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Background Hepatocellular carcinoma tends to present at a late clinical stage with poor prognosis.Therefore, it is urgent to explore and develop a simple, rapid diagnostic method, which has high sensitivity and specificity for hepatocellular carcinoma at an early stage.In this study, the serum proteins in patients with hepatocellular carcinoma or liver cirrhosis and in normal controls were analysed.Surface enhanced laser desorption/ionization time-of-flight mass (SELDI-TOF-MS) spectrometry was used to fingerprint serum protein using the protein chip technique and explore the value of the fingerprint, coupled with artificial neural network, to diagnose hepatocellular carcinoma.Methods Of the 106 serum samples obtained, 52 were from patients with hepatocellular carcinoma, 22 from patients with liver cirrhosis and 32 from healthy volunteers.The samples were randomly assigned into a training group (n=70, 35 patients with hepatocellular carcinoma, 14 with liver cirrhosis, and 21 normal controls) and a testing group (n=36, 17 patients with hepatocellular carcinoma, 8 with liver cirrhosis, and 11 normal controls).An artificial neural network was trained on data from 70 individuals in the training group to develop an artificial neural network diagnostic model and this model was tested.The 36 sera in the testing group were analysed with blind prediction by using the same flowchart and procedure of data collection.The 36 serum protein spectra were clustered with the preset clustering method and the same mass/charge (M/Z) peak values as those in the training group.Matrix transfer was performed after data were output.Then the data were input into the previously built artificial neural network model to get the prediction value.The M/Z peaks of the samples with more than 2000 M/Z were normalized with biomarker wizard of ProteinChip Software version 3.1 for noise filtering.The first threshold for noise filtering was set at 5, and the second was set at 2.The 10% was the minimum threshold for clustering.The statistical analysis of the data of serum protein mass spectrum was performed in the groups (normal vs.hepatocellular carcinoma, and liver cirrhosis vs.hepatocellular carcinoma) with the t test.Results Comparison between the groups of hepatocellular carcinoma and normal control: The mass spectra from 56 samples (hepatocellular carcinoma and normal controls) in the training group were analysed and 241 peaks were obtained.In addition, 21 peaks from them were used for comparison between the groups of hepatocellular carcinoma and normal controls (P<0.01).Only 2 peaks at 3015 M/Z and 5900 M/Z were selected with significant difference (P<10-9).A model was developed based on these two proteins with different M/Z.It was confirmed that this artificial neural network model can be used for comparison between the groups of hepatocellular carcinoma and normal controls.The sensitivity was 100% (17/17), and the specificity was 100% (11/11).Comparison between the groups of hepatocellular carcinoma and liver cirrhosis: The mass spectra from 49 samples in the training group (including patients with hepatocellular carcinoma and liver cirrhosis) were analysed and 208 peaks were obtained.In addition, 21 peaks from them were used for comparison between the groups of hepatocellular carcinoma and liver cirrhosis (P<0.01).Only 2 peaks at 7759 M/Z, 13134 M/Z were selected with significant difference (P<10-9).A model was developed based on these two proteins with dfferent M/Z.It was confirmed that this artificial neural network model can be used for comparison between the groups of hepatocellular carcinoma and liver cirrhosis.The sensitivity was 88.2% (15/17), and the specificity was 100% (8/8).Conclusions The specific biomarkers selected with the SELDI technology could be used for early diagnosis of hepatocellular carcinoma.