A centrifugal ultrafiltration strategy for isolating the low-molecular weight (≤ 25 K) component of human plasma proteome

The low-molecular weight fraction (LMF) of the human plasma proteome is an invaluable source of biological information, especially in the context of identifying plasma-based biomarkers of disease. In this study, a separation and enrichment strategy based on centrifugal ultrafiltration was developed for the LMF (i.e., ≤ 25 K) of plasma routinely prepared from normal, healthy volunteers. Four commercially-available filter membranes of similar nominal molecular weight cut-off (NMWC), but differing membrane chemistries and filter orientations (Microcon®, Millipore; Centrisart®, Sartorius; Amicon Ultra®, Millipore; Vivaspin®, Sartorius), were evaluated. Of these filtration devices, only the Sartorius Vivaspin® tangential membrane, NMWC 20 K was effective in the non-retention of Mr > 50 K, and recovery and enrichment of low-Mr components from human plasma. This filter membrane device was further optimized with respect to plasma buffer composition, centrifugal force, duration and temperature. Optimal ultrafiltration conditions were obtained using 100 μL of normal plasma in 10% acetonitrile, and a centrifugation force of 4000 × g for 35 min at 20 °C. In this LMF, 44 proteins (from 266 unique peptides) were identified using a combination of 1D-SDS-PAGE / nano-LC-MS/MS and a stringent level of identification (FDR < 1%). We report the identification of several proteins (e.g., protein KIAA0649 (Q9Y4D3), rheumatoid factor D5, serine protease inhibitor A3, and transmembrane adapter protein PAG) previously not reported in extant high-confidence Human Proteome Organization (HUPO) Plasma Proteome Project datasets. When compared with the low-Mr human plasma/serum proteome datasets of Zhou et al. (Electrophoresis, 2004. 25, 1289-98), Gundry et al. (Proteomics Clin. Appl., 2007. 1, 73-88) and Villanueva et al. (Anal Chem, 2004. 76, 1560-70), 64% of our identifications (28 proteins) were novel; these include cofilin-1, PPIase A, and the SH3 domain-binding glutamic acid-rich-like protein 3. In addition to intact proteins, many peptide fragments from high-abundance proteins (e.g., fibrinogen, clusterin, Factor XIIIa, transferrin, kinogen-1, and inter-alpha-trypsin inhibitor), presumably derived by ex vivo proteolysis, were observed. © 2009 Elsevier B.V. All rights reserved.