Protein arrays are assays measuring abundances of large number of proteins in a sample in one experiment. There is number of protein array types. Description of one particular approach follows:
Protein bead arrays consists of beads covered with antibodies. One bead has antibodies of only one specificity. Each array contains many bead types which differ in their fluorescence properties forming thus colour code. This colour code is used to distinguish between beads later. In an experiment the sample (e.g. peripheral blood) is lysed to yield complex mixture of cellular proteins - lysate. Proteins in a lysate are uniformly flourescently labelled (with different fluorophore than beads). Therefore the amount of proteins bound to particular bead type via specific antibody can be measured.
Protein bead arrays are analysed with flow cytometers. First, bead types are identified (gated) based on their colour code. Currently about 1700 bead types can be measured. Then the protein fluorescence, proportionate to its amount, is measured on each bead type. Therefore, abundances of 1700 different proteins can be assessed with single assay.
Antibody array analysis with label-based detection and resolution of protein size. Wu W, Slåstad H, de la Rosa Carrillo D, Frey T, Tjønnfjord G, Boretti E, Aasheim HC, Horejsi V, Lund-Johansen F. Mol Cell Proteomics. 2009 Feb;8(2):245-57 pdf