Ruedi Aebersold

Summary

Affiliation: Swiss Federal Institute of Technology
Country: Switzerland

Publications

  1. doi request reprint Mass Spectrometry Applied to Bottom-Up Proteomics: Entering the High-Throughput Era for Hypothesis Testing
    Ludovic C Gillet
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland Email
    Annu Rev Anal Chem (Palo Alto Calif) 9:449-72. 2016
  2. pmc PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells
    Bernd Bodenmiller
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 3:139. 2007
  3. pmc Selected reaction monitoring for quantitative proteomics: a tutorial
    Vinzenz Lange
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 4:222. 2008
  4. pmc The quantitative proteome of a human cell line
    Martin Beck
    European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 7:549. 2011
  5. pmc Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage
    Stefan Jennebach
    Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich CIPSM, Ludwig Maximilians Universitat Munchen, Feodor Lynen Str 25, 81377 Munich, Germany
    Nucleic Acids Res 40:5591-601. 2012
  6. pmc Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells
    Samuel Marguerat
    University College London, Department of Genetics, Evolution and Environment and UCL Cancer Institute, London WC1E 6BT, UK
    Cell 151:671-83. 2012
  7. doi request reprint The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community
    Ruedi Aebersold
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    J Proteome Res 12:23-7. 2013
  8. pmc openBIS: a flexible framework for managing and analyzing complex data in biology research
    Angela Bauch
    Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology ETH Zurich, Switzerland
    BMC Bioinformatics 12:468. 2011
  9. pmc High-accuracy proteome maps of human body fluids
    Alexander Schmidt
    Institute for Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Strasse 16, CH 8093 Zurich, Switzerland
    Genome Biol 7:242. 2006
  10. pmc Proteomics studies confirm the presence of alternative protein isoforms on a large scale
    Michael L Tress
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, C, Melchor Fernandez Almagro, Madrid 28029, Spain
    Genome Biol 9:R162. 2008

Detail Information

Publications94

  1. doi request reprint Mass Spectrometry Applied to Bottom-Up Proteomics: Entering the High-Throughput Era for Hypothesis Testing
    Ludovic C Gillet
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland Email
    Annu Rev Anal Chem (Palo Alto Calif) 9:449-72. 2016
    ..We believe that this shift will have a profound impact for the field of proteomics and life science research in general. ..
  2. pmc PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells
    Bernd Bodenmiller
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 3:139. 2007
    ....
  3. pmc Selected reaction monitoring for quantitative proteomics: a tutorial
    Vinzenz Lange
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 4:222. 2008
    ..Furthermore, normalization and various factors affecting sensitivity and accuracy are discussed...
  4. pmc The quantitative proteome of a human cell line
    Martin Beck
    European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 7:549. 2011
    ..We discuss how protein abundance is linked to function and evolution...
  5. pmc Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage
    Stefan Jennebach
    Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich CIPSM, Ludwig Maximilians Universitat Munchen, Feodor Lynen Str 25, 81377 Munich, Germany
    Nucleic Acids Res 40:5591-601. 2012
    ..This indicates that Pol I and also Pol III are distantly related to a Pol II-TFIIS-TFIIF-TFIIE complex...
  6. pmc Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells
    Samuel Marguerat
    University College London, Department of Genetics, Evolution and Environment and UCL Cancer Institute, London WC1E 6BT, UK
    Cell 151:671-83. 2012
    ..Upon transition to quiescence, the proteome changes substantially, but, in stark contrast to mRNAs, proteins do not uniformly decrease but scale with cell volume...
  7. doi request reprint The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community
    Ruedi Aebersold
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    J Proteome Res 12:23-7. 2013
    ..The B/D-HPP is highly complementary to the C-HPP and will provide datasets and biological characterization useful to the C-HPP teams. In this manuscript we describe the goals, the plans, and the current status of the of the B/D-HPP...
  8. pmc openBIS: a flexible framework for managing and analyzing complex data in biology research
    Angela Bauch
    Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology ETH Zurich, Switzerland
    BMC Bioinformatics 12:468. 2011
    ..Ease of integration with data analysis pipelines and other computational tools is a key requirement for it...
