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

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.