexander; Lau, Andy M; David, Stefan-Sebastian; Chernev, Aleksandar; Kramer, Katharina

  • FLASHDeconv: ultrafast, high-quality feature deconvolution for top-down proteomics

    Cell Systems · 2020

    Jeong, Kyowon; Kim, Jihyung; Gaikwad, Manasi; Hidayah, Siti Nurul; Heikaus, Laura; Schlüter, Hartmut; Kohlbacher, Oliver

  • Feature-based molecular networking in the GNPS analysis environment

    Nature methods · 2020

    Nothias, Louis-Félix; Petras, Daniel; Schmid, Robin; Dührkop, Kai; Rainer, Johannes; Sarvepalli, Abinesh; Protsyuk, Ivan; Ernst, Madeleine; Tsugawa, Hiroshi; Fleischauer, Markus

  • Metabolomics data processing using OpenMS

    Computational Methods and Data Analysis for Metabolomics · 2020

    Rurik, Marc; Alka, Oliver; Aicheler, Fabian; Kohlbacher, Oliver

  • OpenPepXL: an open-source tool for sensitive identification of cross-linked peptides in XL-MS

    Molecular & Cellular Proteomics · 2020

    Netz, Eugen; Dijkstra, Tjeerd MH; Sachsenberg, Timo; Zimmermann, Lukas; Walzer, Mathias; Monecke, Thomas; Ficner, Ralf; Dybkov, Olexandr; Urlaub, Henning; Kohlbacher, Oliver

  • Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells

    Cell Communication and Signaling · 2020

    Scheidt, Tamara; Alka, Oliver; Gonczarowska-Jorge, Humberto; Gruber, Wolfgang; Rathje, Florian; Dell’Aica, Margherita; Rurik, Marc; Kohlbacher, Oliver; Zahedi, René P; Aberger, Fritz

  • SmartPeak automates targeted and quantitative metabolomics data processing

    Analytical Chemistry · 2020

    Kutuzova, Svetlana; Colaianni, Pasquale; Rost, Hannes; Sachsenberg, Timo; Alka, Oliver; Kohlbacher, Oliver; Burla, Bo; Torta, Federico; Schrubbers, Lars; Kristensen, Mette

  • Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities

    Journal of Proteomics · 2020

    Starke, Robert; Oliphant, Kaitlyn; Jehmlich, Nico; Schäpe, Stephanie Serena; Sachsenberg, Timo; Kohlbacher, Oliver; Allen-Vercoe, Emma; von Bergen, Martin

  • Automated SWATH data analysis using targeted extraction of ion chromatograms

    Proteomics: Methods and Protocols · 2017

    Röst, Hannes L; Aebersold, Ruedi; Schubert, Olga T

  • BioContainers: an open-source and community-driven framework for software standardization

    Bioinformatics · 2017

    da Veiga Leprevost, Felipe; Grüning, Björn A; Alves Aflitos, Saulo; Röst, Hannes L; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas

  • In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics

    Journal of proteomics · 2017

    Audain, Enrique; Uszkoreit, Julian; Sachsenberg, Timo; Pfeuffer, Julianus; Liang, Xiao; Hermjakob, Henning; Sanchez, Aniel; Eisenacher, Martin; Reinert, Knut; Tabb, David L

  • OpenMS–a platform for reproducible analysis of mass spectrometry data

    Journal of biotechnology · 2017

    Pfeuffer, Julianus; Sachsenberg, Timo; Alka, Oliver; Walzer, Mathias; Fillbrunn, Alexander; Nilse, Lars; Schilling, Oliver; Reinert, Knut; Kohlbacher, Oliver

  • Targeted feature detection for data-dependent shotgun proteomics

    Journal of proteome research · 2017

    Weisser, Hendrik; Choudhary, Jyoti S

  • The mzIdentML data standard version 1.2, supporting advances in proteome informatics

    Molecular & Cellular Proteomics · 2017

    Vizcaíno, Juan Antonio; Mayer, Gerhard; Perkins, Simon R; Barsnes, Harald; Vaudel, Marc; Perez-Riverol, Yasset; Ternent, Tobias; Uszkoreit, Julian; Eisenacher, Martin; Fischer, Lutz

  • An automated pipeline for high-throughput label-free quantitative proteomics

    Journal of proteome research · 2013

    Weisser, Hendrik; Nahnsen, Sven; Grossmann, Jonas; Nilse, Lars; Quandt, Andreas; Brauer, Hendrik; Sturm, Marc; Kenar, Erhan; Kohlbacher, Oliver; Aebersold, Ruedi

  • The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics

    Molecular & Cellular Proteomics · 2013

    Walzer, Mathias; Qi, Da; Mayer, Gerhard; Uszkoreit, Julian; Eisenacher, Martin; Sachsenberg, Timo; Gonzalez-Galarza, Faviel F; Fan, Jun; Bessant, Conrad; Deutsch, Eric W

  • Tools for label-free peptide quantification

    Molecular & Cellular Proteomics · 2013

    Nahnsen, Sven; Bielow, Chris; Reinert, Knut; Kohlbacher, Oliver

  • Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics

    Journal of proteome research · 2010

    Bertsch, Andreas; Jung, Stephan; Zerck, Alexandra; Pfeifer, Nico; Nahnsen, Sven; Henneges, Carsten; Nordheim, Alfred; Kohlbacher, Oliver