  9. pmc High-accuracy proteome maps of human body fluids
    Alexander Schmidt
    Institute for Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Strasse 16, CH 8093 Zurich, Switzerland
    Genome Biol 7:242. 2006
    ..Three recent large-scale proteomic analyses of tears, urine and seminal plasma using the latest mass spectrometric technology will provide useful datasets for biomarker discovery...
  10. pmc Proteomics studies confirm the presence of alternative protein isoforms on a large scale
    Michael L Tress
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, C, Melchor Fernandez Almagro, Madrid 28029, Spain
    Genome Biol 9:R162. 2008
    ..Although there is extensive evidence for large scale alternative splicing at the transcript level, there have been no comparable studies demonstrating the existence of alternatively spliced protein isoforms...
  11. pmc UniPep--a database for human N-linked glycosites: a resource for biomarker discovery
    Hui Zhang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Genome Biol 7:R73. 2006
    ..Here, we describe UniPep http://www.unipep.org--a database of human N-linked glycosites--as a resource for biomarker discovery...
  12. pmc Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome
    Timo Glatter
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 7:547. 2011
    ..Subsequent genetic studies in flies suggest a role for dTTT in controlling cell growth via a dTORC1- and dTORC2-dependent mechanism...
  13. pmc Absolute quantification of microbial proteomes at different states by directed mass spectrometry
    Alexander Schmidt
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Str 16, Zurich, Switzerland
    Mol Syst Biol 7:510. 2011
    ..interrogans. This is the first study that describes the absolute quantitative behavior of any proteome over multiple states, and represents the most comprehensive proteome abundance pattern comparison for any organism to date...
  14. ncbi request reprint Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation
    Delphine Pflieger
    Institute for Molecular Systems Biology, ETH, 8093 Zurich, Switzerland
    Mol Cell Proteomics 7:326-46. 2008
    ....
  15. doi request reprint Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system
    Ben C Collins
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Nat Methods 10:1246-53. 2013
    ..We therefore establish AP-SWATH as a tool to quantify dynamic changes in protein-complex interaction networks. ..
  16. pmc An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures
    Alexander Schmidt
    Institute of Molecular Systems Biology and section signCompetence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, Wolfgang Pauli Str 16, 8093 Zurich, Switzerland
    Mol Cell Proteomics 7:2138-50. 2008
    ..Compared with conventional DDA LC-MS/MS experiments, a substantially higher number of peptides could be identified from a sample, and this increase was more pronounced for low intensity precursor ions...
  17. doi request reprint False discovery rate estimation for cross-linked peptides identified by mass spectrometry
    Thomas Walzthoeni
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Nat Methods 9:901-3. 2012
    ..Here we describe an automated target-decoy strategy and the software tool xProphet, which solve this problem for large multicomponent protein complexes...
  18. pmc Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis
    Ludovic C Gillet
    Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, 8093 Zurich, Switzerland
    Mol Cell Proteomics 11:O111.016717. 2012
    ....
  19. pmc Visual proteomics of the human pathogen Leptospira interrogans
    Martin Beck
    Institute of Molecular Systems Biology, The Swiss Federal Institute of Technology ETH Zurich, Zurich, Switzerland
    Nat Methods 6:817-23. 2009
    ..We describe a scoring function for visual proteomics and assess its performance and accuracy under realistic conditions. We discuss current and general limitations of the approach, as well as expected improvements in the future...
  20. pmc Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast
    Bernd Bodenmiller
    Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    Sci Signal 3:rs4. 2010
    ..Our results serve to constrain future models of cellular signaling and reinforce the idea that simple linear representations of signaling pathways might be insufficient for drug development and for describing organismal homeostasis...
  21. pmc A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis
    Paola Picotti
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH 8093, Switzerland
    Nature 494:266-70. 2013
    ..Our results suggest that selective pressure favours the acquisition of sets of polymorphisms that adapt protein levels but also maintain the stoichiometry of functionally related pathway members...
  22. ncbi request reprint SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling
    Lukas N Mueller
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Proteomics 7:3470-80. 2007
    ..We show that the program automatically detects profiling trends in an unsupervised manner and is able to associate proteins to their correct theoretical dilution profile...
