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Plant Methods. 2019 Apr 24;15:40. doi: 10.1186/s13007-019-0427-7. eCollection 2019.

Quantitative assay of targeted proteome in tomato trichome glandular cells using a large-scale selected reaction monitoring strategy.

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1Department of Bioresource Production Science, The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, 790-8566 Japan.
2Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan.
3Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, 739-8528 Japan.
4Advanced Research Support Center, Ehime University, Toon, 791-0295 Japan.
5Plant Biophysics/Biochemistry Research Laboratory, Faculty of Agriculture, Ehime University, Matsuyama, 790-8566 Japan.
6Division of Proteomics Research, Proteo-Science Center, Ehime University, Toon, 791-0295 Japan.



Glandular trichomes found in vascular plants are called natural cell factories because they synthesize and store secondary metabolites in glandular cells. To systematically understand the metabolic processes in glandular cells, it is indispensable to analyze cellular proteome dynamics. The conventional proteomics methods based on mass spectrometry have enabled large-scale protein analysis, but require a large number of trichome samples for in-depth analysis and are not suitable for rapid and sensitive quantification of targeted proteins.


Here, we present a high-throughput strategy for quantifying targeted proteins in specific trichome glandular cells, using selected reaction monitoring (SRM) assays. The SRM assay platform, targeting proteins in type VI trichome gland cells of tomato as a model system, demonstrated its effectiveness in quantifying multiple proteins from a limited amount of sample. The large-scale SRM assay uses a triple quadrupole mass spectrometer connected online to a nanoflow liquid chromatograph, which accurately measured the expression levels of 221 targeted proteins contained in the glandular cell sample recovered from 100 glandular trichomes within 120 min. Comparative quantitative proteomics using SRM assays of type VI trichome gland cells between different organs (leaves, green fruits, and calyx) revealed specific organ-enriched proteins.


We present a targeted proteomics approach using the established SRM assays which enables quantification of proteins of interest with minimum sampling effort. The remarkable success of the SRM assay and its simple experimental workflow will increase proteomics research in glandular trichomes.


AQUA peptide; Mass spectrometry; Plant defense mechanism; Protein quantification; Proteotypic peptide; QconCAT; Secondary metabolism; Selected reaction monitoring; Targeted proteomics; Tomato type VI glandular trichome

Conflict of interest statement

The authors declare that they have no competing interests.

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