Zheng R, Stejskal K, Pynn C, Mechtler K, Boychenko A. Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS.
J Proteome Res 2022;
21:2545-2551. [PMID:
36068014 PMCID:
PMC9552226 DOI:
10.1021/acs.jproteome.2c00270]
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Abstract
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This study demonstrates how the latest ultrahigh-performance
liquid
chromatography (UHPLC) technology can be combined with high-resolution
accurate-mass (HRAM) mass spectrometry (MS) and long columns packed
with fully porous particles to improve bottom-up proteomics analysis
with nanoflow liquid chromatography–mass spectrometry (nanoLC-MS)
methods. The increased back pressures from the UHPLC system enabled
the use of 75 μm I.D. × 75 cm columns packed with 2 μm
particles at a typical 300 nL/min flow rate as well as elevated and
reduced flow rates. The constant pressure pump operation at 1500 bar
reduced sample loading and column washing/equilibration stages and
overall overhead time, which maximizes MS utilization time. The versatility
of flow rate optimization to balance the sensitivity, throughput with
sample loading amount, and capability of using longer gradients contributes
to a greater number of peptide and protein identifications for single-shot
bottom-up proteomics experiments. The routine proteome profiling and
precise quantification of >7000 proteins with single-shot nanoLC-MS
analysis open possibilities for large-scale discovery studies with
a deep dive into the protein level alterations. Data are available
via ProteomeXchange with identifier PXD035665.
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