Abstract The review describes chemical space, i.e. the set of known and possible compounds, and presents the use of corresponding chemical data in non-target analysis. Its implementation is briefly considered. General and dedicated chemical databases are outlined. Citation and co-citation of chemical compounds in databases are considered. The data transfer from high resolution mass spectrometry to chemical databases is noted to be the key stage of modern non-target analysis. Searched structures are further filtered with the use of reference and computational data. Related issues are also addressed.