Publications

LC-MS Data Processing Using OpenMS

Methods in molecular biology (Clifton, N.J.)2026

Walter, Axel; Kontou, Eftychia E; Emami, Payam; Kohlbacher, Oliver

pmultiqc: An Open-Source, Lightweight, and Metadata-Oriented QC Reporting Library for MS Proteomics

Molecular & cellular proteomics : MCP2026

Yue, Qi-Xuan; Dai, Chengxin; Kamatchinathan, Selvakumar; Bandla, Chakradhar; Webel, Henry; Larrea, Asier; Bittremieux, Wout; Uszkoreit, Julian; Müller, Tom David; Xiao, Jinqiu; Cox, Juergen; Yu, Fengchao; Ewels, Philip; Demichev, Vadim; Kohlbacher, Oliver; Sachsenberg, Timo; Bielow, Chris; Bai, Mingze; Perez-Riverol, Yasset

Proteomics Using Draft Genomes: A Case Study in Spotted Hyena

Journal of proteome research2026

Tabb, David L; Swartz, Aidan; Higgitt, Roxanne L; Bell, Liam; Guryev, Victor; Miller, Michele A

Harmonized nucleoside mass spectrometry enables reproducible cross-platform RNA modification quantification

bioRxiv : the preprint server for biology2026

Dalwigk, Jan Felix; Kerkhoff, Kira; Knittelfelder, Oskar; Ross, Robert L; Petrella, Maria Cristina; Kuśnierczyk, Anna; Bhandari, Tulsi; Attina, Aurore; Burkard, Alicia; Brás-Costa, Carolina; DeMott, Michael S; Johnson, Kitty; Kerkhoff-Bernaciak, Xenia; Kist, Jennifer; Kögel, Ken; Krämer, Martina; Moreno-Ballesteros, Ricardo; Podoprygorina, Ganna; Simcox, Kaley; Simsir, Özge; Skriba, Anton; Wein, Sam; Cahova, Hana; Garcia, Benjamin A; Helm, Mark; David, Alexandre; Höfer, Katharina; Leidel, Sebastian; Limbach, Patrick A; Novoa, Eva; Sabidó, Eduard; Schneider, Sabine; Wolff, Philippe; Dedon, Peter; Cheung, Vivian; Kaiser, Stefanie

onsite: An Integrated Framework for Phosphosite Localization and False Localization Rate Estimation

Journal of proteome research2026

Yue, Qi-Xuan; Wei, Zhongchun; Dai, Chengxin; Bai, Mingze; Perez-Riverol, Yasset; Sachsenberg, Timo

Human 28S rRNA analysed by state-of-the-art oligonucleotide mass spectrometry: benchmarking current capabilities and a call to action for MS-Seq

bioRxiv : the preprint server for biology2026

Schicktanz, Jannick; Qi, Yuyang; Wu, Junzhou; Hamal, Bibek; Lechner, Antony; Wein, Sam; Knittelfelder, Oskar; Yesiltac-Tosun, Nur; Dalwigk, Felix; Hoja, Katharina; Rusling, Leona; Obersteiner, Sofia; Bellenberg, Ella; Kerkhoff, Kira; DeMott, Michael S; Ross, Robert; Wolff, Philippe; Breuker, Kathrin; Limbach, Patrick A; Dedon, Peter; Kaiser, Stefanie

OpenMS WebApps: Building User-Friendly Solutions for MS Analysis

Journal of Proteome Research2025

Müller, Tom David; Siraj, Arslan; Walter, Axel; Kim, Jihyung; Wein, Samuel; von Kleist, Johannes; Feroz, Ayesha; Pilz, Matteo; Jeong, Kyowon; Sing, Justin Cyril; Charkow, Joshua; Röst, Hannes Luc; Sachsenberg, Timo

pyOpenMS-viz: Streamlining Mass Spectrometry Data Visualization with pandas

Journal of Proteome Research2025

Sing, Justin Cyril; Charkow, Joshua; Walter, Axel; Gao, Mingxuan; Muller, Tom David; Bittremieux, Wout; Sachsenberg, Timo; Röst, Hannes Luc

