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Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage

Florian Meier, Andreas-David Brunner, Max Frank, Annie Ha, Isabell Bludau, Eugenia Voytik, Stephanie Kaspar-Schoenefeld, Markus Lubeck, Oliver Raether, Ruedi Aebersold, Ben C. Collins, Hannes L. Röst, Matthias Mann
doi: https://doi.org/10.1101/656207
Florian Meier
1Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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Andreas-David Brunner
1Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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Max Frank
2Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
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Annie Ha
2Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
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Isabell Bludau
1Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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Eugenia Voytik
1Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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Stephanie Kaspar-Schoenefeld
3Bruker Daltonik GmbH, Bremen, Germany
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Markus Lubeck
3Bruker Daltonik GmbH, Bremen, Germany
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Oliver Raether
3Bruker Daltonik GmbH, Bremen, Germany
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Ruedi Aebersold
4Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
5Faculty of Science, University of Zurich, Zurich, Switzerland
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Ben C. Collins
4Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
6School of Biological Sciences, Queen’s University of Belfast, UK
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  • For correspondence: ben.collins@qub.ac.uk hannes.rost@utoronto.ca mmann@biochem.mpg.de
Hannes L. Röst
2Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
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  • For correspondence: ben.collins@qub.ac.uk hannes.rost@utoronto.ca mmann@biochem.mpg.de
Matthias Mann
1Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
7NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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  • For correspondence: ben.collins@qub.ac.uk hannes.rost@utoronto.ca mmann@biochem.mpg.de
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ABSTRACT

Data independent acquisition (DIA) modes isolate and concurrently fragment populations of different precursors by cycling through segments of a predefined precursor m/z range. Although these selection windows collectively cover the entire m/z range, overall only a few percent of all incoming ions are sampled. Making use of the correlation of molecular weight and ion mobility in a trapped ion mobility device (timsTOF Pro), we here devise a novel scan mode that samples up to 100% of the peptide precursor ion current. We extend an established targeted data extraction workflow by including the ion mobility dimension for both signal extraction and scoring, thereby increasing the specificity for precursor identification. Data acquired from whole proteome digests and mixed organism samples demonstrate deep proteome coverage and a very high degree of reproducibility as well as quantitative accuracy, even from 10 ng sample amounts.

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Posted March 11, 2020.
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Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage
Florian Meier, Andreas-David Brunner, Max Frank, Annie Ha, Isabell Bludau, Eugenia Voytik, Stephanie Kaspar-Schoenefeld, Markus Lubeck, Oliver Raether, Ruedi Aebersold, Ben C. Collins, Hannes L. Röst, Matthias Mann
bioRxiv 656207; doi: https://doi.org/10.1101/656207
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Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage
Florian Meier, Andreas-David Brunner, Max Frank, Annie Ha, Isabell Bludau, Eugenia Voytik, Stephanie Kaspar-Schoenefeld, Markus Lubeck, Oliver Raether, Ruedi Aebersold, Ben C. Collins, Hannes L. Röst, Matthias Mann
bioRxiv 656207; doi: https://doi.org/10.1101/656207

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