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.