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Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

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Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. / Collins, Ben C; Hunter, Christie L; Liu, Yansheng; Schilling, Birgit; Rosenberger, George; Bader, Samuel L; Chan, Daniel W; Gibson, Bradford W; Gingras, Anne-Claude; Held, Jason M; Hirayama-Kurogi, Mio; Hou, Guixue; Krisp, Christoph; Larsen, Brett; Lin, Liang; Liu, Siqi; Molloy, Mark P; Moritz, Robert L; Ohtsuki, Sumio; Schlapbach, Ralph; Selevsek, Nathalie; Thomas, Stefani N; Tzeng, Shin-Cheng; Zhang, Hui; Aebersold, Ruedi.

in: NAT COMMUN, Jahrgang 8, Nr. 1, 21.08.2017, S. 291.

Publikationen: SCORING: Beitrag in Fachzeitschrift/Zeitung › SCORING: Zeitschriftenaufsatz › Forschung › Begutachtung

Harvard

Collins, BC, Hunter, CL, Liu, Y, Schilling, B, Rosenberger, G, Bader, SL, Chan, DW, Gibson, BW, Gingras, A-C, Held, JM, Hirayama-Kurogi, M, Hou, G, Krisp, C, Larsen, B, Lin, L, Liu, S, Molloy, MP, Moritz, RL, Ohtsuki, S, Schlapbach, R, Selevsek, N, Thomas, SN, Tzeng, S-C, Zhang, H & Aebersold, R 2017, 'Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry', NAT COMMUN, Jg. 8, Nr. 1, S. 291. https://doi.org/10.1038/s41467-017-00249-5

APA

Collins, B. C., Hunter, C. L., Liu, Y., Schilling, B., Rosenberger, G., Bader, S. L., Chan, D. W., Gibson, B. W., Gingras, A-C., Held, J. M., Hirayama-Kurogi, M., Hou, G., Krisp, C., Larsen, B., Lin, L., Liu, S., Molloy, M. P., Moritz, R. L., Ohtsuki, S., ... Aebersold, R. (2017). Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. NAT COMMUN, 8(1), 291. https://doi.org/10.1038/s41467-017-00249-5

Vancouver

Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL et al. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. NAT COMMUN. 2017 Aug 21;8(1):291. https://doi.org/10.1038/s41467-017-00249-5

Bibtex

@article{f204e44f75b8464aaf152658e42c527b,
title = "Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry",
abstract = "Quantitative proteomics employing mass spectrometry is an indispensable tool in life science research. Targeted proteomics has emerged as a powerful approach for reproducible quantification but is limited in the number of proteins quantified. SWATH-mass spectrometry consists of data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics (accuracy, sensitivity, and selectivity) of targeted proteomics at large scale. While previous SWATH-mass spectrometry studies have shown high intra-lab reproducibility, this has not been evaluated between labs. In this multi-laboratory evaluation study including 11 sites worldwide, we demonstrate that using SWATH-mass spectrometry data acquisition we can consistently detect and reproducibly quantify >4000 proteins from HEK293 cells. Using synthetic peptide dilution series, we show that the sensitivity, dynamic range and reproducibility established with SWATH-mass spectrometry are uniformly achieved. This study demonstrates that the acquisition of reproducible quantitative proteomics data by multiple labs is achievable, and broadly serves to increase confidence in SWATH-mass spectrometry data acquisition as a reproducible method for large-scale protein quantification.SWATH-mass spectrometry consists of a data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics on the scale of thousands of proteins. Here, using data generated by eleven groups worldwide, the authors show that SWATH-MS is capable of generating highly reproducible data across different laboratories.",
keywords = "HEK293 Cells, Humans, Laboratories, Laboratory Proficiency Testing, Mass Spectrometry, Proteome, Proteomics, Reproducibility of Results, Journal Article, Multicenter Study, Research Support, Non-U.S. Gov't",
author = "Collins, {Ben C} and Hunter, {Christie L} and Yansheng Liu and Birgit Schilling and George Rosenberger and Bader, {Samuel L} and Chan, {Daniel W} and Gibson, {Bradford W} and Anne-Claude Gingras and Held, {Jason M} and Mio Hirayama-Kurogi and Guixue Hou and Christoph Krisp and Brett Larsen and Liang Lin and Siqi Liu and Molloy, {Mark P} and Moritz, {Robert L} and Sumio Ohtsuki and Ralph Schlapbach and Nathalie Selevsek and Thomas, {Stefani N} and Shin-Cheng Tzeng and Hui Zhang and Ruedi Aebersold",
year = "2017",
month = aug,
day = "21",
doi = "10.1038/s41467-017-00249-5",
language = "English",
volume = "8",
pages = "291",
journal = "NAT COMMUN",
issn = "2041-1723",
publisher = "NATURE PUBLISHING GROUP",
number = "1",

