MS/MS Search:
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  • The MS/MS Search program allows a user to search one experimental MS/MS spectrum or a batch of MS/MS spectra against a library of predicted MS/MS spectra of possible human metabolites. The current MCID spectral library consists of predicted spectra of all the known endogenous human metabolites in the Human Metabolome Database (HMDB) (8,021 metabolites) and their predicted metabolic products via one metabolic reaction in the Evidence-based Metabolome Library (EML) (375,809 predicted metabolites).

  • MCID MS/MS spectral search cannot always produce one unique structure match. However, one of the top 3 matches from a MS/MS spectrum with a fit score of greater than 0.700 (out of 1.000) is most likely a correct structure.

  • The ability of using MS/MS search to narrow down a MS/MS spectral match to a few structure candidates should save time and efforts to find or synthesize authentic compound standards of these candidates for positive identification.


  • Single-mode spectral search using the precursor ion and fragment ion masses and their intensities.

  • Batch-mode spectral search using all MS/MS spectra collected from a study. The MS/MS spectral data are uploaded as a CSV file and the search results can be saved as a CSV in a local computer.

  • The server does not store any search file or search results. However, in the saved search results file in CSV which can be opened in Excel, there is a link column containing long names for all the individual matches. By copying and pasting a link name of a match to the web, the user can retrieve the search result in MCID for the match.