RT Journal Article
SR Electronic
T1 Scanning SWATH acquisition enables high-throughput proteomics with chromatographic gradients as fast as 30 seconds
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 656793
DO 10.1101/656793
A1 Christoph B. Messner
A1 Vadim Demichev
A1 Nic Bloomfield
A1 Matthew White
A1 Marco Kreidl
A1 Gordana Ivosev
A1 Fras Wasim
A1 Aleksej Zelezniak
A1 Kathryn S. Lilley
A1 Stephen Tate
A1 Markus Ralser
YR 2020
UL http://biorxiv.org/content/early/2020/07/15/656793.abstract
AB Bridging genotype to phenotype, the proteome has increasingly become of major importance to generate large, longitudinal sample series for data-driven biology and personalized medicine. Major improvements in laboratory automation, chromatography and software have increased the scale and precision of proteomics. So far missing are however mass spectrometric acquisition techniques that could deal with very fast chromatographic gradients. Here we present scanning SWATH, a data-independent acquisition (DIA) method, in which the DIA-typical stepwise windowed acquisition is replaced by a continuous movement of the precursor isolation window. Scanning SWATH accelerates the duty cycles to a few hundreds of milliseconds, and enables precursor mass assignment to the MS2 fragment traces for improving true positive precursor identification in fast proteome experiments. In combination with 800 µL/min high-flow chromatography, we report the quantification of 270 precursors per second, increasing the precursor identifications by 70% or more compared to previous methods. Scanning SWATH quantified 1,410 Human protein groups in conjunction with chromatographic gradients as fast as 30 seconds, 2,250 with 60-second gradients, and 4,586 in conjunction with 5-minute gradients. At high quantitative precision, our method hence increases the proteomic throughput to hundreds of samples per day per mass spectrometer. Scanning SWATH hence enables a broad range of new proteomic applications that depend on large numbers of cheap yet quantification precise proteomes.Competing Interest StatementN.B, G.I., F.W and S.T. are employees of SCIEX