  23. doi request reprint Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome
    Bruno Domon
    Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    J Proteome Res 8:2633-9. 2009
    ..Finally, we have applied a directed tandem mass spectrometric workflow using inclusion lists to increase the number of identified peptides...
  24. pmc Regulation of yeast central metabolism by enzyme phosphorylation
    Ana Paula Oliveira
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 8:623. 2012
    ..These results demonstrate the role of phosphorylation in controlling the metabolic flux realised by these three enzymes...
  25. pmc Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry
    Ralph Schiess
    Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule ETH Zurich, 8093 Zurich, Switzerland
    Mol Cell Proteomics 8:624-38. 2009
    ..The data revealed insulin-dependent cell surface glycoprotein dynamics, including insulin receptor internalization, and linked these changes to intracellular signaling networks...
  26. pmc Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1
    Simon Hauri
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 9:713. 2013
    ..Collectively, our systematic analysis greatly enhances our insights into the biochemical landscape underlying human Hippo signaling and emphasizes multifaceted roles of cell polarity complexes in Hippo-mediated tissue growth control. ..
  27. pmc N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications
    Ruth Hüttenhain
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    Mol Cell Proteomics 12:1005-16. 2013
    ..Together, the established N-glycoprotein SRMAtlas resource facilitates parallel, efficient, consistent, and sensitive evaluation of proposed biomarker candidates in large clinical sample cohorts...
  28. pmc Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet
    Eduard Sabidó
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 9:681. 2013
    ....
  29. pmc Generic comparison of protein inference engines
    Manfred Claassen
    Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology Zurich, Zurich, Switzerland
    Mol Cell Proteomics 11:O110.007088. 2012
    ....
  30. doi request reprint Automated workflow for large-scale selected reaction monitoring experiments
    Lars Malmström
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    J Proteome Res 11:1644-53. 2012
    ..We apply the technology to a large-scale experiment studying how Streptococcus pyogenes remodels its proteome under stimulation of human plasma...
  31. pmc RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans
    Marko Jovanovic
    Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
    Genome Res 22:1360-71. 2012
    ..Comparison of total mRNA and protein abundance changes in mir-58 mutant and wild-type animals indicated that the direct bantam/miR-58 targets identified here are mainly regulated at the level of protein abundance, not mRNA stability...
  32. pmc A computational tool to detect and avoid redundancy in selected reaction monitoring
    Hannes Röst
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH 8093, Switzerland
    Mol Cell Proteomics 11:540-9. 2012
    ..We expect that the consideration of information content will become a standard step in SRM assay design and analysis, facilitated by the SRMCollider...
  33. pmc Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics
    Roeland Costenoble
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 7:464. 2011
    ..Interpreted through flux balance modeling, the data indicate that S. cerevisiae retains proteins not necessarily used in a particular environment. Further, the data suggest differential functionality for several metabolic isoenzymes...
  34. pmc Defining potentially conserved RNA regulons of homologous zinc-finger RNA-binding proteins
    Tanja Scherrer
    Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Wolfgang Pauli Strasse 10, 8093 Zurich, Switzerland
    Genome Biol 12:R3. 2011
    ..To explore the impact of these proteins on RNA regulation, we undertook a systematic analysis of the RNA targets and of the global implications for gene expression...
  35. pmc The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation
    Sandra N Loevenich
    Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    BMC Bioinformatics 10:59. 2009
    ..Protein databases compiled from high quality empirical protein identifications that are in turn based on correct gene models increase the correctness, sensitivity, and quantitative accuracy of systems biology genome-scale experiments...
  36. pmc A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans
    Marko Jovanovic
    Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
    Nat Methods 7:837-42. 2010
    ....
  37. pmc Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry
    Christina Ludwig
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    Mol Cell Proteomics 11:M111.013987. 2012
    ....
  38. doi request reprint Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS
    Yansheng Liu
    Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
    Proteomics 13:1247-56. 2013
    ..We suggest that SWATH-MS analysis combined with N-glycoproteome enrichment in plasma samples is a promising integrative proteomic approach for biomarker discovery and verification...
  39. doi request reprint Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies
    Silvia Surinova
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Nat Protoc 8:1602-19. 2013
    ..The time frame to realize the protocol is 1-2 weeks, depending on the number of replicates used in the experiment. ..
