George Rosenberger

Computational Systems Biologist

George is a Computational Systems Biologist at Bruker Switzerland AG, Fällanden, Switzerland. His research interests focus on method development in computational proteomics and elucidation of cancer-associated molecular interactions. He conducted his PhD studies in the laboratory of Dr. Ruedi Aebersold at ETH Zurich, Zurich, Switzerland and his postdoctoral research in the group of Dr. Andrea Califano at Columbia University, New York, NY, USA. Prior to joing Bruker, he worked as Senior Scientist at sciCORE, University of Basel, Basel, Switzerland and Senior Scientist, Proteogenomics, at ProFound Therapeutics Inc., Cambridge, MA, USA.


VESPA: Virtual Enrichment-based Signaling Protein Analysis

VESPA reconstructs signaling networks de novo and infers kinase/phosphatase activities based on phosphoproteomic profiles.

SECAT: Size-Exclusion Chromatography Algorithmic Toolkit

SECAT quantifies differential protein-protein interaction states by network-centric analysis of SEC-SWATH-MS profiles.

IPF: Inference of PeptidoForms

IPF integrates MS1 precursor-, MS2 peak group- and transition-level data to mediate peptidoform-specific analysis of DIA datasets.


OpenSWATH is a workflow implemented in the OpenMS C++ framework for mass spectrometric data that applies targeted data extraction to DIA datasets.


PyProphet is an implementation and extension of the popular mProphet semi-supervised learning algorithm.


aLFQ is an R-package (available from CRAN) for label-free estimation of absolute abundances of proteins in LC-MS/MS-based proteomics experiments.


EasyPQP is a library generation workflow, integrating DIA-Umpire, MSFragger, TPP and OpenSWATH.

The Human SWATHAtlas

The Human SWATHAtlas is a repository of assays to quantify 10,000 human proteins by SWATH-MS.


Selected publications

  • Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis.
    Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A.
    Nat Commun. 2024 May 9;15(1):3909. doi: 10.1038/s41467-024-47957-3.
    PMID: 38724493
  • SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles.
    Rosenberger G, Heusel M, Bludau I, Collins BC, Martelli C, Williams EG, Xue P, Liu Y, Aebersold R, Califano A.
    Cell Syst. 2020 Dec 16;11(6):589-607.e8. doi: 10.1016/j.cels.2020.11.006.
    PMID: 33333029
  • Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses.
    Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R.
    Nat Methods. 2017 Sep;14(9):921-927. doi: 10.1038/nmeth.4398. Epub 2017 Aug 21.
    PMID: 28825704
  • Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS.
    Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R.
    Nat Biotechnol. 2017 Aug;35(8):781-788. doi: 10.1038/nbt.3908. Epub 2017 Jun 12.
    PMID: 28604659
  • OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data.
    Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R.
    Nat Biotechnol. 2014 Mar;32(3):219-23. doi: 10.1038/nbt.2841.
    PMID: 24727770

