Due to their multiple involvement in biological systems, peptides are ideal biomarker candidates. According to the NIH definition, "biomarker" has been defined as a characteristic that can be measured and evaluated as an indicator of normal biologic processes, pathologic processes or pharmacologic responses to therapeutic intervention. Since peptides can migrate between compartments of an organism, lots of pathogenic processes can be reflected by characteristic, pathognomonic changes of the composition of peptides in different body fluids. Peptide abundance changes associated with various diseases have already been detected.

Currently two peptidomic approaches for biomarker discovery are under investigation: pattern recognition and mono-/oligo-biomarker detection. For the former, there is no need to obtain identity information of biomarker candidates, to designate patient samples with high specificity and sensitivity, solely based on the MS pattern.

Single/oligo biomarkers are more useful and reliable compared with the pattern recognition, because peptide differences in expression levels can be assigned and validated in biological samples collected from multiple sources. Mass spectrometry has a great potential to enter clinical chemistry. This analytical method is capable to reveal concentrations of analyte molecules simultaneously with an extraordinary high specificity, given by the precise macromolecular mass and sequencing capability.

In order to screen and validate peptide biomarkers, therefore it needs to fulfill two tasks in parallel: to identify the peptides present in a sample (qualitative) and to determine corresponding concentrations (quantitative). Only the combination of both will allow the selection of peptide candidates. Usually this work is not restricted to a specific type of analytical instruments, and lots of analytical techniques are currently used for biomarker detection. But we believe the mass spectrometry coupled to various liquid chromatography, such as UPLC and nanoLC, can be taken as the optimal analytical platform with high resolution, sensitivity, throughput and quantitation capabilities.

http://www.creative-proteomics.com/services/characterization-of-peptide-biomarkers.htm