How do I decide whether to use the Accurate Mass Metabolite Spectral Library by SCIEX or use METLIN in XCMS Plus?
The Accurate Mass Metabolite Spectral Library (AMMSL) was generated on metabolites (mostly endogenous) that are biologically relevant in human biology. The library contains over 500 of these metabolites which also include key exogenous and xenobiotic compounds which are typically found in the human metabolome such as caffeine and theophylline (found in coffee). It is a very focused set of metabolites which are routinely measured in metabolomics experiments.
Using MasterView™ Software, reference spectra from the AMMSL is automatically matched to your data, using the MS1 mass and isotope distribution pattern, the MS/MS spectral pattern as well as retention time. Matching results are combined into a library score, a score of over 70 is deemed acceptable. Where so many metabolites share the same accurate masses, differentiating on MS1 alone does not unambiguously identify your feature of interest. Using the MS/MS fragmentation pattern automatically on a large number of samples allows more confident identification, as well as significantly accelerating your time to results over manual matching.
Contrary to this the METLIN database houses over 240,000 compounds, these include metabolites but also pesticides, di-peptides and many other classes of compounds such as plant metabolites and secondary metabolites. If you are studying other species or looking for compounds outside of the core metabolites in human biology, XCMSplus is a great solution. Note though while this database houses MS/MS spectra, XCMSplus or XCMS online software does not automatically match the MS/MS spectra with the experimental MS/MS for identification.