Other publications

  • OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data.
    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.
    Nat Methods. 2024 Mar;21(3):365-367. doi: 10.1038/s41592-024-02197-7.
    PMID: 38366242
  • Network-centric analysis of co-fractionated protein complex profiles using SECAT.
    Bokor BJ, Gorhe D, Jovanovic M, Rosenberger G.
    STAR Protoc. 2023 May 12;4(2):102293. doi: 10.1016/j.xpro.2023.102293.
    PMID: 37182203
  • Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities.
    Salovska B, Gao E, Müller-Dott S, Li W, Cordon CC, Wang S, Dugourd A, Rosenberger G, Saez-Rodriguez J, Liu Y.
    Clin Transl Med. 2023 Feb;13(2):e1179. doi: 10.1002/ctm2.1179.
    PMID: 36781298
  • dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts.
    Demichev V, Szyrwiel L, Yu F, Teo GC, Rosenberger G, Niewienda A, Ludwig D, Decker J, Kaspar-Schoenefeld S, Lilley KS, Mülleder M, Nesvizhskii AI, Ralser M.
    Nat Commun. 2022 Jul 8;13(1):3944. doi: 10.1038/s41467-022-31492-0.
    PMID: 35803928
  • Interferon lambda 4 impairs hepatitis C viral antigen presentation and attenuates T cell responses.
    Chen Q, Coto-Llerena M, Suslov A, Teixeira RD, Fofana I, Nuciforo S, Hofmann M, Thimme R, Hensel N, Lohmann V, Ng CKY, Rosenberger G, Wieland S, Heim MH.
    Nat Commun. 2021 Aug 12;12(1):4882. doi: 10.1038/s41467-021-25218-x.
    PMID: 34385466
  • Systematic detection of functional proteoform groups from bottom-up proteomic datasets.
    Bludau I, Frank M, Dörig C, Cai Y, Heusel M, Rosenberger G, Picotti P, Collins BC, Röst H, Aebersold R.
    Nat Commun. 2021 Jun 21;12(1):3810. doi: 10.1038/s41467-021-24030-x.
    PMID: 34155216
  • DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics.
    Bichmann L, Gupta S, Rosenberger G, Kuchenbecker L, Sachsenberg T, Ewels P, Alka O, Pfeuffer J, Kohlbacher O, Röst H.
    J Proteome Res. 2021 Jul 2;20(7):3758-3766. doi: 10.1021/acs.jproteome.1c00123.
    PMID: 34153189
  • Global and Site-Specific Effect of Phosphorylation on Protein Turnover.
    Wu C, Ba Q, Lu D, Li W, Salovska B, Hou P, Mueller T, Rosenberger G, Gao E, Di Y, Zhou H, Fornasiero EF, Liu Y.
    Dev Cell. 2020 Nov 18:S1534-5807(20)30875-3. doi: 10.1016/j.devcel.2020.10.025.
    PMID: 33238149
  • Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease.
    Robinson AE, Binek A, Venkatraman V, Searle BC, Holewinski RJ, Rosenberger G, Parker SJ, Basisty N, Xie X, Lund PJ, Saxena G, Mato JM, Garcia BA, Schilling B, Lu SC, Van Eyk JE.
    J Proteome Res. 2020 Oct 2;19(10):4163-4178. doi: 10.1021/acs.jproteome.0c00685. Epub 2020 Sep 23.
    PMID: 32966080
  • Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases.
    Buljan M, Ciuffa R, van Drogen A, Vichalkovski A, Mehnert M, Rosenberger G, Lee S, Varjosalo M, Pernas LE, Spegg V, Snijder B, Aebersold R, Gstaiger M.
    Mol Cell. 2020 Aug 6;79(3):504-520.e9. doi: 10.1016/j.molcel.2020.07.001. Epub 2020 Jul 23.
    PMID: 32707033
  • Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes.
    Bludau I, Heusel M, Frank M, Rosenberger G, Hafen R, Banaei-Esfahani A, van Drogen A, Collins BC, Gstaiger M, Aebersold R.
    Nat Protoc. 2020 Aug;15(8):2341-2386. doi: 10.1038/s41596-020-0332-6. Epub 2020 Jul 20.
    PMID: 32690956
  • Isoform-resolved correlation analysis between mRNA abundance regulation and protein level degradation.
    Salovska B, Zhu H, Gandhi T, Frank M, Li W, Rosenberger G, Wu C, Germain PL, Zhou H, Hodny Z, Reiter L, Liu Y.
    Mol Syst Biol. 2020 Mar;16(3):e9170. doi: 10.15252/msb.20199170.
