Applications

An important facet of contemporary bioanalysis is to develop techniques and methodologies that expedite the process of proteomics research. Mass spectrometry (MS) has emerged as one of these core techniques and it is a promising diagnostic tool for identifying biomarkers related to human diseases. A widely accepted approach in this field is to separate protein components from clinical specimens (such as humoral fluids) by one- or two-dimensional gel electrophoresis, followed by in-gel proteolytic digestion and then MS identification. Alternatively, the entire protein mixture can be digested either enzymatically or chemically, and the resulting complicated peptide mixture is submitted to liquid chromatography (LC)-MS/MS analysis. In the latter approach, removal of physiological and processing contaminants such as salts, detergents and chemical reagents is usually required to prevent adverse interference of these compounds in proteolysis. Moreover, concentration of diluted sample solutions is needed prior to ensuing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and MS analyses. However, the commonly used procedures for protein purification and concentration such as trichloroacetic acid (TCA) precipitation and dialysis with a molecular size cut-off membrane are generally time-consuming, incomplete in removing contaminants, and plagued with high sample loss to membranes or the walls of containers. Furthermore, the presence of high-abundance proteins often spoils the MS identification of minute components and, therefore, additional steps for depletion of these abundant proteins have to be undertaken.
 
Solid-phase extraction (SPE) is a popular solution to overcoming these difficulties. Hydrophobic particles and chemically modified matrixes are typical adsorbents used for such purpose. However, the extraction capabilities of hydrophobic surfaces have been shown to deteriorate greatly in solutions containing more than 0.02% SDS. MS analysis of trypsinized peptides from these extracted proteins revealed less information than proteins concentrated from SDS-free solutions. Moreover, a significant fraction of peptide fragments after the tryptic digestion was trapped in the porous material, resulting in low peptide recovery efficiency.
 
The “solid-phase extraction and elution on diamond (SPEED)” platform provides speedy extraction of soluble proteins, membrane proteins, viruses, and other proteinaceous compounds. Compared with conventional methods, the platforms facilitate not only purification and concentration of intact proteins but also their ensuing analysis of enzymatic digests by SDS-PAGE and matrix-assisted laser desorption/ionization (MALDI) MS without prior removal of the adsorbent. One-pot work flow involving reduction of disulfide bonds, protection of free cysteine residues, washing off residual chemicals, and proteolytic digestion of adsorbed proteins can be performed directly on the particles.
 
Further reading:
C.-C. Wu, C.-C. Han, and H.-C. Chang, “Applications of surface-functionalized diamond nanoparticles for mass-spectrometry-based proteomics,” J. Chin. Chem. Soc. 57, 583–594 (2010).