The Aebersold group focuses on both the development and the application of the SWATH MS technology. SWATH MS is a data independent acquisition (DIA) method which aims to complement traditional mass spectrometry-based proteomics techniques such as shotgun and SRM methods. In essence, it allows a complete and permanent recording of all fragment ions of the detectable peptide precursors present in a biological sample. It thus combines the advantages of shotgun (high throughput) with those of SRM (high reproducibility and consistency).

Using SWATH MS, the TB group aims at 1) identify naturally presented HLA class I and class II peptides encoded by Mtb genomes, 2) quantify proteomes of immune cells in response to Mtb infection, and 3) study diversity and mechanisms of drug resistance in Mtb clinical isolates

Read more about SWATH-MS

Read more about Microbial Proteomics

Group ETH

The Aebersold’s group. Annual scientific retreat (Tschamut, Switzerland, 2014).


Programme Leader: Prof. Ruedi Aebersold

Prof. Ruedi Aebersold is one of the pioneers in the field of proteomics. He is known for developing a series of methods that have found wide application in analytical protein chemistry and proteomics like a new class of reagents termed Isotope Coded Affinity Tag (ICAT) reagents used in quantitative mass spectrometry. Prof. Dr. Aebersold and his team of researchers use the protein profiles determined by this method to differentiate cells in different states, such as noncancerous versus cancerous cells, and to systematically study how cells respond to external stimuli. These “snapshot” profiles indicate which cells contain abnormal levels of certain proteins. This is expected to lead to new diagnostic markers for disease and to a more complete understanding of the biochemical processes that control and constitute cell physiology.
Prof. Aebersold serves on the Scientific Advisory Committees of numerous academic and private sector research organizations and is a member of several editorial boards in the fields of protein science, genomics, and proteomics.

TB Group


Dr Etienne Caron

Etienne was born in Canada. He did a PhD in Systems Immunology at the University of Montreal where he worked on the analysis of the cellular immunopeptidome. In 2013, he received a Marie Curie Intra-European Fellowship to carry out research in the group of Ruedi Aebersold in Switzerland. In 2015, he launched the Human Immuno-Peptidome Project (HIPP) initiative as part of the Human Proteome Project. His current research focuses on how cutting edge technologies in mass spectrometry can be applied to identify and quantify MHC-associated peptides. Research on this topic will have an impact on the development of vaccines against infectious diseases and cancers.

Dr Ben Collins

Ben is a native of Ireland where he studied chemistry and applied chemistry at the National University or Ireland, Galway, for his bachelors degree. After working as an analytical chemist in Schering-Plough, Ireland, he undertook an MSc in Molecular Medicine at Trinity College Dublin. Ben’s PhD entitled ‘Mass Spectrometry-Based Proteomics to Support Pre-Clinical Pharmaceutical Toxicology Evaluation’ was completed at University College Dublin in 2009 where he remained for 1 year as the Agilent Technologies Newman Fellow (postdoctoral) in Quantitative Proteomics. Ben moved to the Institute of Molecular Systems Biology at ETH Zurich in Autumn 2010 as postdoctoral researcher under the supervision of Prof. Ruedi Aebersold and Dr Matthias Gstaiger, where his current research focus is on the application of quantitative interaction proteomics in signaling and the development of SWATH mass spectrometry.

Amir Banaei-Esfahani

Amir was born in Iran where he obtained his master’s degree in biotechnology from the University of Tehran. For his master thesis, he worked with Prof. Elahe Elahi to consider how Glaucoma-related genes expression is regulated by ocular microRNAs. Amir was introduced to concept of systems biology when he joined School of Biological Sciences at IPM. He followed up this first experience by visiting the group of Prof. Jens Nielsen to be involved in a project entitled systems biology of secretory machinery. There, he was focused on GTPase superfamily especially Rab GTPase and also worked on the HCSD (the human cancer secretome database) project.

In the Aebersold group, he will be involved in the investigation of multidrug-resistant (MDR) strains of Mycobacterium tuberculosis (Mtb) in the context of a larger Swiss consortium namely TbX.


Dr Michal Bassani-Sternberg (CHUV, Lausanne, Switzerland)


Prof. Alessandro Sette (LaJolla, CA, USA)


Dr Witold E Wolski (FGCZ, Zürich, Switzerland)

ETH Zurich

Human Immuno-Peptidome Project (HIPP)
Biology and Disease-Driven Groups of the HPP (B/D – HPP)




Caron E, Kowalewski D, Koh CC, Sturm T, Shuster H, Aebersold R. Analysis of MHC immunopeptidomes using mass spectrometry. Mol. Cell. Proteomics. in revision.

Esterhuysea MM, Weiner J 3rd, Caron E, Loxton AG, Iannaccone M, Wagman C, Saikali P, Stanley K, Wolski WE, Mollenkopf HJ, Schick M, Aebersold R, Linhart H, Walzl G, Kaufmann SHE. Epigenetics and proteomics join transcriptomics in the quest for tuberculosis biomarkers. mBio. 2015, 6e01187-15.

Schubert OT, Ludwig C, Kogadeeva M, Zimmermann M, Rosenberger G, Gengenbacher M, Gillet LC, Collins BC, Röst HL, Kaufmann SH, Sauer U, Aebersold R. Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis. Cell Host Microbe. 2015 18:96-108.

Caron E, Espona L, Kowalewski D, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Lindestam CSA, Koh CC, Gillet L, Rabsteyn A, Sturm T, Navarro P, Kim S, Lam H, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R. An open-source computational and data resource to analyze quantitative digital maps of immunopeptidomes. eLife. 2015, 4:e07661.

Gubin MM, Zhang X, Schuster H, Caron E, Noguchi T, Ward JP, Ivanova Y, Hundal J, Arthur CD, Krebber WJ, Mulder GE, Vesely MD, Lam SSK, Korman AJ, Allison JP, Freeman GJ, Sharpe AH, Pearce EL, Aebersold R, Rammensee HG, Melief CJM, Mardis ER, Gillanders WE, Artyomov MN, Schreiber RD. Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens. Nature. 2014, 515:577-581.

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 tuberculosis. Cell Host Microbe. 2013 13:602-612.