Abstract
In biomarker discovery, the detection of proteins with low abundance in the serum proteome can be achieved by optimization of protein separation methods as well as selective depletion of the higher abundance proteins such as immunoglobins (e.g. IgG) and albumin. A relative newcomer to the proteomic separation arena is the commercial instrument PF2D from Beckman Coulter that separates proteins in the first dimension using chromatofocusing followed in line by reversed phase chromatography in the second dimension, thereby separating intact proteins based on pI and hydrophobicity. In this study, assessment and optimization of serum separation (undepleted serum and albumin-IgG-depleted serum) by the PF2D is presented. Protein databases were created for serum obtained from a healthy individual under traditional and optimized methods and under different sample preparation protocols. Separation of the doubly depleted serum using the PF2D with 20% isopropanol present in the first dimension running buffer allowed us to unambiguously identify 150 non-redundant serum proteins (excluding all immunoglobulin and albumin, a minimum of two peptide matches with acceptable Mascot score) in which 81 have not been identified previously in serum. Among them, numerous cellular proteins were identified to be specifically the skeletal muscle isoform, such as skeletal muscle fast twitch isoforms of troponin T, myosin alkali light chain 1, and sarcoplasmic/endoplasmic reticulum calcium ATPase. The detection of specific skeletal muscle protein isoforms in the serum from healthy individuals reflects the physiological turnover that occurs in skeletal muscle, which will have an impact on the ability to use generic "cellular" proteins as biomarkers without further characterization of the precise isoforms or post-translational modifications present.
Highlights
From the Departments of ‡Medicine, §Biological Chemistry, and ʈBiomedical Engineering and ¶The Technical Implementation and Coordination Core of NHLBI Proteomics Center, The Johns Hopkins University, Baltimore, Maryland 21224
A relative newcomer to the proteomic separation arena is the commercial instrument PF2D from Beckman Coulter that separates proteins in the first dimension using chromatographic focusing followed in line by reversed phase chromatography in the second dimension, thereby separating intact proteins based on pI and hydrophobicity
LC proteomic methods have focused on separating complex mixtures of peptides obtained following digestion of the serum proteome, whereas separation of proteins has been relegated primarily to electrophoresis in both one and two dimensions (2DE)1 (2, 3). 2DE has an advantage over peptide-based LC methods as it enhances the ability to identify the precise isoforms of proteins that are present and/or post-translational modifications (PTMs) that may alter the pI or mass of a protein (1)
Summary
From the Departments of ‡Medicine, §Biological Chemistry, and ʈBiomedical Engineering and ¶The Technical Implementation and Coordination Core of NHLBI Proteomics Center, The Johns Hopkins University, Baltimore, Maryland 21224. It is necessary to maximize the observation of the plasma or serum proteome to detect proteins with low abundance. This can be achieved by optimization of protein separation methods as well as selective depletion of the proteins at high abundance such as immunoglobins (e.g. IgG) and albumin. The PF2D system (Beckman Coulter) is a two-dimensional LC system that uses chromatographic focusing to separate intact proteins in the first dimension by pI (from 8.5– 4.0) and in the second dimension by reversed phase chromatography, which separates based on hydrophobicity, enhancing the precise detection of isoforms and/or PTMs that alter the pI and/or hydrophobicity of a protein. To assess the utility of the PF2D, protein databases were created for serum obtained from a healthy individual under traditional and optimized methods and under different sample preparation protocols to remove lipids, albumin, and immunoglobulins
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