Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
Collins, Ben C.
Hunter, Christie L.
Bader, Samuel L.
Chan, Daniel W.
Gibson, Bradford W.
Held, Jason M.
Molloy, Mark P.
Moritz, Robert L.
Thomas, Stefani N.
- Journal Article
Rights / licenseCreative Commons Attribution 4.0 International
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 Show more
Journal / seriesNature Communications
PublisherNature Publishing Group
Organisational unit03663 - Aebersold, Rudolf
02207 - Functional Genomics Center Zürich / Functional Genomics Center Zürich
166435 - MitoModules: Biomarkers in context (SNF)
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