Ultra-fast proteomics with Scanning SWATH

Christoph B Messner; Vadim Demichev; Nic Bloomfield; Jason S L Yu; Matthew White; Marco Kreidl; Anna-Sophia Egger; Anja Freiwald; Gordana Ivosev; Fras Wasim; Aleksej Zelezniak; Linda Jürgens; Norbert Suttorp; Leif Erik Sander; Florian Kurth; Kathryn S Lilley; Michael Mülleder; Stephen Tate; Markus Ralser

doi:10.1038/s41587-021-00860-4

Ultra-fast proteomics with Scanning SWATH

Standard

Ultra-fast proteomics with Scanning SWATH. / Messner, Christoph B; Demichev, Vadim; Bloomfield, Nic; Yu, Jason S L; White, Matthew; Kreidl, Marco; Egger, Anna-Sophia; Freiwald, Anja; Ivosev, Gordana; Wasim, Fras; Zelezniak, Aleksej; Jürgens, Linda; Suttorp, Norbert; Sander, Leif Erik; Kurth, Florian; Lilley, Kathryn S; Mülleder, Michael; Tate, Stephen; Ralser, Markus.

In: NAT BIOTECHNOL, Vol. 39, No. 7, 07.2021, p. 846-854.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Messner, CB, Demichev, V, Bloomfield, N, Yu, JSL, White, M, Kreidl, M, Egger, A-S, Freiwald, A, Ivosev, G, Wasim, F, Zelezniak, A, Jürgens, L, Suttorp, N, Sander, LE, Kurth, F, Lilley, KS, Mülleder, M, Tate, S & Ralser, M 2021, 'Ultra-fast proteomics with Scanning SWATH', NAT BIOTECHNOL, vol. 39, no. 7, pp. 846-854. https://doi.org/10.1038/s41587-021-00860-4

APA

Messner, C. B., Demichev, V., Bloomfield, N., Yu, J. S. L., White, M., Kreidl, M., Egger, A-S., Freiwald, A., Ivosev, G., Wasim, F., Zelezniak, A., Jürgens, L., Suttorp, N., Sander, L. E., Kurth, F., Lilley, K. S., Mülleder, M., Tate, S., & Ralser, M. (2021). Ultra-fast proteomics with Scanning SWATH. NAT BIOTECHNOL, 39(7), 846-854. https://doi.org/10.1038/s41587-021-00860-4

Vancouver

Messner CB, Demichev V, Bloomfield N, Yu JSL, White M, Kreidl M et al. Ultra-fast proteomics with Scanning SWATH. NAT BIOTECHNOL. 2021 Jul;39(7):846-854. https://doi.org/10.1038/s41587-021-00860-4

Bibtex

@article{139081bab80c4f5c920b3ee2e080fd78,

title = "Ultra-fast proteomics with Scanning SWATH",

abstract = "Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min-1) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.5-5-min chromatographic gradients. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening and plasma proteomics. Scanning SWATH proteomes capture the mode of action of fungistatic azoles and statins. Moreover, we confirm 43 and identify 11 new plasma proteome biomarkers of COVID-19 severity, advancing patient classification and biomarker discovery. Thus, our results demonstrate a substantial acceleration and increased depth in fast proteomic experiments that facilitate proteomic drug screens and clinical studies.",

keywords = "Arabidopsis/metabolism, Biomarkers/metabolism, COVID-19/blood, Cell Line, Humans, Peptides/analysis, Proteome/analysis, Proteomics/methods, Saccharomyces cerevisiae/metabolism, Saccharomyces cerevisiae Proteins/metabolism, Severity of Illness Index, Tandem Mass Spectrometry",

author = "Messner, {Christoph B} and Vadim Demichev and Nic Bloomfield and Yu, {Jason S L} and Matthew White and Marco Kreidl and Anna-Sophia Egger and Anja Freiwald and Gordana Ivosev and Fras Wasim and Aleksej Zelezniak and Linda J{\"u}rgens and Norbert Suttorp and Sander, {Leif Erik} and Florian Kurth and Lilley, {Kathryn S} and Michael M{\"u}lleder and Stephen Tate and Markus Ralser",

note = "{\textcopyright} 2021. The Author(s), under exclusive licence to Springer Nature America, Inc. part of Springer Nature.",

year = "2021",

month = jul,

doi = "10.1038/s41587-021-00860-4",

language = "English",

volume = "39",

pages = "846--854",

journal = "NAT BIOTECHNOL",

issn = "1087-0156",

publisher = "NATURE PUBLISHING GROUP",

number = "7",

}

RIS

TY - JOUR

T1 - Ultra-fast proteomics with Scanning SWATH

AU - Messner, Christoph B

AU - Demichev, Vadim

AU - Bloomfield, Nic

AU - Yu, Jason S L

AU - White, Matthew

AU - Kreidl, Marco

AU - Egger, Anna-Sophia

AU - Freiwald, Anja

AU - Ivosev, Gordana

AU - Wasim, Fras

AU - Zelezniak, Aleksej

AU - Jürgens, Linda

AU - Suttorp, Norbert

AU - Sander, Leif Erik

AU - Kurth, Florian

AU - Lilley, Kathryn S

AU - Mülleder, Michael

AU - Tate, Stephen

AU - Ralser, Markus

PY - 2021/7

Y1 - 2021/7

N2 - Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min-1) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.5-5-min chromatographic gradients. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening and plasma proteomics. Scanning SWATH proteomes capture the mode of action of fungistatic azoles and statins. Moreover, we confirm 43 and identify 11 new plasma proteome biomarkers of COVID-19 severity, advancing patient classification and biomarker discovery. Thus, our results demonstrate a substantial acceleration and increased depth in fast proteomic experiments that facilitate proteomic drug screens and clinical studies.

AB - Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min-1) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.5-5-min chromatographic gradients. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening and plasma proteomics. Scanning SWATH proteomes capture the mode of action of fungistatic azoles and statins. Moreover, we confirm 43 and identify 11 new plasma proteome biomarkers of COVID-19 severity, advancing patient classification and biomarker discovery. Thus, our results demonstrate a substantial acceleration and increased depth in fast proteomic experiments that facilitate proteomic drug screens and clinical studies.

KW - Arabidopsis/metabolism

KW - Biomarkers/metabolism

KW - COVID-19/blood

KW - Cell Line

KW - Humans

KW - Peptides/analysis

KW - Proteome/analysis

KW - Proteomics/methods

KW - Saccharomyces cerevisiae/metabolism

KW - Saccharomyces cerevisiae Proteins/metabolism

KW - Severity of Illness Index

KW - Tandem Mass Spectrometry

U2 - 10.1038/s41587-021-00860-4

DO - 10.1038/s41587-021-00860-4

M3 - SCORING: Journal article

C2 - 33767396

VL - 39

SP - 846

EP - 854

JO - NAT BIOTECHNOL

JF - NAT BIOTECHNOL

SN - 1087-0156

IS - 7

ER -