Immunoassays detect proteins that are manufactured in the cell according to the information coded by the transgenic (GMO) DNA.  For example, Roundup Ready GM soy has been genetically engineered to be resistant to the glyphosate herbicide Roundup via insertion of a gene that codes for a glyphosate tolerant version of a plant enzyme, CP4 epsps.  Once successfully inserted into the soybean genome, the introduced gene is able to code for the protein enzyme which confers on the plant the ability to survive treatment with glyphosate.  The presence of the CP4 epsps protein in Roundup Ready soybean plants provides the option to test for this genetic modification by immunological protein detection techniques.
Immunological techniques often use antibodies to detect the protein of interest. An antibody is an immune system related protein that is highly specific for a particular protein.  Antibodies that recognize specific GMO proteins can be synthesized ex vivo in large amounts by genetic engineering of transformed mammalian cells and are therefore highly suited for protein detection methodologies.  Antibodies are the basis for the specificity of two protein based GMO detection methods, the strip test (also known as a lateral flow device) and ELISA.
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