List of OpenMS Publications

2025

Müller, Tom David; Siraj, Arslan; Walter, Axel; Kim, Jihyung; Wein, Samuel; von Kleist, Johannes; Feroz, Ayesha; Pilz, Matteo; Jeong, Kyowon; Sing, Justin Cyril; OpenMS WebApps: Building User-Friendly Solutions for MS Analysis. Journal of Proteome Research. 2025. Link
Sing, Justin Cyril; Charkow, Joshua; Walter, Axel; Gao, Mingxuan; Muller, Tom David; Bittremieux, Wout; Sachsenberg, Timo; Röst, Hannes Luc; pyOpenMS-viz: Streamlining Mass Spectrometry Data Visualization with pandas. Journal of Proteome Research. 2025. Link

2024

Kim, Jihyung; Jeong, Kyowon; Kaulich, Philipp T; Winkels, Konrad; Tholey, Andreas; Kohlbacher, Oliver; FLASHQuant: a fast algorithm for proteoform quantification in top-down proteomics. Analytical Chemistry. 2024. Link
Siraj, Arslan; Bouwmeester, Robbin; Declercq, Arthur; Welp, Luisa; Chernev, Aleksandar; Wulf, Alexander; Urlaub, Henning; Martens, Lennart; Degroeve, Sven; Kohlbacher, Oliver; Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links. Proteomics. 2024. Link
Pfeuffer, Julianus; Bielow, Chris; Wein, Samuel; Jeong, Kyowon; Netz, Eugen; Walter, Axel; Alka, Oliver; Nilse, Lars; Colaianni, Pasquale Domenico; McCloskey, Douglas; OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nature methods. 2024. Link
Dai, Chengxin; Pfeuffer, Julianus; Wang, Hong; Zheng, Ping; Käll, Lukas; Sachsenberg, Timo; Demichev, Vadim; Bai, Mingze; Kohlbacher, Oliver; Perez-Riverol, Yasset; quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data. Nature Methods. 2024. Link

2023

Kontou, Eftychia E; Walter, Axel; Alka, Oliver; Pfeuffer, Julianus; Sachsenberg, Timo; Mohite, Omkar S; Nuhamunada, Matin; Kohlbacher, Oliver; Weber, Tilmann; UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis. Journal of Cheminformatics. 2023. Link
Bittremieux, Wout; Levitsky, Lev; Pilz, Matteo; Sachsenberg, Timo; Huber, Florian; Wang, Mingxun; Dorrestein, Pieter C; Unified and standardized mass spectrometry data processing in Python using spectrum_utils. Journal of proteome research. 2023. Link

2022

Luo, Xiyang; Bittremieux, Wout; Griss, Johannes; Deutsch, Eric W; Sachsenberg, Timo; Levitsky, Lev I; Ivanov, Mark V; Bubis, Julia A; Gabriels, Ralf; Webel, Henry; A comprehensive evaluation of consensus spectrum generation methods in proteomics. Journal of proteome research. 2022. Link
Jeong, Kyowon; Babović, Maša; Gorshkov, Vladimir; Kim, Jihyung; Jensen, Ole N; Kohlbacher, Oliver; FLASHIda enables intelligent data acquisition for top–down proteomics to boost proteoform identification counts. Nature communications. 2022. Link
Umer, Husen M; Audain, Enrique; Zhu, Yafeng; Pfeuffer, Julianus; Sachsenberg, Timo; Lehtiö, Janne; Branca, Rui M; Perez-Riverol, Yasset; Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides. Bioinformatics. 2022. Link
Jeong, Kyowon; Kim, Jihyung; Kohlbacher, Oliver; Mass Deconvolution of Top-Down Mass Spectrometry Datasets by FLASHDeconv. Proteoform Identification: Methods and Protocols. 2022. Link

