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

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 acqu...

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Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5566333/
https://www.ncbi.nlm.nih.gov/pubmed/28827567
http://dx.doi.org/10.1038/s41467-017-00249-5
Descripción
Sumario: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.