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

Bian, Yangyang; Zheng, Runsheng; Bayer, Florian P.; Wong, Cassandra; Chang, Yun-Chien; Meng, Chen; Zolg, Daniel P.; Reinecke, Maria; Zecha, Jana; Wiechmann, Svenja; Heinzlmeir, Stephanie; Scherr, Johannes; Hemmer, Bernhard; Baynham, Mike; Gingras, Anne-Claude; Boychenko, Oleksandr und Kuster, Bernhard (2020): Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS. In: Nature Communications, Bd. 11, Nr. 1, 157

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 1x150 mm column shows excellent reproducibility of chromatographic retention time (<0.3% coefficient of variation, CV) and protein quantification (<7.5% CV) using data from >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.

• Dokumententyp: Zeitschriftenartikel
• Fakultät: Medizin > Munich Cluster for Systems Neurology (SyNergy)
• Themengebiete: 600 Technik, Medizin, angewandte Wissenschaften > 610 Medizin und Gesundheit
• Sprache: Englisch
• DFG: Gefördert durch die Deutsche Forschungsgemeinschaft (DFG) - 390857198