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SWATHAtlas Publications



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A repository of assays to quantify 10,000 human proteins by SWATH-MS
George Rosenberger, Ching Chiek Koh, Tiannan Guo, Hannes Röst, Petri Kouvonen, Ben Collins, Moritz Heusel, Yansheng Liu, Etienne Caron, Anton Vychalkovskiy, Marco Faini, Olga Schubert, Pouya Faridi, H Alexander Ebhardt, Mariette Matondo, Henry Lam, Samuel Bader, David Campbell, Eric Deutsch, Robert Moritz, Stephen Tate, and Ruedi Aebersold
Nature Scientific Data (SDATA-14-00107A)

An open-source computational and data resource to analyze digital maps of immunopeptidomes
Etienne Caron, Lucia Espona, Daniel J Kowalewski, Heiko Schuster, Nicola Ternette, Adán Alpízar, Ralf B Schittenhelm, Sri H Ramarathinam, Cecilia S Lindestam Arlehamn, Ching Chiek Koh, Ludovic C Gillet, Armin Rabsteyn, Pedro Navarro, Sangtae Kim, Henry Lam, Theo Sturm, Miguel Marcilla, Alessandro Sette, David S Campbell, Eric W Deutsch, Robert L Moritz, Anthony W Purcell, Hans-Georg Rammensee, Stefan Stevanovic, Ruedi Aebersold
eLife Sciences

Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis
Olga T. Schubert, Christina Ludwig, Maria Kogadeeva, Michael Zimmermann, George Rosenberger, Martin Gengenbacher, Ludovic C. Gillet, Ben C. Collins, Hannes L. Röst, Stefan H.E. Kaufmann, Uwe Sauer, Ruedi Aebersold
Cell Host & Microbe - 8 July 2015 (Vol. 18, Issue 1, pp. 96-108)

Systems-level proteomics of two ubiquitous leaf commensals reveals complementary adaptive traits for phyllosphere colonization
Müller, DB, Schubert, OT, Röst HL, Aebersold R, and Vorholt, J
Molecular & Cellular Proteomics 15:10.1074/mcp.M116.058164, 1-14, 2016 (PMID: 27457762)

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis
Paola Picotti, Mathieu Clément-Ziza, Henry Lam, David S. Campbell, Alexander Schmidt, Eric W. Deutsch, Hannes Röst, Zhi Sun, Oliver Rinner, Lukas Reiter, Qin Shen, Jacob J. Michaelson, Andreas Frei, Simon Alberti, Ulrike Kusebauch, Bernd Wollscheid, Robert L. Moritz, Andreas Beyer & Ruedi Aebersold
Nature 494, 266-270 (14 February 2013)

Co-first authors

SWATH-related publications

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.
Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R.
Mol Cell Proteomics. 2012 Jun;11(6):O111.016717. Epub 2012 Jan 18.

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 10;32(3):219-23. doi: 10.1038/nbt.2841.


General related publications

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
Eric W Deutsch, Henry Lam & Ruedi Aebersold
EMBO reports 9, 5, 429–434 (2008)

Mass spectrometry and protein analysis.
Domon B, Aebersold R.
Science. 2006 Apr 14;312(5771):212-7

Integration of Peptide Sequences Obtained by High-Throughput Mass Spectrometry with the Human Genome
Frank Desiere, Eric W. Deutsch, Alexey I. Nesvizhskii, Parag Mallick, Nichole King, Jimmy K. Eng, Alan Aderem, Rose Boyle, Erich Brunner, Samuel Donohoe, Nelson Fausto, Ernst Hafen, Lee Hood, Michael G. Katze, Kathleen Kennedy, Floyd Kregenow, Hookeun Lee, Biaoyang Lin, Dan Martin, Jeff Ranish, David J. Rawlings, Lawrence E. Samelson, Yuzuru Shiio, Julian Watts, Bernd Wollscheid, Michael E. Wright, Wei Yan, Lihong Yang, Eugene Yi, Hui Zhang and Ruedi Aebersold
Genome Biology 2004, 6:R9

The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis
Olga T. Schubert, Jeppe Mouritsen, Christina Ludwig, Hannes L. Röst, George Rosenberger, Patrick K. Arthur, Manfred Claassen, David S. Campbell, Zhi Sun, Terry Farrah, Martin Gengenbacher, Alessio Maiolica, Stefan H.E. Kaufmann, Robert L. Moritz, Ruedi Aebersold
Cell Host & Microbe - 15 May 2013 (Vol. 13, Issue 5, pp. 602-612)







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