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Proteomic Technology

  • Schubert OT, Gillet LC, Collins BC, Navarro P, Rosenberger G, Wolski WE, Lam H, Amodei D, Mallick P, MacLean B, Aebersold R. Building high-quality assay libraries for targeted analysis of SWATH MS data. Nat Protoc. 2015 Mar;10(3):426-441. Pubmed

  • Liu Y, Buil A, Collins BC, Gillet LC, Blum LC, Cheng LY, Vitek O, Mouritsen J, Lachance G, Spector TD, Dermitzakis ET, Aebersold R. Quantitative variability of 342 plasma proteins in a human twin population.  Mol Syst Biol. 2015 Feb 4;11(2):786. Pubmed

  • Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R. Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast. Mol Syst Biol. 2014 Dec 9;10:767 Pubmed

  • Collins BC, Gillet LC, Rosenberger G, Röst HL, Vichalkovski A, Gstaiger M, Aebersold R. Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system. Nat Methods. 2013 Dec;10(12):1246-53. Pubmed
  • 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. The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosisCell Host Microbe. 2013 May 15;13(5):602-12. Pubmed
  • Picotti P, Clément-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Röst H, Sun Z, Rinner O, Reiter L, Shen Q, Michaelson JJ, Frei A, Alberti S, Kusebauch U, Wollscheid B, Moritz RL, Beyer A, Aebersold R. A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysisNature. 2013 Feb 14;494(7436):266-70. Pubmed
  • Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysisMol Cell Proteomics. 2012 Jun;11(6):O111.016717. Pubmed
  • Ludwig C, Claassen M, Schmidt A, Aebersold R. Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometryMol Cell Proteomics. 2012 Mar;11(3):M111.013987. Pubmed
  • Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A, Herzog F, Rinner O, Ellenberg J, Aebersold R. The quantitative proteome of a human cell lineMol Syst Biol. 2011 Nov 8;7:549. Pubmed
  • Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directionsNat Methods. 2012 May 30;9(6):555-66. Pubmed
  • Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, Colman-Lerner A, Nolan GP, Nesvizhskii AI, Peter M, Loewith R, von Mering C, Aebersold R.Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal. 2010 Dec 21;3(153):rs4. Pubmed
  • Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R. Full dynamic range proteome analysis of S. cerevisiae by targeted proteomicsCell. 2009 Aug 21;138(4):795-806. Pubmed



  • Rosenberger G, Ludwig C, Röst HL, Aebersold R, Malmström L. aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Bioinformatics. 2014 Sep 1;30(17):2511-3. Pubmed

  • 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.  Nat Biotechnol. 2014 Mar;32(3):219-23. Pubmed


  • Chang CY, Sabidó E, Aebersold R, Vitek O. Targeted protein quantification using sparse reference labeling. Nat Methods. 2014 Mar;11(3):301-4. Pubmed
  • Kahraman A, Herzog F, Leitner A, Rosenberger G, Aebersold R, Malmström L. Cross-link guided molecular modeling with ROSETTA. PLoS One. 2013 Sep 17;8(9):e73411. Pubmed
  • Walzthoeni T, Claassen M, Leitner A, Herzog F, Bohn S, Förster F, Beck M, Aebersold R. False discovery rate estimation for cross-linked peptides identified by mass spectrometry. Nat Methods. 2012 Sep;9(9):901-3. Pubmed
  • Röst H, Malmström L, Aebersold R. A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol Cell Proteomics. 2012 Aug;11(8):540-9. Pubmed
  • Kahraman A, Malmström L, Aebersold R. Xwalk: computing and visualizing distances in cross-linking experiments. Bioinformatics. 2011 Aug 1;27(15):2163-4. Pubmed
  • Reiter L, Rinner O, Picotti P, Hüttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods. 2011 May;8(5):430-5. Pubmed
  • Rinner O, Seebacher J, Walzthoeni T, Mueller LN, Beck M, Schmidt A, Mueller M, Aebersold R. Identification of cross-linked peptides from large sequence databases. Nat Methods. 2008 Apr;5(4):315-8. Pubmed
  • Mueller LN, Rinner O, Schmidt A, Letarte S, Bodenmiller B, Brusniak MY, Vitek O, Aebersold R, Müller M. SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics. 2007 Oct;7(19):3470-80. Pubmed
  • Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R.Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol. 2007 Jan;25(1):125-31. Pubmed


