Objective To analyze plasma proteome in hepatitis B virus (HBV)related liver fibrosis patients using various surface-enhanced laser desorption/ionization (SELDI) chips and multi data analysis methods.
Methods Protein expressions of the plasma samples from healthy donates were compared by various kinds of SELDI chips. Three kinds of chips were chosen for further analysis of 110 samples divided into 4 groups (no fibrosis, low fibrosis, high fibrosis and cirrhosis). Besides t test analysis by Biomarker Wizard software provided by manufacture, PCA(principal component analysis), PLSR(palletized load system regression), SIMCA (soft modeling of class independent analogy)and clustering analysis were used for data analysis.
Results WCX2 (weak cation exchange), SAX2 (strong anion exchange), IMAC-N(i immobilized nickel chelate affinity chromatography) chips were used for protein profiling. Twenty differential protein peaks were found by t test. However, 105, 98 and 62 differential protein peaks were found by PCA, PLSR and SIMCA, respectively. The validity of these differential peaks was also analyzed. By clustering analysis, the protein expression patterns were divided into three kinds.
Conclusion The combination of multi SELDI chips and multi data analysis methods could enhance the ability of SELDI technology in disease biomarker discovery.
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