| Background and ObjectiveHepatocellular carcinoma (HCC) is one of the common cancers in China. Although alpha fetoprotein (AFP) has been regarded as a most useful serum marker on HCC diagnosis, its sensitivity is only about 70%. The early detection of HCC in those who have been infected by hepatitis virus remains a challenge. Most patients with HCC present late and are not suitable for curative treatment when been determined. There is a tremendous interest and urgency to identify novel HCC diagnostic marker(s) for early detection.Biomarkers are important tools for cancer detection and monitoring. An effective, clinically useful biomarker should be measurable in a readily accessible body fluid such as serum, urine or saliva. Gene mutations or alterations in gene transcription and translation, and alterations in their protein products can all potentially serve as specific biomarkers for disease. However, several studies have illustrated a poor correlation between gene expression and protein abundance. Knowledge of gene sequence or the quantity of gene expression cannot be used to predict expression level and function of a protein. To identify the structure, interaction and function of the cellular proteins is the main goal in the post-genome era. The character of the proteome in body fluid can be used as a tool on early diagnosis. Certain body fluids such as serum, urine, and saliva can be described in terms of their protein composition and their retrieval are considered to be non-invasive. Therefore there is a clear need for the direct analysis of protein expression in these samples to find some disease related proteins which can be used as tools on early diagnosis and screening.The discovery, identification and validation of proteins associated with aparticular disease state are difficult and laborious tasks, and often require hundreds of samples, if not thousands, to be analyzed. 2D-PAGE and related technologies have proven to be a very reliable tool for discovery-based proteomics approaches, but these technologies require significant time and effort on the part of the investigator, which makes them unsuitable for use in clinical testing. It needs for high throughput and high sensitivity tests for the early detection of cancer. Surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), which was emerged in the beginning of 1990 is especially well suited for the discovery and implementation of these biomarkers. The Protein Chip Biology System use SELDI-TOF-MS to retain proteins on a special solid-phase chromatographic surface that are subsequently ionized and detected by time-of-flight mass spectrometry. It allows for protein profiling from a variety of complex biological materials such as serum, urine and cell lysates with limited sample preparation and for protein-protein and protein-DNA interactions. This technology has rapidly developed since 1993 and has been used to discover biomarkers for diseases and has proven to be useful in the discovery of potential diagnostic markers for prostate, bladder, breast, and ovarian cancers. To identify protein(s) in the HCC proteome that could potentially be used for early detection of the cancer using proteomic technology, Here we use weak cation exchange (WCX2) array of Ciphergen Corporation to detect proteomes in serum from HCC, liver cirrhosis, chronic hepatitis patients and normal controls by SELDI-TOF MS and try to use software to identify proteomic difference in HCC and the controls.MethodsSerum samples were collected from 59 HCC, 18 liver cirrhosis, 21 hepatitis and 52 normal people, and were stored at -80 until use. The samples were profiled by SELDI-TOF MS using WCX2 array of Ciphergen Corporation. Ciphergen Biosystems software was used to analyze theproteomic profiles in order to find proteins related to HCC. The diagnosis value would be compared to that of AFP.ResultsAmong a total of 95 qualified protein mass peaks (signal-to-noise ratio >5) detected, 58 peaks had m/z values between 2000-10000...
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