Analysis of Macromolecular Complexes

  • Efremov RG, Leitner A, Aebersold R, Raunser S. Architecture and conformational switch mechanism of the ryanodine receptor. Nature. 2015 Jan 1;517(7532):39-43 Pubmed
  • Leitner A, Joachimiak LA, Unverdorben P, Walzthoeni T, Frydman J, Förster F, Aebersold R. Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes.  Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9455-60. doi: 10.1073/pnas.1320298111. Epub 2014 Jun 17. Pubmed

  • Politis A, Stengel F, Hall Z, Hernández H, Leitner A, Walzthoeni T, Robinson CV, Aebersold R. A mass spectrometry-based hybrid method for structural modeling of protein complexesNat Methods. 2014 Apr;11(4):403-6. Pubmed
  • Greber BJ, Boehringer D, Leitner A, Bieri P, Voigts-Hoffmann F, Erzberger JP, Leibundgut M, Aebersold R, Ban N. Architecture of the large subunit of the mammalian mitochondrial ribosome. Nature. 2014 Jan 23;505(7484):515-9. Pubmed
  • Hauri S, Wepf A, van Drogen A, Varjosalo M, Tapon N, Aebersold R, Gstaiger M. Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1. Mol Syst Biol. 2013 Dec 22;9:713. Pubmed
  • Nguyen VQ, Ranjan A, Stengel F, Wei D, Aebersold R, Wu C, Leschziner AE. Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1. Cell. 2013 Sep 12;154(6):1220-31. Pubmed
  • Tosi A, Haas C, Herzog F, Gilmozzi A, Berninghausen O, Ungewickell C, Gerhold CB, Lakomek K, Aebersold R, Beckmann R, Hopfner KP. Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex. Cell. 2013 Sep 12;154(6):1207-19. Pubmed
  • Herzog F, Kahraman A, Boehringer D, Mak R, Bracher A, Walzthoeni T, Leitner A, Beck M, Hartl FU, Ban N, Malmström L, Aebersold R. Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Science. 2012 Sep 14;337(6100):1348-52. Pubmed
  • Rinner O, Seebacher J, Walzthoeni T, Mueller LN, Beck M, Schmidt A, Mueller M, Aebersold R. Identification of cross-linked peptides from large sequence databases. Nat Methods. 2008 Apr;5(4):315-8. Pubmed
  • Rinner O, Mueller LN, Hubálek M, Müller M, Gstaiger M, Aebersold R. An integrated mass spectrometric and computational framework for the analysis of protein interaction networks. Nat Biotechnol. 2007 Mar;25(3):345-52. Pubmed


Biomarker and Clinical Research

  • Shao S, Guo T, Aebersold R. Mass spectrometry-based proteomic quest for diabetes biomarkers. Biochim Biophys Acta. 2014 Dec 30. pii: S1570-9639(14)00328-8. Pubmed

  • Liu Y, Chen J, Sethi A, Li QK, Chen L, Collins B, Gillet LC, Wollscheid B, Zhang H, Aebersold R. Glycoproteomic analysis of prostate cancer tissues by SWATH mass spectrometry discovers N-acylethanolamine acid amidase and protein tyrosine kinase 7 as signatures for tumor aggressiveness. Mol Cell Proteomics. 2014 Jul;13(7):1753-68 Pubmed

  • Cerciello F, Choi M, Nicastri A, Bausch-Fluck D, Ziegler A, Vitek O, Felley-Bosco E, Stahel R, Aebersold R, Wollscheid B. Identification of a seven glycopeptide signature for malignant pleural mesothelioma in human serum by selected reaction monitoring. Clin Proteomics. 2013 Nov 8;10(1):16. Pubmed

