Protein microarrays types

Most important protein microarray types 3.4.3.1 Glass microarray slides... 

Currently, protein microarrays can be divided into various types depending on the strategies to be chosen. For example, according to the array structure and shape, protein microarrays include 3D-surface structure [30, 31], nanowell [32], and plain chips [33-36], Meanwhile, considering the field of application, protein microarrays can be classified into five categories antibody array, antigen or reserve array, functional array, capture array, and solute array. Table 11.6 shows the differences among them. 

The proteomics field is currently wide open. Only a few protein microarray products have been commercialized. Unlike DNA microarrays that are commonly constructed on essentially two platforms (GeneChip or slide array) employing oligonucleotides or cDNA probes, the protein microarray appears on a variety of platforms and with different types of probes. 

In the following sections, the major types of substrates currently used for DNA and protein microarrays will be discussed. Much of what is known regarding microarray surface chemistry and the immobilization of biomolecules comes from work with DNA microarrays. Therefore, many of the examples cited here will be from these studies. Zhu and Snyder (2003) in their review provide good insight into the manufacture and utility of protein microarrays. Here are some points to consider when choosing a substrate for protein microarrays ... 

How do we then envision the protein microarray as a proteomics tool We now estimate the human genome to comprise around 30,000 genes. For gene expression analysis using DNA microarrays, 1000 to 10,000 gene elements are often used. Since proteins undergo posttranslational modification (>200 different types see McDonald and Yates, 2000, Reference 40) and can occur as isoforms and multiprotein complexes, the number of protein expression elements needs to be much larger. 

VanMeter AJ, Rodriguez AS, Bowman ED et al (2008) Laser capture microdissection and protein microarray analysis of human non-smaU cell lung cancer differential epidermal growth factor receptor (EGPR) phosphorylation events associated with mutated EGFR compared with wild type. Mol Cell Proteomics 7 1902-1924... 

Analogous to but not yet as technically developed as the genomic microarray, the protein microarray is another emerging technique that holds great analytical promise (93,94), especially with respect to throughput. In general, two types of microarrays are used in proteomics the antibody array (95) and the functional protein microarray (96) (Fig. 7). 

Figure 7.1 Types of protein microarrays and their applications.

A protein microarray study by Jones et al. (33) was designed to test the affinity of all proteins that contain SH2 and PTB domains, which specify binding to the phosphorylated domains of all four ErbB family members. The study uncovered that some ErbB family members were more promiscuous than others, which has important implications for the ErbB signaling network in general and specifically in that the promiscuous ErbB family members are much more commonly overexpressed in several cancer cell types. Eurthermore, 116 new ErbB interaction partners were discovered. Another study by Schulze et al. (34) was also designed to identify all interaction partners for the phosphorylated ErbB family members but using a novel methodology that combines SILAC and LC-MS/MS. This study defined the specific ErbB sites where the interaction partners bind. 

FIGURE 1 Major types of protein microarrays (A) targeted protein arrays, (B) reverse-phase protein arrays, and (C) in situ expressed protein arrays. 

Fig. 2 Common types of microarrays DNA microarray (a), carbohydrate microarray (b), antibody microarray (c), functional protein microarray (d), biomembrane and membrane protein microarray (e), and cellular microarray (f)...

Protein microarray has been useful in examining the relative abundance of a large number of proteins from two different cell types or from a cell type grown under two different condition. The ability to visualize these differences in a large number of proteins from two cell types at the same time makes this method ideally suitable for proteomic analyses. 

Because each cell cluster expresses a particular protein, and cell clusters are spatially separated, the TCA can be considered a particular type of protein microarray. The TCA utilizes eukaryotic cells, allowing for PTMs of expressed proteins. Utilization of different cell lines provides opportunities to screen for protein function in situations where ceU-type-dependent PTMs and PPIs are important. Hence, the investigation of protein function within... 

To prepare porous silicon microarrays in the Laurell group, 380 pm-thick <100> silicon wafers were utilized. The p-type boron-doped wafer with a resistivity of 10-15 Qcm was mounted in an in-house-made electrochemical etch cell. The porosification was made in an electrolyte solution of HF/DMF 1 10, and the wafer was illuminated by a 100 W halogen lamp at a distance of 10 cm. A current density of 2 mA/cm was applied for 1 h. The macropores in the porous layer produced for protein microarrays typically measured 0.5-1.5 pm with a fine side branching network of nanopores (Ressine et al. 2005). 

---