Clinical research relies on reproducible measurement of molecules for the purpose of lab testing and to answer general research questions. Our laboratory uses mass spectrometry to analyze molecules from biofluids for the purpose of biomarker discovery and targeted quantitation of known biomarkers. Because this is a relatively new field, several questions concerning quality control and sample collection remain to be addressed. For example, what is the effect on metabolites if plasma is collected and left at room temperature for 10 minutes versus 30 minutes. To what extent does saliva contaminate sputum and breath samples. We are using mass spectrometry-based metabolomics to answer these questions in the context of several on-going clinical studies. Our studies primarily focus on lung diseases such as COPD and asthma.