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

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 (<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.

SUBMITTER: Bian Y 

PROVIDER: S-EPMC6952431 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature