HPLC is probably the most common method used for targeted analysis of plant materials, and for metabolic profiling of individual classes. A derivatisation step is not essential (unless needed for detection), since involatile and volatile substances may be measured equally well. Selection of compounds arises initially from the type of solvent used for extraction (as with all methods that use an extraction step), and then from the type of column & detector. For example HPLC/UV will only detect compounds with a suitable chromophore, a column selected for its ability to separate one class of compounds will not generally be useful for other types. HPLC profiling methods all rely to a great extent on comparisons with reference compounds. The full UV spectrum (measured for each peak when UV-diode array detectors are used) gives some useful information on the nature of compounds in complex profiles, but often indicates the class of the compound rather than its exact identity.

The development of robust high-performance liquid chromatography (HPLC) technologies continues to improve the detailed analysis and sequencing of glycan structures released from glycoproteins. A database (GlycoBase) & analytical tool (autoGU) to assist the interpretation and assignment of HPLC-glycan profiles is presented. GlycoBase is a relational database which contains the HPLC elution positions for over 350 2-AB labelled N-glycan structures together with predicted products of exoglycosidase digestions. AutoGU assigns provisional structures to each integrated HPLC peak and, when used in combination with exoglycosidase digestions, progressively assigns each structure automatically based on the footprint data. These tools are potentially very promising and facilitate basic research, as well as the quantitative high-throughput analysis of low concentrations of glycans released from glycoproteins

A database was developed to store, organize & retrieve the data associated with electrophoresis and chromatography separations. It allows laboratories to store extensive data on separation techniques (analytical & preparative). The data for gel electrophoresis includes gel composition, staining methods, electric fields, analysis & samples loaded. The database stores data on chromatography conditions, the samples used and the fractions collected. The data structure of this database was designed to maintain the link between samples (including fractions) from chromatography separations and their analysis by gel electrophoresis. The database will allow laboratories to organize and maintain a large amount of separation & sample data in a uniform data environment. It will facilitate the retrieval of the separation history of important samples and the separation conditions used.