  • Templeton AJ, Dutoit V, Cathomas R, Rothermundt C, Bärtschi D, Dröge C, Gautschi O, Borner M, Fechter E, Stenner F, Winterhalder R, Müller B, Schiess R, Wild PJ, Rüschoff JH, Thalmann G, Dietrich PY, Aebersold R, Klingbiel D, Gillessen S; Swiss Group for Clinical Cancer Research (SAKK). Phase 2 trial of single-agent everolimus in chemotherapy-naive patients with castration-resistant prostate cancer (SAKK 08/08)Eur Urol. 2013 Jul;64(1):150-8. 
  • Sabidó E, Wu Y, Bautista L, Porstmann T, Chang CY, Vitek O, Stoffel M, Aebersold R. Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat dietMol Syst Biol. 2013 Jul 16;9:681. Pubmed
  • 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. N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. Mol Cell Proteomics. 2013 Apr;12(4):1005-16. Pubmed
  • Liu Y, Hüttenhain R, Surinova S, Gillet LC, Mouritsen J, Brunner R, Navarro P, Aebersold R. Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MSProteomics. 2013 Apr;13(8):1247-56. Pubmed
  • Hüttenhain R, Soste M, Selevsek N, Röst H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL, Niméus-Malmström E, Rinner O, Aebersold R. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomicsSci Transl Med. 2012 Jul 11;4(142):142ra94. Pubmed
  • Ossola R, Schiess R, Picotti P, Rinner O, Reiter L, Aebersold R. Biomarker validation in blood specimens by selected reaction monitoring mass spectrometry of N-glycosites. Methods Mol Biol. 2011;728:179-94. Pubmed
  • Surinova S, Schiess R, Hüttenhain R, Cerciello F, Wollscheid B, Aebersold R. On the development of plasma protein biomarkers. J Proteome Res. 2011 Jan 7;10(1):5-16. Pubmed
  • Hüttenhain R, Malmström J, Picotti P, Aebersold R. Perspectives of targeted mass spectrometry for protein biomarker verification. Curr Opin Chem Biol. 2009 Dec;13(5-6):518-25. Pubmed


Protocols and Tutorials

  • Ebhardt HA, Nan J, Chaulk SG, Fahlman RP, Aebersold R. Enzymatic generation of peptides flanked by basic amino acids to obtain MS/MS spectra with 2× sequence coverage. Rapid Commun Mass Spectrom. 2014 Dec 30;28(24):2735-43. Pubmed
  • Leitner A, Walzthoeni T, Aebersold R. Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipelineNat Protoc. 2014 Jan;9(1):120-37. Pubmed
  • Surinova S, Hüttenhain R, Chang CY, Espona L, Vitek O, Aebersold R. Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studiesNat Protoc. 2013 Aug;8(8):1602-19. Pubmed
  • Leitner A, Aebersold R. SnapShot: mass spectrometry for protein and proteome analyses. Cell. 2013 Jul 3;154(1):252-252.e1. DOI  Pubmed
  • Farrah T, Deutsch EW, Kreisberg R, Sun Z, Campbell DS, Mendoza L, Kusebauch U, Brusniak MY, Hüttenhain R, Schiess R, Selevsek N, Aebersold R, Moritz RL. PASSEL: the PeptideAtlas SRMexperiment libraryProteomics. 2012 Apr;12(8):1170-5. Pubmed
  • Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. A guided tour of the Trans-Proteomic PipelineProteomics. 2010 Mar;10(6):1150-9. Pubmed
  • Deutsch EW, Lam H, Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflowsEMBO Rep. 2008 May;9(5):429-34. Pubmed
  • Bodenmiller B, Campbell D, Gerrits B, Lam H, Jovanovic M, Picotti P, Schlapbach R, Aebersold R. PhosphoPep--a database of protein phosphorylation sites in model organismsNat Biotechnol. 2008 Dec;26(12):1339-40. Pubmed
  • Aebersold R, Mann M. Mass spectrometry-based proteomicsNature. 2003 Mar 13;422(6928):198-207. Pubmed


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