List of OpenMS Publications

2025

  • Damiani T, Jarmusch AK, Aron AT, Petras D, Phelan VV, Zhao HN, Bittremieux W, Acharya DD, Ahmed MMA, Bauermeister A, Bertin MJ, Boudreau PD, Borges RM, Bowen BP, Brown CJ, Chagas FO, Clevenger KD, Correia MSP, Crandall WJ, Crüsemann M, Fahy E, Fiehn O, Garg N, Gerwick WH, Gilbert JR, Globisch D, Gomes PWP, Heuckeroth S, James CA, Jarmusch SA, Kakhkhorov SA, Kang KB, Kessler N, Kersten RD, Kim H, Kirk RD, Kohlbacher O, Kontou EE, Liu K, Lizama-Chamu I, Luu GT, Luzzatto Knaan T, Mannochio-Russo H, Marty MT, Matsuzawa Y, McAvoy AC, McCall LI, Mohamed OG, Nahor O, Neuweger H, Niedermeyer THJ, Nishida K, Northen TR, Overdahl KE, Rainer J, Reher R, Rodriguez E, Sachsenberg TT, Sanchez LM, Schmid R, Stevens C, Subramaniam S, Tian Z, Tripathi A, Tsugawa H, van der Hooft JJJ, Vicini A, Walter A, Weber T, Xiong Q, Xu T, Pluskal T, Dorrestein PC, Wang M A universal language for finding mass spectrometry data patterns. Nature methods. 2025 Link

  • Zheng P, Audain E, Webel H, Dai C, Klein J, Hitz MP, Sachsenberg T, Bai M, Perez-Riverol Y Ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata. Journal of proteomics. 2025 Link

  • Scheid J, Lemke S, Hoenisch-Gravel N, Dengler A, Sachsenberg T, Declerq A, Gabriels R, Bauer J, Wacker M, Bichmann L, Martens L, Dubbelaar ML, Nahnsen S, Walz JS MHCquant2 refines immunopeptidomics tumor antigen discovery. Genome biology. 2025 Link

  • Perez-Riverol Y, Bittremieux W, Noble WS, Martens L, Bilbao A, Lazear MR, Grüning B, Katz DS, MacCoss MJ, Dai C, Eng JK, Bouwmeester R, Shortreed MR, Audain E, Sachsenberg T, Van Goey J, Wallmann G, Wen B, Käll L, Fondrie WE Open-Source and FAIR Research Software for Proteomics. Journal of proteome research. 2025 Link

  • Müller TD, Siraj A, Walter A, Kim J, Wein S, von Kleist J, Feroz A, Pilz M, Jeong K, Sing JC, Charkow J, Röst HL, Sachsenberg T OpenMS WebApps: Building User-Friendly Solutions for MS Analysis. Journal of proteome research. 2025 Link

  • Sachsenberg T, Pino LK, Brunet M, Bludau I, Kohlbacher O, Vizcaino JA, Bittremieux W Perspectives in computational mass spectrometry: recent developments and key challenges. Bioinformatics advances. 2025 Link

  • Van Den Bossche T, Alexandrov T, Bilbao A, Bittremieux W, Brigante FI, Chambers MC, Charkow J, Deutsch E, Dowsey AW, El Abiead Y, Gabriels R, Hecht H, Heuckeroth S, Klein JA, Knierman M, Martens L, Moritz RL, McCall LI, Neumann S, Perez-Riverol Y, Röst HL, Price EJ, Shofstahl J, Tabb DL, Uszkoreit J, Vizcaíno JA, Wang M, Willems S, Winkelhardt D, Kohlbacher O, Wein SP mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format. Journal of proteome research. 2025 Link

  • Sing JC, Charkow J, Walter A, Gao M, Müller TD, Bittremieux W, Sachsenberg T, Röst HL pyOpenMS-viz: Streamlining Mass Spectrometry Data Visualization with pandas. Journal of proteome research. 2025 Link

2024

  • Kim J, Jeong K, Kaulich PT, Winkels K, Tholey A, Kohlbacher O FLASHQuant: A Fast Algorithm for Proteoform Quantification in Top-Down Proteomics. Analytical chemistry. 2024 Link