2021

Dai, Chengxin; Füllgrabe, Anja; Pfeuffer, Julianus; Solovyeva, Elizaveta M; Deng, Jingwen; Moreno, Pablo; Kamatchinathan, Selvakumar; Kundu, Deepti Jaiswal; George, Nancy; Fexova, Silvie; A proteomics sample metadata representation for multiomics integration and big data analysis. Nature Communications. 2021. Link
Bichmann, Leon; Gupta, Shubham; Rosenberger, George; Kuchenbecker, Leon; Sachsenberg, Timo; Ewels, Phil; Alka, Oliver; Pfeuffer, Julianus; Kohlbacher, Oliver; Rost, Hannes; DIAproteomics: A multifunctional data analysis pipeline for data-independent acquisition proteomics and peptidomics. Journal of proteome research. 2021
Marcu, Ana; Bichmann, Leon; Kuchenbecker, Leon; Kowalewski, Daniel Johannes; Freudenmann, Lena Katharina; Backert, Linus; Mühlenbruch, Lena; Szolek, András; Lübke, Maren; Wagner, Philipp; HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy. Journal for immunotherapy of cancer. 2021

2020

Wein, Samuel; Andrews, Byron; Sachsenberg, Timo; Santos-Rosa, Helena; Kohlbacher, Oliver; Kouzarides, Tony; Garcia, Benjamin A; Weisser, Hendrik; A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. Nature communications. 2020. Link
Stützer, Alexandra; Welp, Luisa M; Raabe, Monika; Sachsenberg, Timo; Kappert, Christin; Wulf, Alexander; Lau, Andy M; David, Stefan-Sebastian; Chernev, Aleksandar; Kramer, Katharina; Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nature communications. 2020. Link
Jeong, Kyowon; Kim, Jihyung; Gaikwad, Manasi; Hidayah, Siti Nurul; Heikaus, Laura; Schlüter, Hartmut; Kohlbacher, Oliver; FLASHDeconv: ultrafast, high-quality feature deconvolution for top-down proteomics. Cell Systems. 2020
Nothias, Louis-Félix; Petras, Daniel; Schmid, Robin; Dührkop, Kai; Rainer, Johannes; Sarvepalli, Abinesh; Protsyuk, Ivan; Ernst, Madeleine; Tsugawa, Hiroshi; Fleischauer, Markus; Feature-based molecular networking in the GNPS analysis environment. Nature methods. 2020
Rurik, Marc; Alka, Oliver; Aicheler, Fabian; Kohlbacher, Oliver; Metabolomics data processing using OpenMS. Computational Methods and Data Analysis for Metabolomics. 2020
Netz, Eugen; Dijkstra, Tjeerd MH; Sachsenberg, Timo; Zimmermann, Lukas; Walzer, Mathias; Monecke, Thomas; Ficner, Ralf; Dybkov, Olexandr; Urlaub, Henning; Kohlbacher, Oliver; OpenPepXL: an open-source tool for sensitive identification of cross-linked peptides in XL-MS. Molecular & Cellular Proteomics. 2020. Link
Scheidt, Tamara; Alka, Oliver; Gonczarowska-Jorge, Humberto; Gruber, Wolfgang; Rathje, Florian; Dell’Aica, Margherita; Rurik, Marc; Kohlbacher, Oliver; Zahedi, René P; Aberger, Fritz; Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells. Cell Communication and Signaling. 2020
Kutuzova, Svetlana; Colaianni, Pasquale; Rost, Hannes; Sachsenberg, Timo; Alka, Oliver; Kohlbacher, Oliver; Burla, Bo; Torta, Federico; Schrubbers, Lars; Kristensen, Mette; SmartPeak automates targeted and quantitative metabolomics data processing. Analytical Chemistry. 2020. Link
Starke, Robert; Oliphant, Kaitlyn; Jehmlich, Nico; Schäpe, Stephanie Serena; Sachsenberg, Timo; Kohlbacher, Oliver; Allen-Vercoe, Emma; von Bergen, Martin; Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. Journal of Proteomics. 2020

