RT Journal Article
SR Electronic
T1 Arabidopsis Proteome and the Mass Spectral Assay Library
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 665547
DO 10.1101/665547
A1 Huoming Zhang
A1 Pei Liu
A1 Tiannan Guo
A1 Huayan Zhao
A1 Dalila Bensaddek
A1 Reudi Aebersold
A1 Liming Xiong
YR 2019
UL http://biorxiv.org/content/early/2019/06/11/665547.abstract
AB Arabidopsis is an important model organism and the first plant with its genome completely sequenced. Much knowledge from studying this species has either direct or indirect applications to agriculture and human health. Quantitative proteomics based on data-independent acquisition (SWATH/DIA-MS) that was recently developed and considered as a high-throughput targeted-like approach for accurate proteome quantitation is an ideal tool for studying proteome dynamics. In this approach, a high quality and comprehensive library is a prerequisite. Here, we presented an Arabidopsis library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups represent ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We subsequently applied DIA-mass spectrometry using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8793 protein groups with 1787 of them being differentially expressed which includes 65 proteins known to respond to abscisic acid stress. Mass spectrometry data are available via ProteomeXchange with identifier PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses. View this table: