**2.3.2 MATLAB**

MATLAB is a piece of commercial software integrating statistical analysis and engineering computation. Taking MATLAB as the development platform, it will be possible to realize the pretreatment, display and statistical analysis of MS data. In the research of serum peptidome profiling of prostatic cancer, breast cancer and bladder cancer, this tool together with the GENESPRING of Agilent has achieved good results in data analysis (Villanueva et al, 2005).

Serum Peptidomics 377

will be performed over the training set with t-test, Pearson correlation analysis and genetic algorithm, to find peaks of higher specificity to build a sorter. Then, the testing set makes tests, which shall be repeated and optimized. Finally, the validating data are used for

Softwares based on the TOF-MS system mainly includes: (1) for the SELDI system, the ProteinChip Software 3.1 and Biomarker Wizard taking the decision tree as the core; (2) for the ClinProt system, the ClinProTools software taking cluster analysis as the core; (3) for the ClinTOF system, the BioExploerTM software taking specific vector machine (SVM), decision,

Other bioinformatics tools for MS correlation analysis include: MapQuant, MASPECTRAS, SpecArray, msInspect and MZMine. These tools or softwares haven't realized seamless connection with serum peptidomics data, so they fail to perfectly accomplish the data

Nowadays in clinical detection, the serum biochemical indicators fail to accomplish the task of diagnosing complex diseases. For instance, there are only one or two serological diagnosis indicators available for specific cancers; even worse, these indicators cannot diagnose diseases independently and sometimes confuse the cancer with benign tumors or inflammation. For example, the prostate specific antigen (PSA) is a major diagnosis indicator for prostatic cancer, but not a biomarker for the prostatic cancer specificity, for the reason that 15%~25% prostatic cancer patients see their serum PSA falling into the normal range. Besides, PSA may also rise due to the benign hyperplasia of prostate, urinary infection, acute prostatitis, retention of urine and the per rectum operations. Accordingly, serum peptidomics analysis, as a new clinical diagnosis method, has made great progress in early diagnosis of complex diseases like tumor, neurological degenerative diseases and

Ovarian cancer is the most maligne tumor among all malignant tumors of the reproductive system, with the pathogenic factors unclear yet but possibly relating to the reproductive and hereditary factors. Most ovarian cancer cases are detected in the late stage and seldom cured. For the moment, the universally-ratified specificity biomarker CA125 for ovarian cancer diagnosis, as the single biomarker, sees the positive predicted value less than 10%. Therefore it is urgent to develop an approach for the early-stage clinical diagnosis so as to enhance the survival rate. The serum based peptidomics has seen great progress in

Pleasantly, based on findings of the SELDI system, the US Vermilion Company and Quest Diagnostics worked together to develop the OVA1, which can determine the onset of ovarian cancer by detecting the cavum pelvis enclosed mass and decide whether operations

validating to get a stable model.

autoimmune disease.

**3.1.1 Ovarian cancer** 

researches of ovarian cancer diagnosis.

**3.1 Tumor** 

4. TOF-MS System Based Softwares

tree, neural networks and k nearest neighbor (kNN) as the core.

management and analysis based on MS serum peptidome profiling.

**3. Disease serum peptidomics research progress** 
