Arabidopsis
is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of
Arabidopsis
and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on
Arabidopsis
. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.
Measurement(s)
Proteome
Technology Type(s)
mass spectrometry assay • computational modeling technique
Sample Characteristic - Organism
Arabidopsis thaliana
Machine-accessible metadata file describing the reported data:
https://doi.org/10.6084/m9.figshare.9959036...

Arabidopsis proteome and the mass spectral assay library

10.1038/s41597-019-0294-0