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.