Various approaches for removal of high-abundance components in body fluids are 
currently available. While most methods are constructed for plasma depletion, 
there is a need for body-fluid-specific strategies. The aim of the present study 
was to design an affinity matrix suitable for the depletion of high-abundance 
proteins in CSF (cerebrospinal fluid). Hence, molecules with specific affinity 
towards proteins present at high concentration in CSF were desired. Affibody 
molecules are specific binders of small size that have shown high stability 
under various conditions and are therefore good candidates for such a matrix. 
The protein composition in CSF resembles that in plasma. However, 20% of the 
proteins are brain-derived and are therefore present in higher proportions in 
CSF than in plasma, whereas larger plasma-derived proteins are less abundant in 
CSF. Therefore five high-abundance CSF proteins were chosen for the design of a 
CSF-specific depletion setup. Affibody molecules with specificity towards HSA 
(human serum albumin), IgG, transferrin and transthyretin were combined in an 
affinity column. In addition, polyclonal antibodies against cystatin C were 
coupled to chromatographic beads and packed in a separate column. Highly 
reproducible and efficient removal of the five target proteins was observed. The 
proportion of depleted proteins were estimated to be 99, 95, 74, 92 and 83% for 
HSA, IgG, transferrin, transthyretin and cystatin C respectively. SDS/PAGE 
analysis was used for monitoring and identifying proteins in native CSF, 
depleted CSF samples and the captured fractions. Moreover, shotgun proteomics 
was used for protein identification in native as well as depleted CSF and the 
achieved data were compared. Enhanced identification of lower-abundance 
components was observed in the depleted fraction, in terms of more detected 
peptides per protein.