2019

Pfeuffer, Julianus; Sachsenberg, Timo; Dijkstra, Tjeerd MH; Serang, Oliver; Reinert, Knut; Kohlbacher, Oliver; EPIFANY-A method for efficient high-confidence protein inference. Journal of proteome research. 2019
Cain, Nicolas; Alka, Oliver; Segelke, Torben; von Wuthenau, Kristian; Kohlbacher, Oliver; Fischer, Markus; Food fingerprinting: Mass spectrometric determination of the cocoa shell content (Theobroma cacao L.) in cocoa products by HPLC-QTOF-MS. Food chemistry. 2019. Link
Bichmann, Leon; Nelde, Annika; Ghosh, Michael; Heumos, Lukas; Mohr, Christopher; Peltzer, Alexander; Kuchenbecker, Leon; Sachsenberg, Timo; Walz, Juliane S; Stevanovic, Stefan; MHCquant: automated and reproducible data analysis for immunopeptidomics. Journal of proteome research. 2019. Link
Löffler, Markus W; Mohr, Christopher; Bichmann, Leon; Freudenmann, Lena Katharina; Walzer, Mathias; Schroeder, Christopher M; Trautwein, Nico; Hilke, Franz J; Zinser, Raphael S; Mühlenbruch, Lena; Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma. Genome medicine. 2019. Link
Gruening, Bjorn; Sallou, Olivier; Moreno, Pablo; da Veiga Leprevost, Felipe; Ménager, Hervé; Søndergaard, Dan; Röst, Hannes; Sachsenberg, Timo; O’connor, Brian; Madeira, Fábio; Recommendations for the packaging and containerizing of bioinformatics software. F1000Research. 2019. Link
Hulstaert, Niels; Shofstahl, Jim; Sachsenberg, Timo; Walzer, Mathias; Barsnes, Harald; Martens, Lennart; Perez-Riverol, Yasset; ThermoRawFileParser: modular, scalable, and cross-platform RAW file conversion. Journal of proteome research. 2019. Link
Licha, David; Vidali, Silvia; Aminzadeh-Gohari, Sepideh; Alka, Oliver; Breitkreuz, Leander; Kohlbacher, Oliver; Reischl, Roland J; Feichtinger, René G; Kofler, Barbara; Huber, Christian G; Untargeted metabolomics reveals molecular effects of ketogenic diet on healthy and tumor xenograft mouse models. International journal of molecular sciences. 2019. Link

2018

Kahles, André; Lehmann, Kjong-Van; Toussaint, Nora C; Hüser, Matthias; Stark, Stefan G; Sachsenberg, Timo; Stegle, Oliver; Kohlbacher, Oliver; Sander, Chris; Caesar-Johnson, Samantha J; Comprehensive analysis of alternative splicing across tumors from 8,705 patients. Cancer cell. 2018. Link

2017

Röst, Hannes L; Aebersold, Ruedi; Schubert, Olga T; Automated SWATH data analysis using targeted extraction of ion chromatograms. Proteomics: Methods and Protocols. 2017. Link
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; BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017. Link
Audain, Enrique; Uszkoreit, Julian; Sachsenberg, Timo; Pfeuffer, Julianus; Liang, Xiao; Hermjakob, Henning; Sanchez, Aniel; Eisenacher, Martin; Reinert, Knut; Tabb, David L; In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. Journal of proteomics. 2017. Link
Pfeuffer, Julianus; Sachsenberg, Timo; Alka, Oliver; Walzer, Mathias; Fillbrunn, Alexander; Nilse, Lars; Schilling, Oliver; Reinert, Knut; Kohlbacher, Oliver; OpenMS–a platform for reproducible analysis of mass spectrometry data. Journal of biotechnology. 2017
Weisser, Hendrik; Choudhary, Jyoti S; Targeted feature detection for data-dependent shotgun proteomics. Journal of proteome research. 2017
Vizcaíno, Juan Antonio; Mayer, Gerhard; Perkins, Simon R; Barsnes, Harald; Vaudel, Marc; Perez-Riverol, Yasset; Ternent, Tobias; Uszkoreit, Julian; Eisenacher, Martin; Fischer, Lutz; The mzIdentML data standard version 1.2, supporting advances in proteome informatics. Molecular & Cellular Proteomics. 2017

