A systematic N-terminal peptide quantitative labeling strategy for differential proteomic analysis.

Liu, Xin; Zhang, Jiyang; Zheng, Zhaobin; Yang, Xing; Jia, Wei; Li, Lei; Gong, Yan; Cai, Yun; Zhu, Yunping; He, Fuchu; Ying, Wantao; Qian, Xiaohong

PURPOSE The purpose of this study is to develop a new systematic strategy for differential proteomic analysis. EXPERIMENTAL DESIGN The new systematic strategy was developed by coupling the stable isotope-coded N-terminal acetyl labeling for guanidinated peptides with LTQ-FT MS for accurate data acquisition, and an in-house graphic user interface program called "MS-based acetyl quantification" for automatic data processing. RESULTS The standard peptide mixture test showed that this method is easy and highly effective, with a linear dynamic range from 0.1 to 10 (R(2) value >0.999 and slope error <5%), down to 25 fmol. Moreover, the range of quantitative ratios differing from the target value of 1.0 was statistically determined to be (0.6527, 1.5350) for the 99% confidence level in a fraction of plasma samples. The practicability of this method was further demonstrated in a pilot study on the differential proteomic analysis of cerebrospinal fluid, with the uncovering of 33 dysregulated proteins from different development stages. CONCLUSIONS AND CLINICAL RELEVANCE The outcome of the differential proteomic analysis of plasma protein and cerebrospinal fluid confirmed the whole strategy as a promising alternative for exploration of potential biomarker in complex clinical or biological samples.