Identifying biomarker proteins

Proteomics have been used to develop biomarkers. This is achieved by comparative analysis of protein expression in healthy and diseased tissues to identify expressed proteins to be used as new markers, by analysis of secreted proteins in cell lines and primary cultures, and by direct serum protein profiling. MALDI seems to be a good technique for direct protein analysis in biological fluids (e.g., the identification of the small proteins-defensin 1, 2 and 3 as related to the anti-HIV-1 activity of CD8 antiviral factor). 

Genomic information Used to identify possible protein therapies and targets, to develop biomarkers, and to understand more deeply how a given compound interacts with a complex living system. 

Methods are being developed to analyze the proteins in slices of a tissue. Using this procedure, it is possible to compare the protein contents of a normal cell and that of a cell from a person with a disease. This will help to identify the protein biomarker(s) of the disease for diagnostics and for the development of a drug or to follow the effect of a drug during treatment. 

Even though the microfluidic-MS analysis was performed with low injection volumes, it enabled the identification of five putative biomarkers 39,40 proliferating cell nuclear antigen (PCNA), cathepsin D and keratins K8, K18 and K19 (Table 7.1). All corresponding peptides that identified these proteins had p < 0.001, confirming the reliability of the match. PCNA is a protein involved... 

The objective of quantitative proteomics is to identify differentially expressed proteins in a biological sample. Differential expression of proteins is caused by a disease state, stress due to external factors (drugs, toxins, etc.), or experimental manipulation. Quantitative proteomics can help identify biomarkers of a particular disease and aid in an early diagnostic intervention and prevention of a disease. Several strategies have been developed for quantitative proteomics some are exclusively gel-based approaches, and others require mass spectrometry measurements [66]. 

In order to evaluate the proteomic profile of whole cells and to correctly identify proteins based solely on the intact mass, advanced instrumentation offering high mass accuracy is necessary. The application of Fourier transform mass spectrometry (FTMS) to intact cell analysis allowed for unambiguous identification of biomarker proteins due to the high resolution and mass... 

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