A1: When doing proteome profiling, there are two methods for protein fractionation such as SDS-PAGE and strong cation exchange (SCX), both of which are usual methods in our company.
These two methods have their own advantage and shortage. For fractionating by using SDS- PAGE, protein with lower solubility such as hydrophobic protein could be dissolved and fractionated well, while protein with extremely small or large molecular weight could be lost. When using SCX, the losing of protein with extreme molecular weight could be avoided. However the protein with lower solubility could be lost.
Qing, Dongjin, Yang, Zhu, Li, Mingzhe, Wong, Wai Shing, Guo, Guangyu, Liu, Shichang, Guo, Hongwei, Ning Li* (2016) Quantitative and Functional Phosphoproteomic Analysis Reveals that Ethylene Regulates Water Transport via the C-terminal Phosphorylation of Aquaporin PIP2;1 in Arabidopsis. Mol Plant. 9, 158–174.
Yang, Zhu and Li, Ning (2015) Absolute quantitation of protein posttranslational modification isoform. Methods Mol Biol 1306:105-19. doi: 10.1007/978-1-4939-2648-0_8
Qin Hu, Guangyu Guo, Zhu Yang, Yaojun Li, Yiji Xia and Ning Li* (2014) Stable Isotope Metabolic Labeling-Based Quantitative Thiol Redox Proteomic Analysis of Hydrogen Peroxide-treated Arabidopsis plant. Journal of Proteomics & Bioinformatics. 7: 121-133.
Zhu Yang, Guangyu Guo, Manyu Zhang, Claire Y. Liu, Qin Hu, Henry Lam,Han Cheng, Yu Xue, Jiayang Li, and Ning Li * (2013) Stable Isotope Metabolic Labeling-Based Quantitative Phosphoproteomic Analysis of Arabidopsis Mutants Reveals Ethylene-Regulated Time-Dependent Phosphoproteins and Putative Substrates of CONSTITUTIVE TRIPLE RESPONSE 1 Kinase. Mol Cell Proteomics. 12, 3559-3582.
Lin Zhu, Dandan Liu, Yaojun Li, and Ning Li* (2013) Functional Phosphoproteomic Analysis Reveals That a Serine-62-Phosphorylated Isoform of Ethylene Response Factor110 Is Involved in Arabidopsis Bolting. Plant Physiol. 161: 904-917.
Zhu, Lin and Li, Ning*. (2013) Quantitation, networking and function of protein phosphorylation in plant cell Frontiers in plant proteomics. 3, 302. doi: 10.3389/ fpls.2012.00302
Li Y, Shu Y, Peng C, Zhu L, Guo G, Li, Ning* (2012) AQUIP: Absolute Quantitation of Isoforms of Post-translationally modified proteins in transgenic organism. Mol Cell Proteomics. 2012 11: 272-285.
Li, Ning (2012) Quantitative Measurement of Phosphopeptides and Proteins via Stable Isotope Labeling in Arabidopsis and Functional Phosphoproteomic Strategies. Methods Mol Biol., 2012. v. 876, 2012, p. 17-32.
Guo GY and Ning Li* (2011) Relative and Accurate Measurement of Protein Abundance in (15)N Stable Isotope Labeling in Arabidopsis (SILIA). Phytochemistry. 72, 1028-1039.
Li, H, Wong WS, Zhu, L, Guo, HW, Ecker, J and Ning LI* (2009) Phosphoproteomics analysis of ethylene-regulated protein phosphorylation in etiolated seedlings of Arabidopsis mutant ein2 using 2-D-separations coupled with a hybrid Q-TOF mass spectrometry. Proteomics. 9, 1646-1661.
Mehta, R A, Cassol, T, Li, Ning, Ali,N, Handa, AK, and Mattoo, AK (2002) Engineered polyamine accumulation in tomato enhances phytonutrient content, juice quality and vine life. Nature Biotechnology. 20, 613-618.