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Metabolomics spectra databases

A very good overview on databases (including links) can be found at the Metabolomics Society Homepage: Link

Another collection of links to databases can be found at the Fiehn lab homepage: Link. The provided information is much less sorted and partially deprecated.

GC-MS database table (incomplete)

Name Link Licence estimated quality file format(s) comments
Golm DB http://gmd.mpimp-golm.mpg.de/ free + .msl, .msp (Golm style) last update online in 2011, german project (DFG, MaxPlanck)
Fiehn DB non-free (?), several MS vendors have/had licences - .msp (Fiehn style) seems to be deprecated
MassBank of Northern America (MoNA) http://mona.fiehnlab.ucdavis.edu/downloads free ++ JSON (with metadata); .msp (MoNA style) (w/o metadata) .msp (MoNA style) should be compatible with NIST MS Search
MassBank http://www.massbank.jp/en/about.html free provides also software and API
NIST commercial NIST format, can be exported as .msp (NIST style)
Human Metabolome Database (HMDB) http://www.hmdb.ca/ free +++ XML provides also structures and protein DBs

Spectra file format converter

We need a converter to be able to automatically compare and combine the different databases.

  • Inputs: All *.msp formats, HMDB-XML, MoNA-JSON

  • Outputs: to be discussed. Potentially useful outputs: MoNA *.msp, MoNA-JSON (?), HMDB-XML

    • I think we should refrain of defining and using a newly defined format. I see some drawbacks in each of the ones existing, but IMHO it really does not make sense to increase the confusion about the right format.

  • Examples of all formats can be found here: [./Beispiele_SpektrenFormate.zip]

    • Every example uses the same two metabolites, only nist_msSearch_output.msp uses two different ones

More information on single DBs

MoNA: MassBank of Northern America (MoNA) collects spectra from many other free databases (e.g. HMDB, RTX Fiehnlib, LipidBlast) and combines them into one huge library. You can restrict the spectra either based on the method (e.g. GC-MS) or based on the source (e.g. HMDB).

HMDB: Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. Sorted by human body fluids (e.g. serum, saliva). Contains many metadata.

Golm: The 2011 version includes most commercially available metabolites. The group is still integrating new ones, but does not upload them online. Current versions are available directly from the Kopka lab. "Ich würde denken dass unserer öffentlicher Teil ziemlich komplementär zu Fiehnlib und dem GC-MS Anteil der Massbank sind." (Zitat Leiter Golm DB)

MassBank: A collection of free databases from different labs allover the world.