  40. pmc The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis
    Olga T Schubert
    Institute of Molecular Systems Biology, ETH Zurich, Zurich CH 8093, Switzerland
    Cell Host Microbe 13:602-12. 2013
    ..In conclusion, we present a publicly available research resource that supports the sensitive, precise, and reproducible quantification of virtually any Mtb protein by a robust and widely accessible mass spectrometric method...
  41. doi request reprint Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A
    Séverine Bontron
    Department of Biology, Division of Biochemistry, University of Fribourg, 1700 Fribourg, Switzerland
    Cell Rep 3:16-22. 2013
    ..These results close a gap in our perception of and delineate a role for PP2A(Cdc55) in TORC1-/PKA-mediated regulation of quiescence and chronological life span...
  42. doi request reprint High-throughput generation of selected reaction-monitoring assays for proteins and proteomes
    Paola Picotti
    Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, Zurich, Switzerland
    Nat Methods 7:43-6. 2010
    ..We illustrate the power of the approach by generating and applying validated SRM assays for all Saccharomyces cerevisiae kinases and phosphatases...
  43. pmc Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics
    Ruth Hüttenhain
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    Sci Transl Med 4:142ra94. 2012
    ..The generated expandable reference map of SRM assays for cancer-associated proteins will be a valuable resource for accelerating and planning biomarker verification studies...
  44. doi request reprint mProphet: automated data processing and statistical validation for large-scale SRM experiments
    Lukas Reiter
    Biognosys AG, Zurich, Switzerland
    Nat Methods 8:430-5. 2011
    ....
  45. doi request reprint Phosphoproteome resource for systems biology research
    Bernd Bodenmiller
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Methods Mol Biol 694:307-22. 2011
    ..The following will give an overview of the content and usage of the PhosphoPep database...
  46. doi request reprint Quantitative interaction proteomics using mass spectrometry
    Alexander Wepf
    Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, Eidgenossische Technische Hochschule Zurich, Wolfgang Pauli Strasse 16, Zurich, Switzerland
    Nat Methods 6:203-5. 2009
    ..We used this method to quantitatively analyze interaction stoichiometries in the human protein phosphatase 2A network...
  47. pmc Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics
    Alexander Leitner
    Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule ETH Zurich, Zurich, Switzerland
    Mol Cell Proteomics 9:1634-49. 2010
    ..Finally, the impact of protein cross-linking on various biological disciplines is highlighted...
  48. pmc Systematic proteomic analysis identifies β-site amyloid precursor protein cleaving enzyme 2 and 1 (BACE2 and BACE1) substrates in pancreatic β-cells
    Ina Stützer
    Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, CH 8093 Zurich, Switzerland
    J Biol Chem 288:10536-47. 2013
    ....
  49. pmc Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans
    Johan Malmstrom
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Strasse 16, CH 8093 Zurich, Switzerland
    Nature 460:762-5. 2009
    ..Because the strategy is relatively fast and applicable to any cell type, we expect that it will become a cornerstone of quantitative biology and systems biology...
  50. ncbi request reprint An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells
    Bernd Bodenmiller
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Biosyst 3:275-86. 2007
    ..The strategy was applied to the mapping of phosphorylation sites of a purified transcription factor, dFOXO and for the global analysis of protein phosphorylation of Drosophila melanogaster Kc167 cells...
  51. doi request reprint Architecture of the large subunit of the mammalian mitochondrial ribosome
    Basil J Greber
    1 Department of Biology, Institute of Molecular Biology and Biophysics, Schafmattstrasse 20, ETH Zurich, CH 8093 Zurich, Switzerland 2
    Nature 505:515-9. 2014
    ....
  52. pmc Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth
    Claudia Blattner
    Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich CIPSM, Ludwig Maximilians Universitat Munchen, 81377 Munich, Germany
    Genes Dev 25:2093-105. 2011
    ..This reveals the molecular basis of Rrn3-regulated Pol I initiation and cell growth, and indicates a general architecture of eukaryotic transcription initiation complexes...
  53. doi request reprint Biomarker validation in blood specimens by selected reaction monitoring mass spectrometry of N-glycosites
    Reto Ossola
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Methods Mol Biol 728:179-94. 2011
    ..This protocol is intended to give an introduction to SRM-based targeted mass spectrometry with a special focus on the validation of biomarker candidates...
