Received on May 8, 2007
Accepted on August 20, 2007

Proteomics and Protein Markers

Quality Control of Serum Albumin Depletion for Proteomic Analysis

¹ Critical Care Medicine Department, National Institutes of Health, Bethesda, MD
² Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD

^* To whom correspondence should be addressed. E-mail: nseam{at}cc.nih.gov.

Methods: Depletion of albumin from pooled serum, performed using IgY immunoaffinity spin columns, was assessed for 21 runs on each of 4 columns. We measured albumin concentrations, after albumin depletion, by use of an immunoturbidimetric assay on the Beckman LX 20 analyzer and assessed mass spectra of albumin-depleted samples by use of SELDI-TOF mass spectrometry.

Results: There was substantial run-to-run variation in efficiency of albumin depletion, with systematic decline in efficiency after multiple uses of the columns. Mean depletion efficiency was >95% for 15 of 17 runs and <90% for runs 18 to 21. We evaluated the 10 highest-intensity peaks present in all spectra from runs 1, 8, 17, and 21 and assessed the effect of albumin depletion on SELDI-TOF mass spectrometry reproducibility. Comparing the %CV of relative intensities for low and high m/z measurements revealed a significant difference of run 21 compared with runs 1, 8, and 17 (P <0.0001). Six-fold more peaks were found in albumin-depleted than unfractionated serum at both high and low m/z.

Conclusions: Sporadic and systematic variation in efficiency of albumin depletion by spin columns may contribute significant preanalytical bias to proteomic approaches of biomarker discovery. This variation requires ongoing quality control of the albumin depletion process by quantification of albumin concentration to assess depletion efficiency.