  • TOPP goes Rapid The OpenMS Proteomics Pipeline in a Grid-Enabled Web Portal

    Proceedings of the 2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing · 2010

    Gesing, Sandra; van Hemert, Jano; Koetsier, Jos; Bertsch, Andreas; Kohlbacher, Oliver

  • De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation

    Electrophoresis · 2009

    Bertsch, Andreas; Leinenbach, Andreas; Pervukhin, Anton; Lubeck, Markus; Hartmer, Ralf; Baessmann, Carsten; Elnakady, Yasser Abbas; Müller, Rolf; Böcker, Sebastian; Huber, Christian G

  • Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach

    Journal of proteome research · 2009

    Pfeifer, Nico; Leinenbach, Andreas; Huber, Christian G; Kohlbacher, Oliver

  • OpenMS and TOPP: open source software for LC-MS data analysis

    Proteome Bioinformatics · 2009

    Reinert, Knut; Kohlbacher, Oliver

  • SILACAnalyzer-a tool for differential quantitation of stable isotope derived data

    International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics · 2009

    Nilse, Lars; Sturm, Marc; Trudgian, David; Salek, Mogjiborahman; Sims, Paul FG; Carroll, Kathleen M; Hubbard, Simon J

  • TOPPView: an open-source viewer for mass spectrometry data

    Journal of proteome research · 2009

    Sturm, Marc; Kohlbacher, Oliver

  • Analysis of mass spectrometric data: peak picking and map alignment

    Freie Universtaet Berlin · 2008

    Lange, Eva

  • Computational quantification of peptides from LC-MS data

    Journal of Computational Biology · 2008

    Schulz-Trieglaff, Ole; Hussong, Rene; Gröpl, Clemens; Leinenbach, Andreas; Hildebrandt, Andreas; Huber, Christian; Reinert, Knut

  • Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

    BMC bioinformatics · 2008

    Lange, Eva; Tautenhahn, Ralf; Neumann, Steffen; Gröpl, Clemens

  • LC-MSsim–a simulation software for liquid chromatography mass spectrometry data

    BMC bioinformatics · 2008

    Schulz-Trieglaff, Ole; Pfeifer, Nico; Gröpl, Clemens; Kohlbacher, Oliver; Reinert, Knut

  • OpenMS–an open-source software framework for mass spectrometry

    BMC bioinformatics · 2008

    Sturm, Marc; Bertsch, Andreas; Gröpl, Clemens; Hildebrandt, Andreas; Hussong, Rene; Lange, Eva; Pfeifer, Nico; Schulz-Trieglaff, Ole; Zerck, Alexandra; Reinert, Knut

  • A fast and accurate algorithm for the quantification of peptides from mass spectrometry data

    Research in Computational Molecular Biology: 11th Annual International Conference, RECOMB 2007, Oakland, CA, USA, April 21-25, 2007. Proceedings 11 · 2007

    Schulz-Trieglaff, Ole; Hussong, Rene; Gröpl, Clemens; Hildebrandt, Andreas; Reinert, Knut

  • A geometric approach for the alignment of liquid chromatography—mass spectrometry data

    Bioinformatics · 2007

    Lange, Eva; Gröpl, Clemens; Schulz-Trieglaff, Ole; Leinenbach, Andreas; Huber, Christian; Reinert, Knut

  • TOPP The OpenMS Proteomics Pipeline

    Proceedings of the 5th European · 2007

    Sturm, Marc

  • TOPP—the OpenMS proteomics pipeline

    Bioinformatics · 2007

    Kohlbacher, Oliver; Reinert, Knut; Gröpl, Clemens; Lange, Eva; Pfeifer, Nico; Schulz-Trieglaff, Ole; Sturm, Marc

  • Absolute quantification of myoglobin content in blood serum using HPLC/MS through automatic bioinformatics analysis

    MOLECULAR & CELLULAR PROTEOMICS · 2005

    Groepl, Clemens; Lange, Eva; Reinert, Knut; Kohlbacher, Oliver; Sturm, Marc; Huber, Christian G; Mayr, Bettina M; Klein, Christoph L

  • Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples

    Computational Life Sciences: First International Symposium, CompLife 2005, Konstanz, Germany, September 25-27, 2005. Proceedings 1 · 2005

    Gröpl, Clemens; Lange, Eva; Reinert, Knut; Kohlbacher, Oliver; Sturm, Marc; Huber, Christian G; Mayr, Bettina M; Klein, Christoph L

  • OPENMS; a generic open source framework for chromatography/MS-based proteomics

    Molecular & Cellular Proteomics · 2005

    Lange, E; Reinert, K; Groepl, C; Kohlbacher, O; Sturm, M; Hildebrandt, A

  • OpenMS-Software for Mass Spectrometry

    Poster presented at the MBI Workshop on Computational Proteomics and Mass Spectrometry · 2005

    Gröpl, C; Hildebrandt, A; Kohlbacher, O; Lange, E; Lövenich, S; Sturm, M