  54. pmc xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry
    Thomas Walzthoeni
    Department of Biology, Eidgenossische Technische Hochschule ETH Zurich, Zurich, Switzerland
    Nat Methods 12:1185-90. 2015
    ..Our method discovers and explains the structural heterogeneity of protein complexes using only sparse structural information. ..
  55. pmc A repository of assays to quantify 10,000 human proteins by SWATH-MS
    George Rosenberger
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland PhD Program in Systems Biology, University of Zurich and ETH Zurich, CH 8093 Zurich, Switzerland
    Sci Data 1:140031. 2014
    ..9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35). ..
  56. pmc Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry
    Nathalie Selevsek
    From the Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    Mol Cell Proteomics 14:739-49. 2015
    ..Overall, this study demonstrates the ability of SWATH-MS to efficiently generate reproducible, consistent, and quantitatively accurate measurements of a large fraction of a proteome across multiple samples. ..
  57. pmc Identification of cross-linked peptides from large sequence databases
    Oliver Rinner
    Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule ETH Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Nat Methods 5:315-8. 2008
    ..We showed that xQuest can identify cross-linked peptides from a total Escherichia coli lysate with an unrestricted database search...
  58. doi request reprint An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data
    Lukas N Mueller
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    J Proteome Res 7:51-61. 2008
    ..This review therefore serves as a starting point for researchers to choose an appropriate software solution for quantitative proteomic experiments based on their experimental and analytical requirements...
  59. pmc A mass spectrometric-derived cell surface protein atlas
    Damaris Bausch-Fluck
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland Department of Health Sciences and Technology, BMPP, ETH Zurich, Zurich, Switzerland
    PLoS ONE 10:e0121314. 2015
    ..The CSPA will be useful for the evaluation of drug targets, for the improved classification of cell types and for a better understanding of the surfaceome and its concerted biological functions in complex signaling microenvironments. ..
  60. pmc Cross-link guided molecular modeling with ROSETTA
    Abdullah Kahraman
    Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Zurich, Switzerland
    PLoS ONE 8:e73411. 2013
    ....
  61. doi request reprint Mass spectrometry supported determination of protein complex structure
    Thomas Walzthoeni
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Str 16, 8093 Zurich, Switzerland
    Curr Opin Struct Biol 23:252-60. 2013
    ..Hydrogen-deuterium exchange combined with MS has been used to map protein-protein binding sites. Here, we focus on recent developments in CX-MS and native MS and their application to challenging problems in structural biology...
  62. doi request reprint Comprehensive proteomics
    Martin Beck
    European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
    Curr Opin Biotechnol 22:3-8. 2011
    ..Here we discuss the feasibility of this goal in the light of recent technological developments...
  63. pmc Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring
    Vinzenz Lange
    Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
    Mol Cell Proteomics 7:1489-500. 2008
    ..The resulting quantitative protein patterns enabled us to clearly define the subset of virulence proteins that is regulated upon plasma exposure...
  64. ncbi request reprint A proteome catalog of Drosophila melanogaster: an essential resource for targeted quantitative proteomics
    Christian H Ahrens
    Center for Model Organsim Proteomes, University of Zurich, Zurich, Switzerland
    Fly (Austin) 1:182-6. 2007
    ....
  65. pmc Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography
    Alexander Leitner
    Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Mol Cell Proteomics 11:M111.014126. 2012
    ..The benefits of both SEC enrichment and multiprotease digests are demonstrated on a set of model proteins and the improved workflow is applied to the characterization of the 20S proteasome from rabbit and Schizosaccharomyces pombe...
  66. doi request reprint Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry
    Franz Herzog
    Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Science 337:1348-52. 2012
    ..This study establishes XL-MS as an integral part of hybrid structural biology approaches for the analysis of endogenous protein complexes...
  67. pmc Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics
    Paola Picotti
    Institute of Molecular Systems Biology, ETH Zurich, Zurich CH 8093, Switzerland
    Cell 138:795-806. 2009
    ..We therefore demonstrate the potential of SRM-based proteomics to provide assays for the measurement of any set of proteins of interest in yeast at high-throughput and quantitative accuracy...
