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ScanningSWATH enables ultra-fast proteomics using high-flow chromatography and minute-scale gradients

Christoph Messner, Vadim Demichev, Nic Bloomfield, Gordana Ivosev, Fras Wasim, Aleksej Zelezniak, Kathryn Lilley, Steven Tate, View ORCID ProfileMarkus Ralser
doi: https://doi.org/10.1101/656793
Christoph Messner
1The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, United Kingdom
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Vadim Demichev
1The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, United Kingdom
2Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Nic Bloomfield
3SCIEX, Toronto, Canada
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Gordana Ivosev
3SCIEX, Toronto, Canada
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Fras Wasim
3SCIEX, Toronto, Canada
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Aleksej Zelezniak
1The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, United Kingdom
4Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Kathryn Lilley
2Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Steven Tate
3SCIEX, Toronto, Canada
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Markus Ralser
1The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, United Kingdom
5Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
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  • ORCID record for Markus Ralser
  • For correspondence: Markus.Ralser@crick.ac.uk
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Abstract

Rapidly emerging applications in data-driven biology and personalised medicine call for the development of fast and reliable proteomic methods. However, the use of fast chromatographic gradients is limited by the mass spectrometers’ sampling rate and signal interferences. Here we present scanningSWATH, a data-independent acquisition method, in which the DIA-typical stepwise windowed acquisition is replaced by continuous scanning with the first quadrupole. ScanningSWATH enables ultra-fast duty cycles as well as to assign precursor masses to the MS2 fragment traces. Furthermore, we have implemented the support for scanningSWATH in DIA-NN, a fully-automated software suite designed to deconvolute fast DIA experiments, which corrects for signal interferences. We show that the combination of scanningSWATH and DIA-NN enables the efficient application of high-flow liquid chromatography (800 μL/min flow rate) to proteomics. High-flow scanningSWATH increases proteomic sample throughput to the minute-scale, while the use of high-flow chromatography hardware improves reliability and robustness. Benchmarking on yeast and human cell lysates, we demonstrate that the proteomic depth achieved with five-minute high-flow scanningSWATH gradients is comparable to that obtained with several times slower nano- and microflow chromatographic gradients, even if compared to most recent studies that used microflow-SWATH or Evosep-DIA methods. The combination of scanningSWATH, advanced data processing, and industry-standard high-flow LC hardware paves a way for a new generation of cheaper and highly consistent proteomic methods. These allow the recording of hundreds of precise quantitative proteomes per day on a single instrument.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 31, 2019.
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ScanningSWATH enables ultra-fast proteomics using high-flow chromatography and minute-scale gradients
Christoph Messner, Vadim Demichev, Nic Bloomfield, Gordana Ivosev, Fras Wasim, Aleksej Zelezniak, Kathryn Lilley, Steven Tate, Markus Ralser
bioRxiv 656793; doi: https://doi.org/10.1101/656793
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ScanningSWATH enables ultra-fast proteomics using high-flow chromatography and minute-scale gradients
Christoph Messner, Vadim Demichev, Nic Bloomfield, Gordana Ivosev, Fras Wasim, Aleksej Zelezniak, Kathryn Lilley, Steven Tate, Markus Ralser
bioRxiv 656793; doi: https://doi.org/10.1101/656793

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