A new method and apparatus are described for on‐line mass spectrometry that enables real‐time, automated, trace contamination and chemical species analyses focused on semiconductor manufacturing application. The scaleable ion source produces not only elemental ions for ppt quantitative analysis, but also enables quantitative and qualitative elemental, species, ligand, and organic molecular analyses. The system uses a unique calibration methodology permitting automated, continuous, unattended operation for up to a week without intervention. A sample handling system has been developed to automate small sample extraction (2 mL) from wet stations and its transport for up to 30 meters to the instrument using laminar flow techniques. Sample preparation includes the incorporation of stable enriched isotope reference solutions with feedback control for automated optimization of sample and reference mixtures. Instrument data is converted into actionable instructions for manual intervention or for integrated metrology and advanced process control (APC) implementation. Identification of species present in process solutions as a function of time provides new information about processes and mechanisms, offering unique characterization and defect prediction. These new capabilities are expected to enable rapid yield learning, contamination and chemical constituent quantification, and significantly improved process control. © 2003 American Institute of Physics