Methods are disclosed for the capture, detection, separation, isolation and quantification of contaminants in a starting material. Also disclosed are competitive assay methods for the detection and quantification of contaminants in a starting material. Kits for use with the method are disclosed as well. A system for capturing, separating and/or concentrating contaminants from a material is also presented. The system captures, separates and/or concentrates contaminants such as bacteria, viruses, other microorganisms, and/or larger items, such as insects, from a variety of materials, such as food, and environmental and clinical materials. In general, the system uses a rotating magnetic field to mix the material with magnetic particles to capture the target contaminants, and a fixed magnetic field to separate and concentrate the captured target contaminants.