System and method for early detection of contaminants in a fuel processing system

A processing system fuel (10), comprising: a processing unit fuel (12) adapted to produce from a supply reservoir (18) having a product hydrogen stream (34) comprising at least hydrogen gas and select one or more compounds selected from the group consisting of carbon dioxide methane and water; equipment fuel cell (14) including one or more fuel cells, wherein the fuel cell equipment (14) is adapted to receive at least a portion of the product hydrogen stream (34); and a control system (50) adapted to measure the concentration of at least one of or selected components in the product hydrogen stream (34) and prevent flow of the product hydrogen stream (34) to cell fuel (14) if the measure of at least one of / concentration of the selected components exceeds a corresponding threshold value.