Definition of study cohorts: A clinical proteomic study should begin with a well-framed clinical question or problem, followed by selection of the appropriate study populations [CASE (red) vs. CONTROL (green)] and samples to be analysed. Hereby, we focused on urine, since urine is easily accessible, available in large quantities and long-term stable during storage at -20°C, yielding comparable datasets. Furthermore, urinary polypeptides display the “status” of the kidney, bladder, prostate and vascular architecture and are capable to depict systemic diseases. Other specimens, such as cerebrospinal fluid and tissue culture supernatant are suitable for analysis, as well.
Determination of total (compiled) polypeptide patterns: CE/MS (capillary electrophoresis coupled to mass spectrometry) technology is capable to display >1,000 polypeptides in a single CE/MS run without the need for specific reagents. Separation time and mass to charge ratio are used to get a pattern of peptides and proteins for every single sample/patient. A multitude of such individual analyses are considered for compilation yielding the best representative characterisation (compiled patterns).
The compiled patterns are used in a database to identify discriminatory biomarkers, in general 10 to 50 polypeptides, which form a diagnostic pattern. During this early phase, we focus on a well defined study population to establish the discriminatory (polypeptide) patterns by using our proprietary software packages.
After establishment the diagnostic pattern could be applied on a blinded set (cohort) of patient samples.
CE/MS measurement of all urine samples from blinded cohort.
Identification of discriminatory biomarkers in each individual CE/MS analysis.
Comparison of individual discriminatory biomarker patterns with diagnostic polypeptide pattern.
Individual classification of patients form blinded cohort into CASE and CONTROL group
Classification might be used for drug evaluation, therapy monitoring, phenotyping …
… or comparison to other diagnostic methods (determination of sensitivity and specificity).