    PMID: 32175694
  • A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS.
    Heusel M, Frank M, Köhler M, Amon S, Frommelt F, Rosenberger G, Bludau I, Aulakh S, Linder MI, Liu Y, Collins BC, Gstaiger M, Kutay U, Aebersold R.
    Cell Syst. 2020 Feb 26;10(2):133-155.e6. doi: 10.1016/j.cels.2020.01.001. Epub 2020 Feb 5.
    PMID: 32027860
  • Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition.
    Li W, Chi H, Salovska B, Wu C, Sun L, Rosenberger G, Liu Y.
    J Am Soc Mass Spectrom. 2019 Aug;30(8):1396-1405. doi: 10.1007/s13361-019-02243-1. Epub 2019 May 30.
    PMID: 31147889
  • Complex-centric proteome profiling by SEC-SWATH-MS.
    Heusel M, Bludau I, Rosenberger G, Hafen R, Frank M, Banaei-Esfahani A, van Drogen A, Collins BC, Gstaiger M, Aebersold R.
    Mol Syst Biol. 2019 Jan 14;15(1):e8438. doi: 10.15252/msb.20188438.
    PMID: 30642884
  • Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial.
    Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R.
    Mol Syst Biol. 2018 Aug 13;14(8):e8126. doi: 10.15252/msb.20178126.
    PMID: 30104418
  • Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry.
    Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng SC, Zhang H, Aebersold R.
    Nat Commun. 2017 Aug 21;8(1):291. doi: 10.1038/s41467-017-00249-5.
    PMID: 28827567
  • Quantitative proteomics: challenges and opportunities in basic and applied research.
    Schubert OT, Röst HL, Collins BC, Rosenberger G, Aebersold R.
    Nat Protoc. 2017 Jul;12(7):1289-1294. doi: 10.1038/nprot.2017.040. Epub 2017 Jun 1.
    PMID: 28569762
  • A multicenter study benchmarks software tools for label-free proteome quantification.
    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.
    Nat Biotechnol. 2016 Nov;34(11):1130-1136. doi: 10.1038/nbt.3685. Epub 2016 Oct 3.
    PMID: 27701404
  • TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.
    Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R.
    Nat Methods. 2016 Sep;13(9):777-83. doi: 10.1038/nmeth.3954. Epub 2016 Aug 1.
    PMID: 27479329
  • OpenMS: a flexible open-source software platform for mass spectrometry data analysis.
    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.
    Nat Methods. 2016 Aug 30;13(9):741-8. doi: 10.1038/nmeth.3959.
    PMID: 27575624
  • xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry.
    Walzthoeni T, Joachimiak LA, Rosenberger G, Röst HL, Malmström L, Leitner A, Frydman J, Aebersold R.
    Nat Methods. 2015 Dec;12(12):1185-90. doi: 10.1038/nmeth.3631. Epub 2015 Oct 26.
    PMID: 26501516
  • Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry.
    Parker SJ, Rost H, Rosenberger G, Collins BC, Malmström L, Amodei D, Venkatraman V, Raedschelders K, Van Eyk JE, Aebersold R.
    Mol Cell Proteomics. 2015 Oct;14(10):2800-13. doi: 10.1074/mcp.O114.042267. Epub 2015 Jul 21.
    PMID: 26199342
  • Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis.
    Schubert OT, Ludwig C, Kogadeeva M, Zimmermann M, Rosenberger G, Gengenbacher M, Gillet LC, Collins BC, Röst HL, Kaufmann SH, Sauer U, Aebersold R.
    Cell Host Microbe. 2015 Jul 8;18(1):96-108. doi: 10.1016/j.chom.2015.06.001. Epub 2015 Jun 18.
    PMID: 26094805
  • A repository of assays to quantify 10,000 human proteins by SWATH-MS.
    Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R.
    Sci Data. 2014 Sep 16;1:140031. doi: 10.1038/sdata.2014.31. eCollection 2014.
    PMID: 25977788
  • Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.
