Mass spectrometry based metabolomics represents a new area for bioinformatics 
technology development. While the computational tools currently available such 
as XCMS statistically assess and rank LC-MS features, they do not provide 
information about their structural identity. XCMS(2) is an open source software 
package which has been developed to automatically search tandem mass 
spectrometry (MS/MS) data against high quality experimental MS/MS data from 
known metabolites contained in a reference library (METLIN). Scoring of hits is 
based on a "shared peak count" method that identifies masses of fragment ions 
shared between the analytical and reference MS/MS spectra. Another functional 
component of XCMS(2) is the capability of providing structural information for 
unknown metabolites, which are not in the METLIN database. This "similarity 
search" algorithm has been developed to detect possible structural motifs in the 
unknown metabolite which may produce characteristic fragment ions and neutral 
losses to related reference compounds contained in METLIN, even if the precursor 
masses are not the same.