Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS

Yangyang Bian, Runsheng Zheng, Florian P. Bayer, Cassandra Wong, Yun-Chien Chang, Chen Meng, Daniel P. Zolg, Maria Reinecke, Jana Zecha, Svenja Wiechmann, Stephanie Heinzlmeir, Johannes Scherr, Bernhard Hemmer, Mike Baynham, Anne-Claude Gingras, Oleksandr Boychenko and Bernhard Kuster ()
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Yangyang Bian: Technical University of Munich
Runsheng Zheng: Technical University of Munich
Florian P. Bayer: Technical University of Munich
Cassandra Wong: Sinai Health System
Yun-Chien Chang: Technical University of Munich
Chen Meng: Technical University of Munich
Daniel P. Zolg: Technical University of Munich
Maria Reinecke: Technical University of Munich
Jana Zecha: Technical University of Munich
Svenja Wiechmann: Technical University of Munich
Stephanie Heinzlmeir: Technical University of Munich
Johannes Scherr: Technical University of Munich
Bernhard Hemmer: Technical University of Munich
Mike Baynham: Thermo Fisher Scientific
Anne-Claude Gingras: Sinai Health System
Oleksandr Boychenko: Thermo Fisher Scientific
Bernhard Kuster: Technical University of Munich

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: Abstract Nano-flow liquid chromatography tandem mass spectrometry (nano-flow LC–MS/MS) is the mainstay in proteome research because of its excellent sensitivity but often comes at the expense of robustness. Here we show that micro-flow LC–MS/MS using a 1 × 150 mm column shows excellent reproducibility of chromatographic retention time ( 2000 samples of human cell lines, tissues and body fluids. Deep proteome analysis identifies >9000 proteins and >120,000 peptides in 16 h and sample multiplexing using tandem mass tags increases throughput to 11 proteomes in 16 h. The system identifies >30,000 phosphopeptides in 12 h and protein-protein or protein-drug interaction experiments can be analyzed in 20 min per sample. We show that the same column can be used to analyze >7500 samples without apparent loss of performance. This study demonstrates that micro-flow LC–MS/MS is suitable for a broad range of proteomic applications.

Date: 2020
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DOI: 10.1038/s41467-019-13973-x

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