A universal language for finding mass spectrometry data patterns

Nature methods2025

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

Ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata

Journal of proteomics2025

Zheng P, Audain E, Webel H, Dai C, Klein J, Hitz MP, Sachsenberg T, Bai M, Perez-Riverol Y

MHCquant2 refines immunopeptidomics tumor antigen discovery

Genome biology2025

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

Open-Source and FAIR Research Software for Proteomics

Journal of proteome research2025

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

Perspectives in computational mass spectrometry: recent developments and key challenges

Bioinformatics advances2025

Sachsenberg T, Pino LK, Brunet M, Bludau I, Kohlbacher O, Vizcaino JA, Bittremieux W

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format

Journal of proteome research2025

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

FLASHQuant: a fast algorithm for proteoform quantification in top-down proteomics

Analytical Chemistry2024

Kim, Jihyung; Jeong, Kyowon; Kaulich, Philipp T; Winkels, Konrad; Tholey, Andreas; Kohlbacher, Oliver

Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links

Proteomics2024

Siraj, Arslan; Bouwmeester, Robbin; Declercq, Arthur; Welp, Luisa; Chernev, Aleksandar; Wulf, Alexander; Urlaub, Henning; Martens, Lennart; Degroeve, Sven; Kohlbacher, Oliver

quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data

Nature Methods2024

Dai, Chengxin; Pfeuffer, Julianus; Wang, Hong; Zheng, Ping; Käll, Lukas; Sachsenberg, Timo; Demichev, Vadim; Bai, Mingze; Kohlbacher, Oliver; Perez-Riverol, Yasset

OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data

Nature methods2024

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

Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top-down proteomics

Proteomics2024

Jeong K, Kaulich PT, Jung W, Kim J, Tholey A, Kohlbacher O

UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis

Journal of Cheminformatics2023

Kontou, Eftychia E; Walter, Axel; Alka, Oliver; Pfeuffer, Julianus; Sachsenberg, Timo; Mohite, Omkar S; Nuhamunada, Matin; Kohlbacher, Oliver; Weber, Tilmann

Unified and standardized mass spectrometry data processing in Python using spectrum_utils

Journal of proteome research2023

Bittremieux, Wout; Levitsky, Lev; Pilz, Matteo; Sachsenberg, Timo; Huber, Florian; Wang, Mingxun; Dorrestein, Pieter C

A comprehensive evaluation of consensus spectrum generation methods in proteomics

Journal of proteome research2022

Luo, Xiyang; Bittremieux, Wout; Griss, Johannes; Deutsch, Eric W; Sachsenberg, Timo; Levitsky, Lev I; Ivanov, Mark V; Bubis, Julia A; Gabriels, Ralf; Webel, Henry

FLASHIda enables intelligent data acquisition for top–down proteomics to boost proteoform identification counts

Nature communications2022

Jeong, Kyowon; Babović, Maša; Gorshkov, Vladimir; Kim, Jihyung; Jensen, Ole N; Kohlbacher, Oliver

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides

Bioinformatics2022

Umer, Husen M; Audain, Enrique; Zhu, Yafeng; Pfeuffer, Julianus; Sachsenberg, Timo; Lehtiö, Janne; Branca, Rui M; Perez-Riverol, Yasset

Mass Deconvolution of Top-Down Mass Spectrometry Datasets by FLASHDeconv

Proteoform Identification: Methods and Protocols2022

Jeong, Kyowon; Kim, Jihyung; Kohlbacher, Oliver

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

Nature Communications2021

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 research2021

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 cancer2021

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 communications2020

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 communications2020

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 Systems2020

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 methods2020

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 Metabolomics2020

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 Proteomics2020

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 Signaling2020

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 Chemistry2020

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 Proteomics2020

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

EPIFANY-A method for efficient high-confidence protein inference

Journal of proteome research2019

Pfeuffer, Julianus; Sachsenberg, Timo; Dijkstra, Tjeerd MH; Serang, Oliver; Reinert, Knut; Kohlbacher, Oliver

Food fingerprinting: Mass spectrometric determination of the cocoa shell content (Theobroma cacao L.) in cocoa products by HPLC-QTOF-MS

Food chemistry2019

Cain, Nicolas; Alka, Oliver; Segelke, Torben; von Wuthenau, Kristian; Kohlbacher, Oliver; Fischer, Markus