  • Siraj A, Bouwmeester R, Declercq A, Welp L, Chernev A, Wulf A, Urlaub H, Martens L, Degroeve S, Kohlbacher O, Sachsenberg T Intensity and retention time prediction improves the rescoring of protein-nucleic acid cross-links. Proteomics. 2024 Link

  • Pfeuffer J, Bielow C, Wein S, Jeong K, Netz E, Walter A, Alka O, Nilse L, Colaianni PD, McCloskey D, Kim J, Rosenberger G, Bichmann L, Walzer M, Veit J, Boudaud B, Bernt M, Patikas N, Pilz M, Startek MP, Kutuzova S, Heumos L, Charkow J, Sing JC, Feroz A, Siraj A, Weisser H, Dijkstra TMH, Perez-Riverol Y, Röst H, Kohlbacher O, Sachsenberg T OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nature methods. 2024 Link

  • Jeong K, Kaulich PT, Jung W, Kim J, Tholey A, Kohlbacher O Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top-down proteomics. Proteomics. 2024 Link

  • Dai C, Pfeuffer J, Wang H, Zheng P, Käll L, Sachsenberg T, Demichev V, Bai M, Kohlbacher O, Perez-Riverol Y quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data. Nature methods. 2024 Link

2023

  • Kontou EE, Walter A, Alka O, Pfeuffer J, Sachsenberg T, Mohite OS, Nuhamunada M, Kohlbacher O, Weber T UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis. Journal of cheminformatics. 2023 Link

  • Bittremieux W, Levitsky L, Pilz M, Sachsenberg T, Huber F, Wang M, Dorrestein PC Unified and Standardized Mass Spectrometry Data Processing in Python Using spectrum_utils. Journal of proteome research. 2023 Link

2022

  • Luo X, Bittremieux W, Griss J, Deutsch EW, Sachsenberg T, Levitsky LI, Ivanov MV, Bubis JA, Gabriels R, Webel H, Sanchez A, Bai M, Käll L, Perez-Riverol Y A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics. Journal of proteome research. 2022 Link

  • Jeong K, Babović M, Gorshkov V, Kim J, Jensen ON, Kohlbacher O FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts. Nature communications. 2022 Link

  • Umer HM, Audain E, Zhu Y, Pfeuffer J, Sachsenberg T, Lehtiö J, Branca RM, Perez-Riverol Y Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides. Bioinformatics (Oxford, England). 2022 Link

  • Jeong K, Kim J, Kohlbacher O Mass Deconvolution of Top-Down Mass Spectrometry Datasets by FLASHDeconv. Methods in molecular biology (Clifton, N.J.). 2022 Link

2021

  • Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y A proteomics sample metadata representation for multiomics integration and big data analysis. Nature communications. 2021 Link

  • Bichmann L, Gupta S, Rosenberger G, Kuchenbecker L, Sachsenberg T, Ewels P, Alka O, Pfeuffer J, Kohlbacher O, Röst H DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics. Journal of proteome research. 2021 Link

  • Marcu A, Bichmann L, Kuchenbecker L, Kowalewski DJ, Freudenmann LK, Backert L, Mühlenbruch L, Szolek A, Lübke M, Wagner P, Engler T, Matovina S, Wang J, Hauri-Hohl M, Martin R, Kapolou K, Walz JS, Velz J, Moch H, Regli L, Silginer M, Weller M, Löffler MW, Erhard F, Schlosser A, Kohlbacher O, Stevanović S, Rammensee HG, Neidert MC HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy. Journal for immunotherapy of cancer. 2021 Link

2020

  • Wein S, Andrews B, Sachsenberg T, Santos-Rosa H, Kohlbacher O, Kouzarides T, Garcia BA, Weisser H A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry. Nature communications. 2020 Link

  • Stützer A, Welp LM, Raabe M, Sachsenberg T, Kappert C, Wulf A, Lau AM, David SS, Chernev A, Kramer K, Politis A, Kohlbacher O, Fischle W, Urlaub H Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nature communications. 2020 Link