  68. pmc Xwalk: computing and visualizing distances in cross-linking experiments
    Abdullah Kahraman
    Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology ETH Zurich, CH 8093 Zurich, Switzerland
    Bioinformatics 27:2163-4. 2011
    ..Chemical cross-linking of proteins or protein complexes and the mass spectrometry-based localization of the cross-linked amino acids in peptide sequences is a powerful method for generating distance restraints on the substrate's topology...
  69. pmc An integrated workflow for charting the human interaction proteome: insights into the PP2A system
    Timo Glatter
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 5:237. 2009
    ..These results show that the presented analytical process will substantially advance throughput and reproducibility in future systematic AP-MS studies on human protein complexes...
  70. doi request reprint Direct identification of ligand-receptor interactions on living cells and tissues
    Andreas P Frei
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
    Nat Biotechnol 30:997-1001. 2012
    ..This technology enables the identification of receptors for many types of ligands under near-physiological conditions and without the need for genetic manipulations...
  71. doi request reprint The protein interaction landscape of the human CMGC kinase group
    Markku Varjosalo
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    Cell Rep 3:1306-20. 2013
    ....
  72. doi request reprint Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome
    Basil J Greber
    Department of Biology, Institute of Molecular Biology and Biophysics, Otto Stern Weg 5, ETH Zurich, CH 8093 Zurich, Switzerland
    Science 348:303-8. 2015
    ..Furthermore, the structure contributes to a mechanistic understanding of aminoglycoside ototoxicity. ..
  73. doi request reprint Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis
    Olga T Schubert
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, CH 8093, Switzerland
    Cell Host Microbe 18:96-108. 2015
    ..Thus, global absolute protein measurements provide a quantitative description of microbial states, which can support the development of therapeutic interventions. ..
  74. pmc Mass spectrometric protein maps for biomarker discovery and clinical research
    Yansheng Liu
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Str 16, 8093 Zurich, Switzerland
    Expert Rev Mol Diagn 13:811-25. 2013
    ..Herein, we demonstrate that the application of the mass spectrometric reference maps and the acquisition of personalized SWATH maps hold a particular promise for accelerating the current process of biomarker discovery. ..
  75. ncbi request reprint Reproducible isolation of distinct, overlapping segments of the phosphoproteome
    Bernd Bodenmiller
    Institute for Molecular Systems Biology, Swiss Federal Institute of Technology, ETH Honggerberg, Wolfgang Pauli Str 16, HPT, CH 8093 Zurich, Switzerland
    Nat Methods 4:231-7. 2007
    ..The results suggest that the three methods detect different, partially overlapping segments of the phosphoproteome and that, at present, no single method is sufficient for a comprehensive phosphoproteome analysis...
  76. doi request reprint Genotype-phenotype relationships in light of a modular protein interaction landscape
    Matthias Gstaiger
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Biosyst 9:1064-7. 2013
    ..These efforts revealed a highly modular organization of the protein landscape. Here we discuss the challenges and implications emerging from a modular protein landscape for a better understanding of complex genotype-phenotype patterns...
  77. pmc Perspectives of targeted mass spectrometry for protein biomarker verification
    Ruth Hüttenhain
    Institute of Molecular Systems Biology, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Curr Opin Chem Biol 13:518-25. 2009
    ..These assays are stored in publicly accessible databases and have the potential to greatly impact the throughput of biomarker verification studies...
  78. doi request reprint Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions
    Paola Picotti
    Department of Biology, Institute of Biochemistry, ETH Zurich, Switzerland
    Nat Methods 9:555-66. 2012
    ..Here we describe how SRM is applied in proteomics, review recent advances, present selected applications and provide a perspective on the future of this powerful technology...
  79. doi request reprint Targeted proteome investigation via selected reaction monitoring mass spectrometry
    Alessio Maiolica
    Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
    J Proteomics 75:3495-513. 2012
    ..This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry...
  80. doi request reprint Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate
    H Alexander Ebhardt
    Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule ETH Zurich, Zurich, Switzerland
    Proteomics 12:1185-93. 2012
    ....