}

RIS

TY - JOUR

T1 - Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

AU - Collins, Ben C

AU - Hunter, Christie L

AU - Liu, Yansheng

AU - Schilling, Birgit

AU - Rosenberger, George

AU - Bader, Samuel L

AU - Chan, Daniel W

AU - Gibson, Bradford W

AU - Gingras, Anne-Claude

AU - Held, Jason M

AU - Hirayama-Kurogi, Mio

AU - Hou, Guixue

AU - Krisp, Christoph

AU - Larsen, Brett

AU - Lin, Liang

AU - Liu, Siqi

AU - Molloy, Mark P

AU - Moritz, Robert L

AU - Ohtsuki, Sumio

AU - Schlapbach, Ralph

AU - Selevsek, Nathalie

AU - Thomas, Stefani N

AU - Tzeng, Shin-Cheng

AU - Zhang, Hui

AU - Aebersold, Ruedi

PY - 2017/8/21

Y1 - 2017/8/21

N2 - Quantitative proteomics employing mass spectrometry is an indispensable tool in life science research. Targeted proteomics has emerged as a powerful approach for reproducible quantification but is limited in the number of proteins quantified. SWATH-mass spectrometry consists of data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics (accuracy, sensitivity, and selectivity) of targeted proteomics at large scale. While previous SWATH-mass spectrometry studies have shown high intra-lab reproducibility, this has not been evaluated between labs. In this multi-laboratory evaluation study including 11 sites worldwide, we demonstrate that using SWATH-mass spectrometry data acquisition we can consistently detect and reproducibly quantify >4000 proteins from HEK293 cells. Using synthetic peptide dilution series, we show that the sensitivity, dynamic range and reproducibility established with SWATH-mass spectrometry are uniformly achieved. This study demonstrates that the acquisition of reproducible quantitative proteomics data by multiple labs is achievable, and broadly serves to increase confidence in SWATH-mass spectrometry data acquisition as a reproducible method for large-scale protein quantification.SWATH-mass spectrometry consists of a data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics on the scale of thousands of proteins. Here, using data generated by eleven groups worldwide, the authors show that SWATH-MS is capable of generating highly reproducible data across different laboratories.

AB - Quantitative proteomics employing mass spectrometry is an indispensable tool in life science research. Targeted proteomics has emerged as a powerful approach for reproducible quantification but is limited in the number of proteins quantified. SWATH-mass spectrometry consists of data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics (accuracy, sensitivity, and selectivity) of targeted proteomics at large scale. While previous SWATH-mass spectrometry studies have shown high intra-lab reproducibility, this has not been evaluated between labs. In this multi-laboratory evaluation study including 11 sites worldwide, we demonstrate that using SWATH-mass spectrometry data acquisition we can consistently detect and reproducibly quantify >4000 proteins from HEK293 cells. Using synthetic peptide dilution series, we show that the sensitivity, dynamic range and reproducibility established with SWATH-mass spectrometry are uniformly achieved. This study demonstrates that the acquisition of reproducible quantitative proteomics data by multiple labs is achievable, and broadly serves to increase confidence in SWATH-mass spectrometry data acquisition as a reproducible method for large-scale protein quantification.SWATH-mass spectrometry consists of a data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics on the scale of thousands of proteins. Here, using data generated by eleven groups worldwide, the authors show that SWATH-MS is capable of generating highly reproducible data across different laboratories.

KW - HEK293 Cells

KW - Humans

KW - Laboratories

KW - Laboratory Proficiency Testing

KW - Mass Spectrometry

KW - Proteome

KW - Proteomics

KW - Reproducibility of Results

KW - Journal Article

KW - Multicenter Study

KW - Research Support, Non-U.S. Gov't

U2 - 10.1038/s41467-017-00249-5

DO - 10.1038/s41467-017-00249-5

M3 - SCORING: Journal article

C2 - 28827567

VL - 8

SP - 291

JO - NAT COMMUN

JF - NAT COMMUN

SN - 2041-1723

IS - 1

ER -