2016

Navarro, Pedro; Kuharev, Jörg; Gillet, Ludovic C; Bernhardt, Oliver M; MacLean, Brendan; Röst, Hannes L; Tate, Stephen A; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; A multicenter study benchmarks software tools for label-free proteome quantification. Nature biotechnology. 2016. Link
Weisser, Hendrik; Wright, James C; Mudge, Jonathan M; Gutenbrunner, Petra; Choudhary, Jyoti S; Flexible data analysis pipeline for high-confidence proteogenomics. Journal of Proteome Research. 2016. Link
Veit, Johannes; Sachsenberg, Timo; Chernev, Aleksandar; Aicheler, Fabian; Urlaub, Henning; Kohlbacher, Oliver; LFQProfiler and RNPxl: open-source tools for label-free quantification and protein–RNA cross-linking integrated into proteome discoverer. Journal of proteome research. 2016. Link
Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature methods. 2016
Perez-Riverol, Yasset; Gatto, Laurent; Wang, Rui; Sachsenberg, Timo; Uszkoreit, Julian; da Veiga Leprevost, Felipe; Fufezan, Christian; Ternent, Tobias; Eglen, Stephen J; Katz, Daniel S; Ten simple rules for taking advantage of Git and GitHub. PLoS computational biology. 2016

2015

Röst, Hannes L; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars; Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Bioinformatics. 2015. Link
Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars; Fast and efficient XML data access for next-generation mass spectrometry. PloS one. 2015. Link
Sachsenberg, Timo; Herbst, Florian-Alexander; Taubert, Martin; Kermer, Rene; Jehmlich, Nico; Von Bergen, Martin; Seifert, Jana; Kohlbacher, Oliver; MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics. Journal of proteome research. 2015. Link
Ranninger, Christina; Rurik, Marc; Limonciel, Alice; Ruzek, Silke; Reischl, Roland; Wilmes, Anja; Jennings, Paul; Hewitt, Philip; Dekant, Wolfgang; Kohlbacher, Oliver; Nephron toxicity profiling via untargeted metabolome analysis employing a high performance liquid chromatography-mass spectrometry-based experimental and computational pipeline. Journal of Biological Chemistry. 2015. Link
Aicheler, Fabian; Li, Jia; Hoene, Miriam; Lehmann, Rainer; Xu, Guowang; Kohlbacher, Oliver; Retention time prediction improves identification in nontargeted lipidomics approaches. Analytical chemistry. 2015. Link
Nilse, Lars; Sigloch, Florian Christoph; Biniossek, Martin L; Schilling, Oliver; Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling. PROTEOMICS–Clinical Applications. 2015. Link
Aiche, Stephan; Sachsenberg, Timo; Kenar, Erhan; Walzer, Mathias; Wiswedel, Bernd; Kristl, Theresa; Boyles, Matthew; Duschl, Albert; Huber, Christian G; Berthold, Michael R; Workflows for automated downstream data analysis and visualization in large‐scale computational mass spectrometry. Proteomics. 2015

