The completion of the human genomic sequence has provided a vast opportunity to study the basis of health and disease. However, the information obtained by gene sequences alone might be insufficient to identify many processes in human beings because the function of a large proportion of human gene sequences is unknown. For this purpose, scientists will need to know the structure and function of the proteins translated from these gene sequences. Consequently, this field of study, called proteomics, has become a major focus in recent medical research.

Two distinctive proteomic approaches are operational, nowadays. The mostly common and well-known approach is the identification of individual proteins. Next to identification, profiling of complex biological samples is applicable and a promising tool in the field of Clinical Proteomics. This profiling technology allows the identification of biomarkers related to disease onset, disease follow-up and therapy-follow-up.

The Nijmegen Proteomics Facility facilitates profiling proteomics. The facility has the disposal of the Surface Enhanced Laser Desorption Ionization and Time of Flight (SELDI-TOF) technology. This technology can be used to identify biomarkers or clusters of biomarkers in complex biological samples such as serum, blood plasma, and tissue extracts. The principal compartment of the technology is the ‘ProteinChip’ allowing the binding of a subset of proteins within complex protein mixtures. Subsequently, the proteins bound to the ProteinChip are eluted using laser desorption and after ionization the molecular masses of the proteinchip bound proteins are measured by time of flight (TOF) mass spectrometry. The readout is a spectrum of peaks. The position of an individual protein in the spectrum corresponds to its ‘time of flight’ because the small proteins fly faster and the larger proteins more slowly. Cluster analysis will be performed between the patient’s protein profiles and the control protein profiles to identify biomarkers or clusters of biomarkers.

The SELDI-TOF platform requires small biological sample volumes and allows the comparison of large cohorts in a limited time schedule. The statistical and bioinformatic analyses can be performed using different software programs. Currently the facility uses Ciphergen Express Data Manager, a software program able to perform univariate as well as multivariate statistical analysis. The SELDI-TOF equipment is located at the Central Hematology Laboratory of Radboud University Nijmegen Medical Centre.

Figure 1: The ProteinChip Biomarker system (PBS IIC) and workstation at the Central Hematology Laboratory.