The term peptide is typically used for polypeptides in the range up to approximately 20 kDa molecular weight. Peptides are usually the products of proteolytic cleavage events (e.g. cleavage of activation peptides from zymogens). Many pathological processes are associated with changes in protease expression or activation and these changes are captured or represented in altered peptide profiles.

In contrast to cell-associated proteases or the precursor protein respectively, peptides exhibit better permeability between tissue compartments due to the relative low molecular weight. Therefore, the probability to detect proteolytic fragments of tissue-born proteins in body fluids is significantly higher than to identify the protein precursor.

Peptides are suitable to encode conditions diametrically opposed to each other (Coagulation versus Fibrinolysis), which are not accessible by classical Proteomics methods (e.g. after Tryptic Digestion).

Peptide of interest do have picomolar concentrations in blood plasma. In order to measure these low abundant entities sophisticated sample preparation techniques (removal of high abundant plasma proteins) and tailored experimental designs are necessary to achieve the required analytical sensitivity.

These properties indicate that peptides as a molecular class are ideal diagnostic marker candidates.

PXBioVisioN has developed a Peptidomics platform to display and interpret peptide patterns in complex body fluids and tissues of various origins. Peptide profiles are systematically and comprehensively measured, compared and interpreted in an appropriate biological context to elucidate knowledge about the biological processes. When applied to relevant disease models, Peptidomics-Technologies have the potential to uncover previously unrecognized factors that may contribute to the pathophysiology.

Data visualization communicates a quantitative message. Visualization of mass spectra is important to mine basic structures in the data. For visualization of complex 2D LC-MALDI-MS datasets, a two-dimensional (chromato-raphic elution and molecular mass) map view has been intro- duced resembling the picture of 2D gel electrophoresis. It allows assessing high density information in a natural and convenient way. Spectra are ordered by the chromatographic retention time (y-coordinate); thus spectra are sorted by hydrophobicity. The m/z values are represented by the x-coordinate whereas the intensity is reflected by a z-scale (coloring).

Visual analysis of mass spectrometric data can deliver important clues for data interpretation since the human brain possesses a strong aptitude for pattern recognition thus enabling the researcher to observe effects present in datasets that might otherwise be difficult to determine using uni- or multivariate methods. The visualization of mass spectrometric data is beneficial to comprehensively assess data to determine various aspects of the measure-ment. For example, the distribution and intensity of signals is accessible and conspicuous features like polymeric components are recognizable. The visualization allows for wide-ranging assessment of signals within a spatial context (e.g., the distribution of signals based on fraction and mass) and interrelations between signals like post- translational modifications become apparent

PXBioVisioN combines state-of-the-art liquid chromatographic separation and mass spectrometry (LC-MS) to separate and profile peptides in biological samples with a high accuracy within the molecular mass range between 950 and 15,000 Da. The LC-MS data are converted into reliable profiling data by proprietary software tools. The integrated Peptidomics data analysis platform Spectromania supports full-resolution visualization of large data sets and full integration of all experimental and process data. The process is supported by rigorous QC/QA measures and is auditable.