2014

Kenar, Erhan; Franken, Holger; Forcisi, Sara; Wörmann, Kilian; Häring, Hans-Ulrich; Lehmann, Rainer; Schmitt-Kopplin, Philippe; Zell, Andreas; Kohlbacher, Oliver; Automated label-free quantification of metabolites from liquid chromatography–mass spectrometry data. Molecular & Cellular Proteomics. 2014. Link
Röst, Hannes L; Rosenberger, George; Navarro, Pedro; Gillet, Ludovic; Miladinović, Saša M; Schubert, Olga T; Wolski, Witold; Collins, Ben C; Malmström, Johan; Malmström, Lars; OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nature biotechnology. 2014
Kramer, Katharina; Sachsenberg, Timo; Beckmann, Benedikt M; Qamar, Saadia; Boon, Kum-Loong; Hentze, Matthias W; Kohlbacher, Oliver; Urlaub, Henning; Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins. Nature methods. 2014. Link
Griss, Johannes; Jones, Andrew R; Sachsenberg, Timo; Walzer, Mathias; Gatto, Laurent; Hartler, Jürgen; Thallinger, Gerhard G; Salek, Reza M; Steinbeck, Christoph; Neuhauser, Nadin; The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Molecular & Cellular Proteomics. 2014. Link
Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars; pyOpenMS: a Python‐based interface to the OpenMS mass‐spectrometry algorithm library. Proteomics. 2014
Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk WP; Staes, An; Vandenbussche, Jonathan; qcML: an exchange format for quality control metrics from mass spectrometry experiments. Molecular & Cellular Proteomics. 2014. Link

2013

Weisser, Hendrik; Nahnsen, Sven; Grossmann, Jonas; Nilse, Lars; Quandt, Andreas; Brauer, Hendrik; Sturm, Marc; Kenar, Erhan; Kohlbacher, Oliver; Aebersold, Ruedi; An automated pipeline for high-throughput label-free quantitative proteomics. Journal of proteome research. 2013
Walzer, Mathias; Qi, Da; Mayer, Gerhard; Uszkoreit, Julian; Eisenacher, Martin; Sachsenberg, Timo; Gonzalez-Galarza, Faviel F; Fan, Jun; Bessant, Conrad; Deutsch, Eric W; The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Molecular & Cellular Proteomics. 2013
Nahnsen, Sven; Bielow, Chris; Reinert, Knut; Kohlbacher, Oliver; Tools for label-free peptide quantification. Molecular & Cellular Proteomics. 2013

2012

Nahnsen, Sven; Kohlbacher, Oliver; In silico design of targeted SRM-based experiments. BMC bioinformatics. 2012. Link
Junker, Johannes; Bielow, Chris; Bertsch, Andreas; Sturm, Marc; Reinert, Knut; Kohlbacher, Oliver; TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data. Journal of proteome research. 2012. Link
Jones, Andrew R; Eisenacher, Martin; Mayer, Gerhard; Kohlbacher, Oliver; Siepen, Jennifer; Hubbard, Simon J; Selley, Julian N; Searle, Brian C; Shofstahl, James; Seymour, Sean L; The mzIdentML data standard for mass spectrometry-based proteomics results. Molecular & cellular proteomics. 2012

2011

Bielow, Chris; Aiche, Stephan; Andreotti, Sandro; Reinert, Knut; MSSimulator: Simulation of mass spectrometry data. Journal of proteome research. 2011. Link
Bertsch, Andreas; Gröpl, Clemens; Reinert, Knut; Kohlbacher, Oliver; OpenMS and TOPP: open source software for LC-MS data analysis. Data Mining in Proteomics: From Standards to Applications. 2011
Nahnsen, Sven; Bertsch, Andreas; Rahnenführer, Jörg; Nordheim, Alfred; Kohlbacher, Oliver; Probabilistic consensus scoring improves tandem mass spectrometry peptide identification. Journal of proteome research. 2011. Link

2010

Bertsch, Andreas; Jung, Stephan; Zerck, Alexandra; Pfeifer, Nico; Nahnsen, Sven; Henneges, Carsten; Nordheim, Alfred; Kohlbacher, Oliver; Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics. Journal of proteome research. 2010. Link
Gesing, Sandra; van Hemert, Jano; Koetsier, Jos; Bertsch, Andreas; 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

