A systematic N-terminal peptide quantitative labeling strategy for differential proteomic analysis.
OBJECTIVE
The purpose of this study is to develop a new systematic strategy for differential proteomic analysis.


METHODS
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
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.
State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China.
Xin
X
Liu
Jiyang
J
Zhang
Zhaobin
Z
Zheng
Xing
X
Yang
Wei
W
Jia
Lei
L
Li
Yan
Y
Gong
Yun
Y
Cai
Yunping
Y
Zhu
Fuchu
F
He
Wantao
W
Ying
Xiaohong
X
Qian
D000107:Acetylation; D000818:Animals; D001798:Blood Proteins / Q000032:analysis*; D002556:Cerebrospinal Fluid Proteins / Q000032:analysis*; D020869:Gene Expression Profiling; D019791:Guanidine / Q000737:chemistry; D006801:Humans; D006816:Huntington Disease / Q000378:metabolism; D007553:Isotope Labeling; D013058:Mass Spectrometry / Q000379:methods; D009211:Myoglobin / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012984:Software
D001798:Blood Proteins; D002556:Cerebrospinal Fluid Proteins; D009211:Myoglobin; D010455:Peptides; D019791:Guanidine