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pmid:31757973
Arabidopsis proteome and the mass spectral assay library.
Huoming Zhang · Pei Liu · Tiannan Guo · Huayan Zhao · Dalila Bensaddek · Ruedi Aebersold · Liming Xiong
Scientific data · 2019 doi:10.1038/s41597-019-0294-0
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Complete file
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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. 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