2009

Bertsch, Andreas; Leinenbach, Andreas; Pervukhin, Anton; Lubeck, Markus; Hartmer, Ralf; Baessmann, Carsten; Elnakady, Yasser Abbas; Müller, Rolf; Böcker, Sebastian; Huber, Christian G; De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation. Electrophoresis. 2009
Pfeifer, Nico; Leinenbach, Andreas; Huber, Christian G; Kohlbacher, Oliver; Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach. Journal of proteome research. 2009. Link
Reinert, Knut; Kohlbacher, Oliver; OpenMS and TOPP: open source software for LC-MS data analysis. Proteome Bioinformatics. 2009
Nilse, Lars; Sturm, Marc; Trudgian, David; Salek, Mogjiborahman; Sims, Paul FG; Carroll, Kathleen M; Hubbard, Simon J; SILACAnalyzer-a tool for differential quantitation of stable isotope derived data. International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics. 2009
Sturm, Marc; Kohlbacher, Oliver; TOPPView: an open-source viewer for mass spectrometry data. Journal of proteome research. 2009. Link

2008

Lange, Eva; Analysis of mass spectrometric data: peak picking and map alignment. Freie Universtaet Berlin. 2008
Schulz-Trieglaff, Ole; Hussong, Rene; Gröpl, Clemens; Leinenbach, Andreas; Hildebrandt, Andreas; Huber, Christian; Reinert, Knut; Computational quantification of peptides from LC-MS data. Journal of Computational Biology. 2008
Lange, Eva; Tautenhahn, Ralf; Neumann, Steffen; Gröpl, Clemens; Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements. BMC bioinformatics. 2008. Link
Schulz-Trieglaff, Ole; Pfeifer, Nico; Gröpl, Clemens; Kohlbacher, Oliver; Reinert, Knut; LC-MSsim–a simulation software for liquid chromatography mass spectrometry data. BMC bioinformatics. 2008. Link
Sturm, Marc; Bertsch, Andreas; Gröpl, Clemens; Hildebrandt, Andreas; Hussong, Rene; Lange, Eva; Pfeifer, Nico; Schulz-Trieglaff, Ole; Zerck, Alexandra; Reinert, Knut; OpenMS–an open-source software framework for mass spectrometry. BMC bioinformatics. 2008

2007

Schulz-Trieglaff, Ole; Hussong, Rene; Gröpl, Clemens; Hildebrandt, Andreas; 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
Lange, Eva; Gröpl, Clemens; Schulz-Trieglaff, Ole; Leinenbach, Andreas; Huber, Christian; Reinert, Knut; A geometric approach for the alignment of liquid chromatography—mass spectrometry data. Bioinformatics. 2007
Sturm, Marc; TOPP The OpenMS Proteomics Pipeline. Proceedings of the 5th European. 2007
Kohlbacher, Oliver; Reinert, Knut; Gröpl, Clemens; Lange, Eva; Pfeifer, Nico; Schulz-Trieglaff, Ole; Sturm, Marc; TOPP—the OpenMS proteomics pipeline. Bioinformatics. 2007. Link

2006

Lange, Eva; Gröpl, Clemens; Reinert, Knut; Kohlbacher, Oliver; Hildebrandt, Andreas; High-accuracy peak picking of proteomics data using wavelet techniques. Biocomputing 2006. 2006. Link

2005

Groepl, Clemens; Lange, Eva; Reinert, Knut; Kohlbacher, Oliver; Sturm, Marc; Huber, Christian G; Mayr, Bettina M; Klein, Christoph L; Absolute quantification of myoglobin content in blood serum using HPLC/MS through automatic bioinformatics analysis. MOLECULAR & CELLULAR PROTEOMICS. 2005
Gröpl, 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
Lange, E; Reinert, K; Groepl, C; Kohlbacher, O; Sturm, M; Hildebrandt, A; OPENMS; a generic open source framework for chromatography/MS-based proteomics. Molecular & Cellular Proteomics. 2005
Gröpl, C; Hildebrandt, A; Kohlbacher, O; Lange, E; Lövenich, S; Sturm, M; OpenMS-Software for Mass Spectrometry. Poster presented at the MBI Workshop on Computational Proteomics and Mass Spectrometry. 2005