Arabidopsis Proteome and the Mass Spectral Assay Library

Arabidopsis is an important model organism and the first plant with its genome sequenced. Knowledge from studying this species has either direct or indirect applications to agriculture and human health. Quantitative proteomics by data-independent acquisition (SWATH/DIA-MS) was recently developed and considered as a high-throughput targetedlike approach for accurate proteome quantitation. In this approach, a high-quality and comprehensive library is a prerequisite. Here, we generated a protein 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 subsequently applied DIA-mass spectrometry using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups with 1,787 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.