MS2 Spectra Reference Databases:

The MS2 databases are curated from multiple public repositories under various licenses as documented below. By downloading these databases from the provided links below, you are considered to have agreed to comply with the original licenses. Please read and ensure compliance with the requirements of these licenses if you decide to reuse any of these databases.
Library Description Download LICENSES
Pathway-related library (136MB) MS2ID_Pathway.zip HMDB (CC BY-NC 4.0)
MoNA (CC BY 4.0)
LipidBlast (CC BY 4.0)
MassBank (CC BY)
GNPS (CC0 / CC BY)
MINEs (MIT)
RIKEN (CC BY 4.0)
BMDMS (CC BY 4.0)
ReSpect (CC BY 4.0)
Vaniya (CC BY 4.0)
Pathway-related library (Neutral Loss, 94MB) MS2ID_Pathway_NL.zip
Biological library (744MB) MS2ID_Biology.zip
Biological library (Neutral Loss, 491MB) MS2ID_Biology_NL.zip
Exposomics library (1.5GB) MS2ID_Exposomics.zip
Exposomics library (Neutral Loss, 1.1GB) MS2ID_Exposomics_NL.zip
Lipids library (1.6GB) MS2ID_Lipids.zip
Lipids library (Neutral Loss, 1.1GB) MS2ID_Lipids_NL.zip
Complete library (7.2GB) MS2ID_Complete.zip
Complete library (Neutral Loss, 6.4GB) MS2ID_Complete_NL.zip

MS2 Fragmentation Formula Databases:

The molecular formulas for the MS2 peaks in the reference database spectra are predicted using the MSBUDDY. This fragmentation formula database was curated from the Complete library and Complete library (Neutral Loss) MS2 spectra databases above.
Library Description Download Curation Tools
Fragmentation formula complete library (1.5GB) FragsAnnotateDB.zip BUDDY and msbuddy (python)
Fragmentation formula complete library (Neutral Loss, 1.3GB) FragsAnnotateDB_NL.zip

PLINK and hapmaps:

These libraries are used for LD Clumping locally, including plink binary file and hapmaps curated from OpenGWAS.
Library Description Download Resources and Licenses
PLINK and Hapmaps (7.9GB) PLINK_Hapmaps.zip PLINK Source, version 1.9 and GNU General Public License (V2)
LD Clumping local hapmaps from OpenGWAS Project.
NSERC CRC CFI TMIC Genome Canada Genome Quebec NIH