  • Pfeuffer J, Sachsenberg T, Dijkstra TMH, Serang O, Reinert K, Kohlbacher O EPIFANY: A Method for Efficient High-Confidence Protein Inference. Journal of proteome research. 2020 Link

  • Jeong K, Kim J, Gaikwad M, Hidayah SN, Heikaus L, Schlüter H, Kohlbacher O FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics. Cell systems. 2020 Link

  • Nothias LF, Petras D, Schmid R, Dührkop K, Rainer J, Sarvepalli A, Protsyuk I, Ernst M, Tsugawa H, Fleischauer M, Aicheler F, Aksenov AA, Alka O, Allard PM, Barsch A, Cachet X, Caraballo-Rodriguez AM, Da Silva RR, Dang T, Garg N, Gauglitz JM, Gurevich A, Isaac G, Jarmusch AK, Kameník Z, Kang KB, Kessler N, Koester I, Korf A, Le Gouellec A, Ludwig M, Martin H C, McCall LI, McSayles J, Meyer SW, Mohimani H, Morsy M, Moyne O, Neumann S, Neuweger H, Nguyen NH, Nothias-Esposito M, Paolini J, Phelan VV, Pluskal T, Quinn RA, Rogers S, Shrestha B, Tripathi A, van der Hooft JJJ, Vargas F, Weldon KC, Witting M, Yang H, Zhang Z, Zubeil F, Kohlbacher O, Böcker S, Alexandrov T, Bandeira N, Wang M, Dorrestein PC Feature-based molecular networking in the GNPS analysis environment. Nature methods. 2020 Link

  • Rurik M, Alka O, Aicheler F, Kohlbacher O Metabolomics Data Processing Using OpenMS. Methods in molecular biology (Clifton, N.J.). 2020 Link

  • Netz E, Dijkstra TMH, Sachsenberg T, Zimmermann L, Walzer M, Monecke T, Ficner R, Dybkov O, Urlaub H, Kohlbacher O OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS. Molecular & cellular proteomics : MCP. 2020 Link

  • Scheidt T, Alka O, Gonczarowska-Jorge H, Gruber W, Rathje F, Dell’Aica M, Rurik M, Kohlbacher O, Zahedi RP, Aberger F, Huber CG Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells. Cell communication and signaling : CCS. 2020 Link

  • Kutuzova S, Colaianni P, Röst H, Sachsenberg T, Alka O, Kohlbacher O, Burla B, Torta F, Schrübbers L, Kristensen M, Nielsen L, Herrgård MJ, McCloskey D SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing. Analytical chemistry. 2020 Link

  • Hulstaert N, Shofstahl J, Sachsenberg T, Walzer M, Barsnes H, Martens L, Perez-Riverol Y ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion. Journal of proteome research. 2020 Link

  • Starke R, Oliphant K, Jehmlich N, Schäpe SS, Sachsenberg T, Kohlbacher O, Allen-Vercoe E, von Bergen M Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. Journal of proteomics. 2020 Link

2019

  • Cain N, Alka O, Segelke T, von Wuthenau K, Kohlbacher O, Fischer M 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 L, Nelde A, Ghosh M, Heumos L, Mohr C, Peltzer A, Kuchenbecker L, Sachsenberg T, Walz JS, Stevanović S, Rammensee HG, Kohlbacher O MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics. Journal of proteome research. 2019 Link

  • Löffler MW, Mohr C, Bichmann L, Freudenmann LK, Walzer M, Schroeder CM, Trautwein N, Hilke FJ, Zinser RS, Mühlenbruch L, Kowalewski DJ, Schuster H, Sturm M, Matthes J, Riess O, Czemmel S, Nahnsen S, Königsrainer I, Thiel K, Nadalin S, Beckert S, Bösmüller H, Fend F, Velic A, Maček B, Haen SP, Buonaguro L, Kohlbacher O, Stevanović S, Königsrainer A, Rammensee HG Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma. Genome medicine. 2019 Link