  81. doi request reprint Quantitative proteomics of microbes: Principles and applications to virulence
    Lars Malmström
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Proteomics 11:2947-56. 2011
    ..Here, we describe the most commonly used techniques and discuss their strengths and weaknesses and illustrate their respective performance for the identification of virulence factors in Streptococcus pyogenes...
  82. doi request reprint Systematic LC-MS analysis of labile post-translational modifications in complex mixtures
    Christine Carapito
    Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    J Proteome Res 8:2608-14. 2009
    ..The technique was applied to the analysis of O-GlcNAc peptides, a very complex mixture of N-linked glycopeptides, and a phosphotyrosine peptide...
  83. doi request reprint Proteome coverage prediction for integrated proteomics datasets
    Manfred Claassen
    Department of Computer Science, ETH Zurich, Zurich, Switzerland
    J Comput Biol 18:283-93. 2011
    ..interrogans dataset. We discuss the implications of our results for determining rational stop criteria and their influence on the design of efficient and reliable proteomics studies...
  84. doi request reprint Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines
    Thomas Bock
    Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
    J Proteome Res 11:4885-93. 2012
    ..The included Skyline Glioblastoma SRM assay library provides an elevated starting point for parallel testing of the abundance level of the detected glioblastoma surfaceome members in future drug perturbation experiments...
  85. doi request reprint Mass spectrometry-based proteomics for systems biology
    Eduard Sabidó
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Curr Opin Biotechnol 23:591-7. 2012
    ..Herein, we review recent contributions of MS to systems biology and discuss several examples that illustrate the importance of mass spectrometry to elucidate the components and interactions of molecular networks...
  86. pmc Proteome coverage prediction with infinite Markov models
    Manfred Claassen
    Department of Computer Science, Institute of Molecular Systems Biology, ETH Zurich, Competence Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
    Bioinformatics 25:i154-60. 2009
    ..Proteome coverage prediction is important to enhance the design of efficient proteomics studies. To date, there does not exist any method to reliably estimate the increase of proteome coverage at an early stage...
  87. doi request reprint Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry-based proteomics
    Bernd Bodenmiller
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Methods Enzymol 470:317-34. 2010
    ..We believe that the protocols and data processing tools described in this chapter will be a valuable resource for biologists interested in the analysis of protein phosphorylation-based signal transduction...
  88. doi request reprint Differential glucose repression in common yeast strains in response to HXK2 deletion
    Anne Kümmel
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    FEMS Yeast Res 10:322-32. 2010
    ....
  89. doi request reprint Directed mass spectrometry: towards hypothesis-driven proteomics
    Alexander Schmidt
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Str 16, 8093 Zurich, Switzerland
    Curr Opin Chem Biol 13:510-7. 2009
    ..In this manuscript we summarize recent technical advances in directed MS and discuss important applications to quantitative proteomics...
  90. ncbi request reprint The implications of proteolytic background for shotgun proteomics
    Paola Picotti
    Institute of Molecular Systems Biology, ETH Zurich, CH 8093, Zurich, Switzerland
    Mol Cell Proteomics 6:1589-98. 2007
    ....
  91. pmc The molecular architecture of the eukaryotic chaperonin TRiC/CCT
    Alexander Leitner
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    Structure 20:814-25. 2012
    ..The structure described here explains all available crosslink experiments, provides a rationale for previously unexplained structural features, and reveals a surprising asymmetry of charges within the chaperonin folding chamber...
  92. pmc Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes
    Sabine P Schrimpf
    Institute of Molecular Biology, University of Zurich, Zurich, Switzerland
    PLoS Biol 7:e48. 2009
    ....
  93. pmc The Drosophila FoxA ortholog Fork head regulates growth and gene expression downstream of Target of rapamycin
    Margret H Bülow
    Institute of Molecular Systems Biology, Swiss Federal Institute of Technology ETH Zurich, Zurich, Switzerland
    PLoS ONE 5:e15171. 2010
    ..In summary, our observations show that an alteration of FKH levels has an effect on cellular and organismal size, and that FKH function is required for the growth inhibition and target gene induction caused by low TOR signaling levels...
  94. doi request reprint Mass spectrometry-based proteomics and network biology
    Ariel Bensimon
    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH 8093, Switzerland
    Annu Rev Biochem 81:379-405. 2012
    ..We discuss future directions for MS-based proteomics within the network biology paradigm...