Proteomics protein chip array

In a more modified approach, differential display proteomics can also be done with no separation of proteins. This is called the protein chip approach. In this method, a variety of bait proteins such as antibodies, peptides, or protein fragments may be immobilized in an array format on specially treated surfaces. The surface is then probed with the samples of interest. Proteins that bind to the relevant target can then be analyzed by direct MALDI readout of the bound material (Nelson, 1997 Davies et ah, 1999). Lor example, well-characterized antibodies can be used as bait. Protein samples from two different cell states are then labeled by different fluorophores, mixed together, and used as probe. In such a case, the fluorescent color acts as an indicator for any change in the abundance of the protein that remains bound to the chip (Lueking et ah, 1999). A number of technical problems would still need to be overcome before applying this technique for large-scale analysis of proteins. 

Another method using protein "chips has also been developed (Haab et al., 2001 Zhao et al., 2001 Zhu et al., 2001). These chips contain ordered arrays of protein-binding molecules with the proteins then bound or enriched on a segment of the chip to be analyzed via various technologies. Antibodies recognizing specific protein sequences or modifications can be used, for example, to separate proteins with a specific activity from a complex mixture. A different version of a protein chip has been created by Zhu et al. (2001) and by Martzen et al. (1999). In these cases, the proteins are arrayed on the chip and the proteome can then be screened for interaction with particular substrates and ligands, and for certain classes of biochemical properties and activities. 

Two hundred and forty-eight serum samples provided from the National Ovarian Cancer Early Detection Program clinic at Northwestern University Hospital (Chicago, IlUnios) were analyzed on the same ProteinChip arrays using both a PBS-II and a Qq-TOF MS fitted with a SELDI interface. The proteomic patterns of the serum samples were acquired on the PBS-II TOF MS, immediately followed by their acquisition on the Qq-TOF MS. The key to this study is that the identical set of serum samples was analyzed on the exact same protein-chip surface, eliminating all experimental variability other than the use of two different instruments. 

Without highly specific binding to proteins on the chip, thorough washing of the array may remove specific binders as well as non-specific binders. Protein bindings cannot offer a universal detection scheme like hybridization used in DNA arrays, which makes it difficult to discover enough probes for proteomics. 

In this chapter, we will present different types of biochips, including protein and antibody arrays, as well as carbohydrate, peptide and living cell arrays. We will discuss recent progress and current bottlenecks in high-throughput generation of chip content, surface chemistry, molecule attachment, detection methods, and also applications in the proteomic field and in drug discovery. 

Gilbert, I. Schiffmann, S. Rubenwolf, S. Jensen, K. Mai, T. Albrecht, C. Lankenau, A. Beste, G. Blank, K. Gaub, H. E. Clausen-Schaumann, H., Double chip protein arrays using recombinant single-chain fv antibody fragments, Proteomics 2004, 4, 1417-1420... 

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