  • Licha D, Vidali S, Aminzadeh-Gohari S, Alka O, Breitkreuz L, Kohlbacher O, Reischl RJ, Feichtinger RG, Kofler B, Huber CG Untargeted Metabolomics Reveals Molecular Effects of Ketogenic Diet on Healthy and Tumor Xenograft Mouse Models. International journal of molecular sciences. 2019 Link

  • Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y, Vizcaíno JA, Salek RM, Neumann S, Jones AR mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics. Analytical chemistry. 2019 Link

2018

  • Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, Rätsch G Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer cell. 2018 Link

  • Gruening B, Sallou O, Moreno P, da Veiga Leprevost F, Ménager H, Søndergaard D, Röst H, Sachsenberg T, O’Connor B, Madeira F, Dominguez Del Angel V, Crusoe MR, Varma S, Blankenberg D, Jimenez RC, Perez-Riverol Y Recommendations for the packaging and containerizing of bioinformatics software. F1000Research. 2018 Link

2017

  • Röst HL, Aebersold R, Schubert OT Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms. Methods in molecular biology (Clifton, N.J.). 2017 Link

  • da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England). 2017 Link

  • Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. Journal of proteomics. 2017 Link

  • Pfeuffer J, Sachsenberg T, Alka O, Walzer M, Fillbrunn A, Nilse L, Schilling O, Reinert K, Kohlbacher O OpenMS - A platform for reproducible analysis of mass spectrometry data. Journal of biotechnology. 2017 Link

  • Weisser H, Choudhary JS Targeted Feature Detection for Data-Dependent Shotgun Proteomics. Journal of proteome research. 2017 Link

  • Vizcaíno JA, Mayer G, Perkins S, Barsnes H, Vaudel M, Perez-Riverol Y, Ternent T, Uszkoreit J, Eisenacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Jones AR The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics. Molecular & cellular proteomics : MCP. 2017 Link

2016

  • Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S A multicenter study benchmarks software tools for label-free proteome quantification. Nature biotechnology. 2016 Link

  • Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS Flexible Data Analysis Pipeline for High-Confidence Proteogenomics. Journal of proteome research. 2016 Link

  • Veit J, Sachsenberg T, Chernev A, Aicheler F, Urlaub H, Kohlbacher O LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer. Journal of proteome research. 2016 Link

  • Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature methods. 2016 Link

2015

  • Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RH, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry. Methods (San Diego, Calif.). 2015 Link

  • Röst HL, Rosenberger G, Aebersold R, Malmström L Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Bioinformatics (Oxford, England). 2015 Link

  • Röst HL, Schmitt U, Aebersold R, Malmström L Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry. PloS one. 2015 Link

  • Sachsenberg T, Herbst FA, Taubert M, Kermer R, Jehmlich N, von Bergen M, Seifert J, Kohlbacher O MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics. Journal of proteome research. 2015 Link

  • Ranninger C, Rurik M, Limonciel A, Ruzek S, Reischl R, Wilmes A, Jennings P, Hewitt P, Dekant W, Kohlbacher O, Huber CG Nephron Toxicity Profiling via Untargeted Metabolome Analysis Employing a High Performance Liquid Chromatography-Mass Spectrometry-based Experimental and Computational Pipeline. The Journal of biological chemistry. 2015 Link

  • Aicheler F, Li J, Hoene M, Lehmann R, Xu G, Kohlbacher O Retention Time Prediction Improves Identification in Nontargeted Lipidomics Approaches. Analytical chemistry. 2015 Link

  • Nilse L, Sigloch FC, Biniossek ML, Schilling O Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling. Proteomics. Clinical applications. 2015 Link

  • Aiche S, Sachsenberg T, Kenar E, Walzer M, Wiswedel B, Kristl T, Boyles M, Duschl A, Huber CG, Berthold MR, Reinert K, Kohlbacher O Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry. Proteomics. 2015 Link

2014

  • Kenar E, Franken H, Forcisi S, Wörmann K, Häring HU, Lehmann R, Schmitt-Kopplin P, Zell A, Kohlbacher O Automated label-free quantification of metabolites from liquid chromatography-mass spectrometry data. Molecular & cellular proteomics : MCP. 2014 Link

  • Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nature biotechnology. 2014 Link

