Many literatures focus on the biological relevance and the identification of biomarkers for disease activity assessment while less attention has been paid to the development of standard procedures for sample preparation and storage based on liquid chromatography technique. The influencing factors including protein precipitation, storage temperature, storage time, and reconstitution by ultra pure water were analyzed employing HPLC-DAD. The effects were investigated from five participants over three months by principal components analysis (PCA) and the values of percent changes (PC). The samples with protein precipitation might slow the rate of bacterial enzymatic conversion. After protein precipitation, the average PC of urine samples ($0.136{pm}0.013$, n = 5) is relatively less than that of the serum samples ($0.173{pm}0.026$, n = 5) for three months. Minimal effects on metabolic profiles of serum and urine (PC < 0.15) are reasonable for metabolomic studies after protein precipitation and storage at $-20^{circ}C$ for two months.