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Wondering if there is an open (freely available) database of Mass Spec Data, particularly for the Substances/Compounds listed in NCBI.

Specifically, I am not sure if NCBI includes the mass spectrometry data / datafiles in their FTP server related to any of their chemicals. So I am just wondering if there is an open database of mass spec datafiles out there somewhere.

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  • $\begingroup$ It's unclear what you are looking for, there are many substances/compounds listed in NCBI. Could you clarify this so the question can be answered? $\endgroup$
    – Michael_A
    Nov 17, 2018 at 18:34

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The Human metabolome database (HMDB) contains many MS/MS and NMR spectra for human metabolites. You can acquire the spectra from the downloads section. The HMDB includes external identifiers for each compound. This includes the PubChem Compound IDs that are given on the NCBI database. There are 2 265 compounds with LC-MS/MS spectra in the HMDB.

The excellent MS-DIAL software package also comes with extensive positive and negative ion mode LC-MS/MS and GC-MS/MS spectral libraries in flat text format; that's also worth a look.

A lot of the raw spectral data is restricted due to multi party agreements (NIST, chemspider).

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