Types of protein chips

Protein chips are miniature devices on which proteins, or reagents that capture proteins from solution, are applied in an array. There are many different types of protein chip, some used to analyze protein abundance and others used to study protein functions. 

This emerging technology has the potential to considerably improve the throughput of protein analysis, particularly with the recent advent of a whole pro-teome chip for the yeast Saccharomyces cerevisiae. The various different types of protein chip that have been described are summarized below ... 

In another study that evaluated the protein fingerprints of HIV-1-infected MDM, cell lysates were directly applied on two types of protein chips weak cation exchange and reverse-phase hydrophobic interaction. After washing to remove the unbound proteins, bound proteins were ionized and their molecular mass/charge ratio was determined using TOP analysis. Analysis of the obtained profiles showed distinct patterns between uninfected and infected MDM [33]. 

Protein Chips Proteins, too, can be immobilized on a solid surface and used to help define the presence or absence of other proteins in a sample. For example, researchers prepare an array of antibodies to particular proteins by immobilizing them as individual spots on a solid surface. A sample of proteins is added, and if the protein that binds any of the antibodies is present in the sample, it can be detected by a solid-state form of the ELISA assay (see Fig. 5-28). Many other types and applications of protein chips are being developed. 

Direct detection of a cytokine protein, recombinant human interferon-y, using an IBIS SPR sensor is presented in [60]. Several types of sensor chip coatings, including self-assembled monolayers and hydrogel-derivatized SAMs, were characterized in terms of their ability to resist non-specific adsorption from plasma. The best results with respect to plasma adsorption and surface regenerability were obtained with antibodies immobilized on the dextran-modified 11-mercaptoimdecanoic acid SAM. The detection limit for detection of human interferon-y in 1 100 diluted plasma was established at 250ngmL . ... 

A protein chip is a glass, plastic or silicon chip onto which different proteins have been attached at separate locations in an ordered manner to form a microscopic array. They are attached mainly by adsorption, absorption, covalent cross-linking or affinity binding. There are two main types of protein arrays analytical arrays and functional protein arrays. In the hrst type the capture molecules are antibodies or antibody mimics which are used to detect the presence and amount of protein in a sample. These are mainly used for diagnostics and expression profiling experiments. The second type of protein array involves immobilising proteins on a chip and using the chip to probe biochemical activity. 

Tissuelysates arrayed on to chip or ted in solution depending on type of protein array used... 

A developing application of DNA technology uses a DNA chip that contains many small segments of bases of known sequence. Such DNA chips are being used to attack cancers. Cancers occur when defective genes cause cells to divide uncontrollably, but usually the process of protein synthesis also is modified. Different types of cancer result in different modifications to protein synthesis, depending on how the DNA... 

A number of different types of ESI sources, known as nanospray sources, have been designed that can operate at lower sample flow rates (10-200 nL min ). These generate smaller droplets and improve the signal intensity of the protein-ligand noncovalent complexes further, with the added benefit of reducing protein consumption up to 100-fold compared to standard ESI flow rates. Nanospray has also been reported to be more tolerant to nonvolatile cations in solution [37]. Recently, an automated fabricated chip nanospray source has been developed. This chip-based device has improved the ease-of-use for nanospray, while the design eliminates carryover effects as the spray is produced directly from an orifice on each sample well of the chip [38]. 

In a related approach, arrays with different types of surface chemistries such as hydrophobic, hydrophilic, anionic, and affinity are used to absorb certain protein groups from biological or patient samples. The chip-absorbed proteins are then directly detected by surface-enhanced laser desorption/ionization time-of-flight MS (SELDl-TOF MS) (Issaq et al. 2002). The resulting protein masses can be used in pattern analysis and thereby provide a useful diagnostic tool. 

Figure 6 The SELDI technology. This type of proteomic analytical tool is a class of mass spectroscopy instrument that is useful in high-throughput proteomic fingerprinting of serum. Using a robotic sample dispenser, 1 p,L of serum is applied to the surface of a protein-binding chip. A subset of the proteins in the sample binds to the surface of the chip. The bound proteins are treated with a matrix-assisted laser desorption and ionization matrix and are washed and dried. The chip, which contains multiple patient samples, is inserted into a vacuum chamber where it is irradiated with a laser. The laser desorbs the adherent proteins and causes them to be launched as ions. The TOF of the ion before detection by an electrode is a measure of the mass-to-charge (m/z) value of the ion. The ion spectra can be analyzed by computer-assisted tools that classify a subset of the spectra by characteristic patterns of relative intensity (adapted from www.evmsdoctors.com).

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