Application of quantitative PTM proteomics SILIA and AQUIP in plant hormone signaling

Guang Yu Guo, Yao Jun LI and Ning Li*

Division of Life Science, The Hong Kong University of Science and Technology, Clear water bay, Hong Kong SAR, China.
*Corresponding Author：Ning Li, 852-2358-7335; boningli@ust.hk

Abstract
Hundreds of protein post-translational modifications (PTM) have been discovered over years. These PTMs are known to play an important role in regulation of growth and development of an organism. As one of the most important PTMs, protein phosphorylation participates in regulating various cellular processes and biological functions. Mass spectrometry-based protein phosphosite identification has emerged as a high-throughput approach in discovery of phosphoproteins involved in regulation of cellular processes. The changes at these novel phosphosites can be accurately measured using a ¹⁵N-stable isotopic labeling in Arabidopsis (SILIA) quantitative proteomic approach. The unique characteristics of the SILIA-based quantitative phosphoproteomics approach are its versatile usages, simplicity in PTM peptide quantitation and the preservation of native PTM status on protein during peptide preparation. Evolved from SILIA is the absolute quantitation of isoforms of post-translationally modified proteins (AQUIP), which was developed by combining the advantages of AQUA and PSAQ with SILIA. Functional validation of phosphosite is performed using point-mutations at phosphosites. The combined use of SILIA and AQUIP provides a novel strategy for investigation of in vivo biological functions of phosphoproteins at a large scale and ultimately for deciphering the combinatorial code and networks of PTM during plant growth and development.

Keywords: SILIA, AQUIP, Arabidopsis, quantitative proteomics, stable isotope labeling, post-translational modification networks.