    Röst H, Rosenberger G, Aebersold R, Malmström L.
    Bioinformatics. 2015 Jul 15;31(14):2415-7. doi: 10.1093/bioinformatics/btv152. Epub 2015 Mar 18.
    PMID: 25788625
  • Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps.
    Guo T, Kouvonen P, Koh CC, Gillet LC, Wolski WE, Röst HL, Rosenberger G, Collins BC, Blum LC, Gillessen S, Joerger M, Jochum W, Aebersold R.
    Nat Med. 2015 Apr;21(4):407-13. doi: 10.1038/nm.3807. Epub 2015 Mar 2.
    PMID: 25730263
  • Building high-quality assay libraries for targeted analysis of SWATH MS data.
    Schubert OT, Gillet LC, Collins BC, Navarro P, Rosenberger G, Wolski WE, Lam H, Amodei D, Mallick P, MacLean B, Aebersold R.
    Nat Protoc. 2015 Mar;10(3):426-441. doi: 10.1038/nprot.2015.015. Epub 2015 Feb 12.
    PMID: 25675208
  • DIANA-algorithmic improvements for analysis of data-independent acquisition MS data.
    Teleman J, Röst HL, Rosenberger G, Schmitt U, Malmström L, Malmström J, Levander F.
    Bioinformatics. 2015 Feb 15;31(4):555-62. doi: 10.1093/bioinformatics/btu686. Epub 2014 Oct 27.
    PMID: 25348213
  • Functional and structural properties of a novel protein and virulence factor (Protein sHIP) in Streptococcus pyogenes.
    Wisniewska M, Happonen L, Kahn F, Varjosalo M, Malmström L, Rosenberger G, Karlsson C, Cazzamali G, Pozdnyakova I, Frick IM, Björck L, Streicher W, Malmström J, Wikström M.
    J Biol Chem. 2014 Jun 27;289(26):18175-88. doi: 10.1074/jbc.M114.565978. Epub 2014 May 13.
    PMID: 24825900
  • aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.
    Rosenberger G, Ludwig C, Röst HL, Aebersold R, Malmström L.
    Bioinformatics. 2014 Sep 1;30(17):2511-3. doi: 10.1093/bioinformatics/btu200. Epub 2014 Apr 20.
    PMID: 24753486
  • Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system.
    Collins BC, Gillet LC, Rosenberger G, Röst HL, Vichalkovski A, Gstaiger M, Aebersold R.
    Nat Methods. 2013 Dec;10(12):1246-53. doi: 10.1038/nmeth.2703. Epub 2013 Oct 27.
    PMID: 24162925
  • Cross-link guided molecular modeling with ROSETTA.
    Kahraman A, Herzog F, Leitner A, Rosenberger G, Aebersold R, Malmström L.
    PLoS One. 2013 Sep 17;8(9):e73411. doi: 10.1371/journal.pone.0073411. eCollection 2013.
    PMID: 24069194
  • The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis.
    Schubert OT, Mouritsen J, Ludwig C, Röst HL, Rosenberger G, Arthur PK, Claassen M, Campbell DS, Sun Z, Farrah T, Gengenbacher M, Maiolica A, Kaufmann SH, Moritz RL, Aebersold R.
    Cell Host Microbe. 2013 May 15;13(5):602-12. doi: 10.1016/j.chom.2013.04.008.
    PMID: 23684311
  • N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications.
    Hüttenhain R, Surinova S, Ossola R, Sun Z, Campbell D, Cerciello F, Schiess R, Bausch-Fluck D, Rosenberger G, Chen J, Rinner O, Kusebauch U, Hajdúch M, Moritz RL, Wollscheid B, Aebersold R.
    Mol Cell Proteomics. 2013 Apr;12(4):1005-16. doi: 10.1074/mcp.O112.026617. Epub 2013 Feb 13.
    PMID: 23408683
  • Automated workflow for large-scale selected reaction monitoring experiments.
    Malmström L, Malmström J, Selevsek N, Rosenberger G, Aebersold R.
    J Proteome Res. 2012 Mar 2;11(3):1644-53. doi: 10.1021/pr200844d. Epub 2012 Feb 10.
    PMID: 22283722

Preprint publications

  • SEC-TMT facilitates quantitative differential analysis of protein interaction networks.
    Doron-Mandel E, Bokor BJ, Ma Y, Street LA, Tang LC, Abdou AA, Shah NH, Rosenberger GA, Jovanovic M.
    bioRxiv. 2023 Jan 13:2023.01.12.523793. doi: 10.1101/2023.01.12.523793.
    PMID: 36711903