Abstract: Objective To analyze the impact of serum high abundant proteins immunodepletion on identification of tissue proteome. Methods Human thyroid and pituitary samples were disposed using 12 high abundant proteins depletion antibody column. The low abundant proteins and raw samples were analyzed by LC/MS. Identified peptides and proteins were qualitatively and quantitatively analyzed. Results The serum high abundant proteins in thyroid and pituitary were respectively depleted by 92.11%±12.87%, 78%±25%. Compared with raw thyroid, the non-redundant peptide and protein identification of low abundant thyroid was respectively increased by 70%, 16.5%. The non-redundant peptide identification of low abundant pituitary was 21.9% higher than raw samples. But the protein identification was unchanged. Conclusions The immunodepletion of serum high abundant proteins can significantly increase peptide and protein identification and is more suitable for the tissues with intensive blood vessel.

Key words: thyroid proteome, pituitary proteome, serum high abundant proteins immunodepletion, LC/MS analysis