TY - JOUR
T1 - Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS
AU - Bian, Yangyang
AU - Zheng, Runsheng
AU - Bayer, Florian P.
AU - Wong, Cassandra
AU - Chang, Yun Chien
AU - Meng, Chen
AU - Zolg, Daniel P.
AU - Reinecke, Maria
AU - Zecha, Jana
AU - Wiechmann, Svenja
AU - Heinzlmeir, Stephanie
AU - Scherr, Johannes
AU - Hemmer, Bernhard
AU - Baynham, Mike
AU - Gingras, Anne Claude
AU - Boychenko, Oleksandr
AU - Kuster, Bernhard
N1 - Publisher Copyright:
© 2020, The Author(s).
PY - 2020/12/1
Y1 - 2020/12/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85077685689&partnerID=8YFLogxK
U2 - 10.1038/s41467-019-13973-x
DO - 10.1038/s41467-019-13973-x
M3 - Article
C2 - 31919466
AN - SCOPUS:85077685689
SN - 2041-1723
VL - 11
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 157
ER -