Journal
NATURE COMMUNICATIONS
Volume 11, Issue 1, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41467-019-13973-x
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Funding
- Alexander von Humboldt Foundation
- Carl Friedrich von Siemens Foundation
- National Natural Science Foundation of China [81600046]
- Chinese Scholarship Council (CSC)
- German Science foundation [DFG-SFB1309]
- ProteomeTools project (BMBF) [031L0008A]
- German Excellence Initiative
- Canadian Institutes of Health Research Foundation Grant (CIHR) [FDN 143301]
- Government of Ontario
- Genome Canada
- Ontario Genomics [OGI-139]
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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.
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