Mass Spectrometry in Peptide Biomarker Discovery and Peptidomics

Biomarkers are defined as characteristics that are objectively measured and evaluated as indicators of normal biologic processes, pathogenic processes or pharmacologic responses to a therapeutic intervention (1). Various studies showed that native peptides from bodily fluids such as blood, urine or cerebrospinal fluid, as well as cells or tissues, could act as biomarkers and be used for diagnostic purposes or for monitoring disease stages (2,3).

Peptides are products of proteolytical protein processing, and their biochemistry reflects the changes of the biological state of any living organism. These changes are indicated by the presence or absence of specific peptides or a significant change in their abundance in biological samples. Furthermore, various peptides have biological activity (such as regulatory function) or are associated with different diseases, so that the probability of finding relevant biomarkers in peptidomes is high (see Figure 1).

The advantage of a biomarker discovery by means of peptidomics is largely due to the high accessibility of biological source material, especially of bodily fluids. However, these samples have extremely high complexity and quantitative diversity. Peptides with biological activity are mainly present in a very low concentration. An additional challenge is that ongoing enzymatic processes or coagulation in the cases of blood samples can affect the peptidome by activation of degradation processes (4,5).

For peptide biomarker discovery, a comprehensive peptide profiling for the identification of biomarker candidates and determination of their amino acid sequence is necessary. Mass spectrometry, such as matrix-assisted laser desorption/ionisation (MALDI) and electrospray ionisation (ESI) techniques for the analysis of intact peptides and protein digests has evolved as a powerful key technology in this area. Hence, the understanding of the utility of mass spectrometry not as a standalone technique but as part of a highly complex discovery process, which starts with the collection of clinical sample material and ends with the biological interpretation of biomarker sequence information, is very important. This understanding avoids failures and minimises and controls the influences of analytical equipment and sample material handling (6).