Protein microarrays are tools that can be used in many different areas of research, including basic and translational research. Protein arrays can take on many different formats and can be used to do more than simple expression profiling of samples.

Recent publications have demonstrated that protein microarrays can be used to phenotype leukemia cells, identify novel protein-protein interactions, screen entire proteomes for new proteins, and profile hundreds of patient samples simultaneously. Whatman has led the way in protein array technology starting with the development of the FAST Slide: the premier protein arraying surface.

Whatman offers kits, reagents, and protocols for scientists who wish to develop their own protein arrays, as well as off-the-shelf arrays and a variety of protein array services.

Proteomic Arrays
Proteomic arrays are typically high-density arrays (> 1000 elements/array) that are used to identify novel proteins or protein-protein interactions. The library that is arrayed can come from many possible sources, including expression libraries, and can contain known, as well as unknown, elements. The sample to probe the array can come from virtually any source.

To detect proteins that are bound to the array, the samples must be labeled directly with a fluorophore or a hapten. Alternatively, in some applications antibodies can be used to detect binding events. One common use is for antibody screening.

Microspot ELISA and Antibody Arrays
Microspot ELISA and antibody arrays are used for quantitative profiling of protein expression in cell cultures or clinical specimens. Typically these arrays are low-density (9 to 100 elements/array). In these arrays, known antibodies are arrayed and used to capture antigens from unknown samples. To detect antigen that is bound to the array, the antigen either needs to be labeled directly with a fluorophore, or a second binder/antibody can be used. The latter option creates a sandwich assay similar to a traditional ELISA, only in a microspot format. The Whatman FAST Quant Cytokine Quantification Kits offer an example of a microspot sandwich assay.

Single-Capture Antibody Arrays
Single-capture antibody arrays consist of multiple, known antibodies arrayed to a solid surface and used to profile the presence of specific antigens from a pooled sample, usually consisting of both a normal and disease-present sample. A single capture antibody array utilizes a direct or hapten labeling system, which does not require a matched antibody. Single-capture antibody arrays offer a qualitative profiling tool to detect binding events. The Whatman Serum Biomarker Chip offers an example of a single-capture antibody array.

Antigen Arrays or Reverse Arrays
One application of antigen arrays is to interrogate research or clinical samples for the presence of auto-antibodies. Normally, a low-density array is probed with serum or plasma samples. The Whatman CombiChip Autoimmune Kit offers an example of an antigen array. Reverse arrays are used to profile dozens or hundreds of samples (research or clinical) for the presence of a small number of antigens (1 to 3). Cell lysates, material from laser capture microdissection or serum samples are arrayed. This creates an array of ‘unknowns’ that can be probed with a small number of antibodies. Visualization can be performed with a detection or ‘top’ antibody linked to a fluorophore or color detection reagent.

Microarray Westerns
An alternative strategy for protein microarrays is to array samples containing multiple proteins on the FAST Slide and probe with a labeled antibody or set of antibodies. The advantage of the micro format is that extracts from various treatments and time points can be arrayed on the same slide. Once arrayed, the levels of multiple proteins can be measured and compared simultaneously.

Protein Binder Arrays
Protein arrays can be used to identify novel protein binding motifs or protein-protein interactions. Engineered or synthetic proteins, or peptides with various binding motifs are arrayed, and the array is probed with complex protein samples. Detection with a known antibody allows the researcher to identify previously unknown binding events.