Evaluation of a Protein-Depletion Kit for Enriching Low Abundant Proteins from Human Sera

The identification of low-abundance serum proteins in human sera can be severely affected by high-abundance proteins (HAPs), so many protein-depletion kits have been developed for enhancing the efficiency of identifying them. The ProteoSpin^™ Abundant Serum Protein Depletion Kit is a fast, simple, and budget-friendly kit for the depletion of HAPs including albumin, alpha-antitrypsin, transferrin, and haptoglobin from serum and plasma samples but its depletion efficiency has not been investigated. Our study aimed to evaluate the efficiency of this kit in processing a pooled serum of hepatocellular carcinoma patients. We conducted a thorough evaluation following criteria: (i) protein recovery rate after depletion, (ii) efficacy of depletion, (iii) specificity of depletion using ProteoSpin^™ Kit. Quantitative determination of total proteins, depleted proteins, and HAPs was performed. SDS-PAGE was used to analyze the serum samples before and after depletion while Shotgun LC–MS/MS was conducted to identify proteins from the depleted serum. The results then were compared with previous research to evaluate the efficiency of depletion. Our results indicated that the ProteoSpin^™ Kit was efficient to deplete HAPs by revealing a protein recovery rate of 5.73% and the identification of 251 serum proteins. It reduced albumin, IgG, transferrin, fibrinogen, haptoglobin, and transthyretin by approximately 60%. The depletion efficacy of ProteoSpin^™ Kit was comparable or even superior to some other commercial kits. It has significantly eliminated HAPs and enhanced the number of identified proteins in a serum sample. Our study can help to facilitate the choice of optimal products for HAP depletion in studying serum proteins.