  • Kramer K, Sachsenberg T, Beckmann BM, Qamar S, Boon KL, Hentze MW, Kohlbacher O, Urlaub H Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins. Nature methods. 2014 Link

  • Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Molecular & cellular proteomics : MCP. 2014 Link

  • Röst HL, Schmitt U, Aebersold R, Malmström L pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics. 2014 Link

  • Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L qcML: an exchange format for quality control metrics from mass spectrometry experiments. Molecular & cellular proteomics : MCP. 2014 Link

2013

  • Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, Malmström L An automated pipeline for high-throughput label-free quantitative proteomics. Journal of proteome research. 2013 Link

  • Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, Jones AR The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Molecular & cellular proteomics : MCP. 2013 Link

  • Nahnsen S, Bielow C, Reinert K, Kohlbacher O Tools for label-free peptide quantification. Molecular & cellular proteomics : MCP. 2013 Link

2012

  • Nahnsen S, Kohlbacher O In silico design of targeted SRM-based experiments. BMC bioinformatics. 2012 Link

  • Junker J, Bielow C, Bertsch A, Sturm M, Reinert K, Kohlbacher O TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data. Journal of proteome research. 2012 Link

  • Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D The mzIdentML data standard for mass spectrometry-based proteomics results. Molecular & cellular proteomics : MCP. 2012 Link

2011

  • Bielow C, Aiche S, Andreotti S, Reinert K MSSimulator: Simulation of mass spectrometry data. Journal of proteome research. 2011 Link

  • Nahnsen S, Bertsch A, Rahnenführer J, Nordheim A, Kohlbacher O Probabilistic consensus scoring improves tandem mass spectrometry peptide identification. Journal of proteome research. 2011 Link

2010

  • Reinert K, Kohlbacher O OpenMS and TOPP: open source software for LC-MS data analysis. Methods in molecular biology (Clifton, N.J.). 2010 Link

  • Bertsch A, Jung S, Zerck A, Pfeifer N, Nahnsen S, Henneges C, Nordheim A, Kohlbacher O Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics. Journal of proteome research. 2010 Link

2009

  • Bertsch A, Leinenbach A, Pervukhin A, Lubeck M, Hartmer R, Baessmann C, Elnakady YA, Müller R, Böcker S, Huber CG, Kohlbacher O De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation. Electrophoresis. 2009 Link

  • Pfeifer N, Leinenbach A, Huber CG, Kohlbacher O Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach. Journal of proteome research. 2009 Link

  • Sturm M, Kohlbacher O TOPPView: an open-source viewer for mass spectrometry data. Journal of proteome research. 2009 Link

2008

  • Schulz-Trieglaff O, Hussong R, Gröpl C, Leinenbach A, Hildebrandt A, Huber C, Reinert K Computational quantification of peptides from LC-MS data. Journal of computational biology : a journal of computational molecular cell biology. 2008 Link

  • Lange E, Tautenhahn R, Neumann S, Gröpl C Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements. BMC bioinformatics. 2008 Link

  • Schulz-Trieglaff O, Pfeifer N, Gröpl C, Kohlbacher O, Reinert K LC-MSsim–a simulation software for liquid chromatography mass spectrometry data. BMC bioinformatics. 2008 Link

  • Sturm M, Bertsch A, Gröpl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O OpenMS - an open-source software framework for mass spectrometry. BMC bioinformatics. 2008 Link

2007

  • Lange E, Gröpl C, Schulz-Trieglaff O, Leinenbach A, Huber C, Reinert K A geometric approach for the alignment of liquid chromatography-mass spectrometry data. Bioinformatics (Oxford, England). 2007 Link

  • Kohlbacher O, Reinert K, Gröpl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M TOPP–the OpenMS proteomics pipeline. Bioinformatics (Oxford, England). 2007 Link

2006

  • Mayr BM, Kohlbacher O, Reinert K, Sturm M, Gröpl C, Lange E, Klein C, Huber CG Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms. Journal of proteome research. 2006 Link

  • Lange E, Gröpl C, Reinert K, Kohlbacher O, Hildebrandt A High-accuracy peak picking of proteomics data using wavelet techniques. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2006 Link