MHCquant: automated and reproducible data analysis for immunopeptidomics

Journal of proteome research2019

Bichmann, Leon; Nelde, Annika; Ghosh, Michael; Heumos, Lukas; Mohr, Christopher; Peltzer, Alexander; Kuchenbecker, Leon; Sachsenberg, Timo; Walz, Juliane S; Stevanovic, Stefan

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

Genome medicine2019

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

Recommendations for the packaging and containerizing of bioinformatics software

F1000Research2019

Gruening, Bjorn; Sallou, Olivier; Moreno, Pablo; da Veiga Leprevost, Felipe; Ménager, Hervé; Søndergaard, Dan; Röst, Hannes; Sachsenberg, Timo; O'connor, Brian; Madeira, Fábio

ThermoRawFileParser: modular, scalable, and cross-platform RAW file conversion

Journal of proteome research2019

Hulstaert, Niels; Shofstahl, Jim; Sachsenberg, Timo; Walzer, Mathias; Barsnes, Harald; Martens, Lennart; Perez-Riverol, Yasset

Untargeted metabolomics reveals molecular effects of ketogenic diet on healthy and tumor xenograft mouse models

International journal of molecular sciences2019

Licha, David; Vidali, Silvia; Aminzadeh-Gohari, Sepideh; Alka, Oliver; Breitkreuz, Leander; Kohlbacher, Oliver; Reischl, Roland J; Feichtinger, René G; Kofler, Barbara; Huber, Christian G

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics

Analytical chemistry2019

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

Comprehensive analysis of alternative splicing across tumors from 8,705 patients

Cancer cell2018

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

Automated SWATH data analysis using targeted extraction of ion chromatograms

Proteomics: Methods and Protocols2017

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

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

Bioinformatics2017

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 proteomics2017

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 biotechnology2017

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 research2017

Weisser, Hendrik; Choudhary, Jyoti S

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

Molecular & Cellular Proteomics2017

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

A multicenter study benchmarks software tools for label-free proteome quantification

Nature biotechnology2016

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

Flexible data analysis pipeline for high-confidence proteogenomics

Journal of Proteome Research2016

Weisser, Hendrik; Wright, James C; Mudge, Jonathan M; Gutenbrunner, Petra; Choudhary, Jyoti S

LFQProfiler and RNPxl: open-source tools for label-free quantification and protein–RNA cross-linking integrated into proteome discoverer

Journal of proteome research2016

Veit, Johannes; Sachsenberg, Timo; Chernev, Aleksandar; Aicheler, Fabian; Urlaub, Henning; Kohlbacher, Oliver

OpenMS: a flexible open-source software platform for mass spectrometry data analysis

Nature methods2016

Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan

Ten simple rules for taking advantage of Git and GitHub

PLoS computational biology2016

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

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR

Bioinformatics2015

Röst, Hannes L; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars

Fast and efficient XML data access for next-generation mass spectrometry

PloS one2015

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

Journal of proteome research2015

Sachsenberg, Timo; Herbst, Florian-Alexander; Taubert, Martin; Kermer, Rene; Jehmlich, Nico; Von Bergen, Martin; Seifert, Jana; 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 Chemistry2015

Ranninger, Christina; Rurik, Marc; Limonciel, Alice; Ruzek, Silke; Reischl, Roland; Wilmes, Anja; Jennings, Paul; Hewitt, Philip; Dekant, Wolfgang; Kohlbacher, Oliver

Retention time prediction improves identification in nontargeted lipidomics approaches

Analytical chemistry2015

Aicheler, Fabian; Li, Jia; Hoene, Miriam; Lehmann, Rainer; Xu, Guowang; Kohlbacher, Oliver

Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling

PROTEOMICS–Clinical Applications2015

Nilse, Lars; Sigloch, Florian Christoph; Biniossek, Martin L; Schilling, Oliver

Workflows for automated downstream data analysis and visualization in large‐scale computational mass spectrometry

Proteomics2015

Aiche, Stephan; Sachsenberg, Timo; Kenar, Erhan; Walzer, Mathias; Wiswedel, Bernd; Kristl, Theresa; Boyles, Matthew; Duschl, Albert; Huber, Christian G; Berthold, Michael R

Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry

Methods (San Diego, Calif.)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

Automated label-free quantification of metabolites from liquid chromatography–mass spectrometry data

Molecular & Cellular Proteomics2014

Kenar, Erhan; Franken, Holger; Forcisi, Sara; Wörmann, Kilian; Häring, Hans-Ulrich; Lehmann, Rainer; Schmitt-Kopplin, Philippe; Zell, Andreas; Kohlbacher, Oliver

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

Nature biotechnology2014

Röst, Hannes L; Rosenberger, George; Navarro, Pedro; Gillet, Ludovic; Miladinović, Saša M; Schubert, Olga T; Wolski, Witold; Collins, Ben C; Malmström, Johan; Malmström, Lars

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

Nature methods2014

Kramer, Katharina; Sachsenberg, Timo; Beckmann, Benedikt M; Qamar, Saadia; Boon, Kum-Loong; Hentze, Matthias W; Kohlbacher, Oliver; Urlaub, Henning

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

Molecular & Cellular Proteomics2014

Griss, Johannes; Jones, Andrew R; Sachsenberg, Timo; Walzer, Mathias; Gatto, Laurent; Hartler, Jürgen; Thallinger, Gerhard G; Salek, Reza M; Steinbeck, Christoph; Neuhauser, Nadin

qcML: an exchange format for quality control metrics from mass spectrometry experiments

Molecular & Cellular Proteomics2014

Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk WP; Staes, An; Vandenbussche, Jonathan

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library

Proteomics2014

Röst HL, Schmitt U, Aebersold R, Malmström L

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

Journal of proteome research2013

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 Proteomics2013

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 Proteomics2013

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

In silico design of targeted SRM-based experiments

BMC bioinformatics2012

Nahnsen, Sven; Kohlbacher, Oliver

TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data

Journal of proteome research2012

Junker, Johannes; Bielow, Chris; Bertsch, Andreas; Sturm, Marc; Reinert, Knut; Kohlbacher, Oliver

The mzIdentML data standard for mass spectrometry-based proteomics results

Molecular & cellular proteomics2012

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

MSSimulator: Simulation of mass spectrometry data

Journal of proteome research2011

Bielow, Chris; Aiche, Stephan; Andreotti, Sandro; Reinert, Knut

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

Data Mining in Proteomics: From Standards to Applications2011

Bertsch, Andreas; Gröpl, Clemens; Reinert, Knut; Kohlbacher, Oliver

Probabilistic consensus scoring improves tandem mass spectrometry peptide identification

Journal of proteome research2011

Nahnsen, Sven; Bertsch, Andreas; Rahnenführer, Jörg; Nordheim, Alfred; Kohlbacher, Oliver

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

Journal of proteome research2010

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 Computing2010

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

Electrophoresis2009

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 research2009

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

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

Proteome Bioinformatics2009

Reinert, Knut; Kohlbacher, Oliver

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

International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics2009

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 research2009

Sturm, Marc; Kohlbacher, Oliver

Analysis of mass spectrometric data: peak picking and map alignment

Freie Universtaet Berlin2008

Lange, Eva

Computational quantification of peptides from LC-MS data

Journal of Computational Biology2008

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 bioinformatics2008

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

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

BMC bioinformatics2008

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

OpenMS–an open-source software framework for mass spectrometry

BMC bioinformatics2008

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 112007

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

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

Bioinformatics2007

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

TOPP The OpenMS Proteomics Pipeline

Proceedings of the 5th European2007

Sturm, Marc

TOPP—the OpenMS proteomics pipeline

Bioinformatics2007

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

High-accuracy peak picking of proteomics data using wavelet techniques

Biocomputing 20062006

Lange, Eva; Gröpl, Clemens; Reinert, Knut; Kohlbacher, Oliver; Hildebrandt, Andreas

Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms

Journal of proteome research2006

Mayr BM, Kohlbacher O, Reinert K, Sturm M, Gröpl C, Lange E, Klein C, Huber CG

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

MOLECULAR & CELLULAR PROTEOMICS2005

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 12005

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 Proteomics2005

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 Spectrometry2005

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