Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
By Ben C. Collins, C. Hunter, Yansheng Liu, B. Schilling, George A. Rosenberger, Samuel L. Bader, D. Chan, B. Gibson, A. Gingras, Jason M. Held and 15 more. Nature Communications, 2016
518 citations recorded by the source corpus.
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.
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/9c55acff92bfc3dfc5b12eddbb845c075896d866
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In Molecular Biology
Citations in the corpus
- Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial (2018, unknown): “An inter-laboratory evaluation study recently showed that an organism-scale spectral library could effectively be used to analyse SWATH-MS data generated from 11 different laboratories worldwide (Collins et al , 2017).”
- A proteomic atlas of senescence-associated secretomes for aging biomarker development (2019, methodology): “519 All samples were analyzed by data-independent acquisitions (DIA), specifically using 520 variable window DIA acquisitions [71].”