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Citation: LIU Zhiwei, ZHU Mingrui, ZHAI Linhui, TAN Minjia. Comparison of reliabilities of mass spectrometry-based label-free quantitation methods for histone post-translational modification analysis[J]. Chinese Journal of Chromatography, ;2016, 34(9): 825-830. doi: 10.3724/SP.J.1123.2016.04040 shu

Comparison of reliabilities of mass spectrometry-based label-free quantitation methods for histone post-translational modification analysis

LIU Zhiwei ^1,2, ,
ZHU Mingrui ^1,2 ,
ZHAI Linhui ^1,3 ,
TAN Minjia ^1,2

1.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China;
2.
University of Chinese Academy of Sciences, Beijing 100049, China;
3.
Shanghai Key Laboratory of Chemical Assessment and Sustainability, Shanghai 200092, China

Received Date: 28 April 2016

Fund Project: Foundation of Shanghai Science and Technology Commission (No. 14DZ2261100)

Histone post-translational modifications (PTMs) play critical roles in epigenetic regulations of cellular physiology. The rapid development of mass spectrometry based on proteomics makes it possible to systematically widely identify and quantify the dynamic changes of histone PTMs. There are three widely used label-free quantitation methods (spectra count, peak area and intensity) for mass spectrometry data analysis, but by which method is the most reliable one for histone PTM quantification has not been systematically investigated. To this goal, we quantified histone acetylome in stable isotope amino acid labeled SH-SY5Y cells by SAHA (a pan histone deacetylase inhibitor) treatment. By comparing the standard deviations (SDs) of quantitation results from the three methods, we showed that quantification based on peak area method is the most reliable one. Therefore, our study provided new insight for label-free histone mark analysis, especially for clinical and large-scale samples.
- histone post-translational modification,
- label-free quantitation,
- reliability
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