OBJECTIVES: Two different depletion strategies for removing albumin from human 
cerebrospinal fluid (CSF), Microcon Centrifugal Filter vs. Montage Albumin 
Deplete kit, were evaluated for improving protein profiling pattern and 
reproducibility in SELDI analysis.
DESIGN AND METHODS: Pooled CSF was divided into 20 aliquots and these aliquots 
were subjected to SELDI analysis either after albumin depletion or without 
preprocessing. Protein profiles were obtained by using CM10, Q10 and IMAC chips.
RESULTS: Both strategies resulted in reliable albumin depletion (<6.2 mg/L, 
filter; 8.1 mg/L, depletion kit). Investigated methods of albumin depletion 
showed no significant differences in coefficients of variation (CVs) of peak 
intensities compared to unprocessed CSF on almost all chip types. Peak 
intensities were significantly higher after albumin depletion compared to CSF 
without preprocessing on Q10 and on CM10 chips. Nevertheless, the two strategies 
of albumin depletion led to a decrease in the number of detected peaks on all 
chip types compared to unprocessed CSF, but several additional peaks, not 
detected in unprocessed CSF, occurred.
CONCLUSIONS: This study demonstrates that reduction of sample complexity by 
albumin depletion of CSF can be performed without CV impairment. However, the 
significance of this strategy needs to be evaluated separately for each 
individual biomarker discovery study.