Human milk oligosaccharides (HMOs) perform a number of functions including serving as prebiotics to stimulate the growth of beneficial intestinal bacteria, as receptor analogues to inhibit binding of pathogens, and as substances that promote postnatal brain development. There is further evidence that HMOs participate in modulating the human immune system. Because the absorption, catabolism, and biological function of oligosaccharides (OS) have strong correlations with their structures, structure elucidation is key to advancing this research. Oligosaccharides are produced by competing enzymes that provide the large structural diversity and heterogeneity that characterizes this class of compounds. Unlike the proteome, there is no template for oligosaccharides, making it difficult to rapidly identify oligosaccharide structures. In this research, annotation of the neutral free oligosaccharides in milk is performed to develop a database for the rapid identification of oligosaccharide structures. Our strategy incorporates high performance nanoflow liquid chromatography and mass spectrometry for characterizing HMO structures. HPLC-Chip/TOF MS provides a sensitive and quantitative method for sample profiling. The reproducible retention time and accurate mass can be used to rapidly identify the OS structures in HMO samples. A library with 45 neutral OS structures has been constructed. The structures include information regarding the epitopes such as Lewis type, as well as information regarding the secretor status.