Table 1.
Metabolomics and Natural Products MS/MS Computational Resources Overview
| Summary | Data repository* | Reference collections^ |
Open online data analysis& |
Reference | |
|---|---|---|---|---|---|
| GNPS | Natural products and metabolomics crowdsourced analysis platform with public reference libraries, public data repository and living data |
Yes, with automated reanalysis, minimal required metadata (220 w/MS2, 274 total) |
Yes, open access, crowdsourced curation |
Can search any number of files, analog searches and molecular networking (G,J,E,NA,R,H,N) |
|
| Reference Collections | |||||
| MassBank Japan | The first public large scale database for metabolomics reference spectra. |
Yes, open access |
Can search up to one file at a time (J) |
5 | |
| MassBank Europe | European counterpart of massbank japan. This public reference spectral library is under construction to include draft structures. |
Yes, open access |
Can search up to one file at a time (J,E) |
||
| MassBank North America | North American public spectral library warehouse and distribution database. |
Yes, open access |
Can search up to one file at a time (G,J,NA,R,H) |
||
| ReSpect | Public reference library for plant metabolites. |
Yes, open access |
Can search single spectrum (R) |
8 | |
| HMDB | Public reference library for human metabolites. |
Yes, open access |
Can search single spectrum (H) |
55 | |
| XCMS-online/Metlin | Reference library for metabolomics. Can be searched but the library is commercial and not available for public redistribution. |
Yes, no reanalysis (10 w/MS2, 23 total) |
Yes, not freely available |
Can search any number of files up to 25Gb (Mt) |
6 |
| NIST/EPA/NIH | Reference libraries for metabolomics. Accessible through purchase but not available for redistribution. |
Yes, not freely available |
|||
| mzCloud | A metabolomics search engine and reference library. The library is not available to the scientific community. |
Yes, not freely available |
|||
| Data Repositories | |||||
| Metabolights | Public data repository for metabolomics data, library capabilities under construction. |
Yes, no reanalysis, experimental metadata (13 w/MS2, 131 total) |
Aggregator only |
34 | |
| Metabolomics workbench | Public data repository for metabolomics data. |
Yes, no reanalysis, extensive metadata required (9 w/open format MS2, 196 total) |
Aggregator only |
56 | |
Data repository – denotes whether a resource is designed to publicly share projects data with the community or between different research groups. Total number of MS/MS datasets and total datasets are shown in parenthesis.
Reference collection of MS/MS spectra – indicates whether resources contribute new MS/MS reference spectra to spectral libraries (rather than redistributing them); mode of access to download the MS/MS reference spectra is clarified.
Online analysis utilizing MS/MS reference spectra available at each resource, with emphasis on batch capabilities; the MS/MS spectral libraries available for searches at each resource are highlighted with the following notation: GNPS libraries (G), MassBank JP libraries (J), MassBank EU libraries (E), MassBank of North America libraries (NA), HMDB libraries (H), ReSpect libraries (R), NIST libraries (N), Metlin libraries (Mt), mzCloud libraries (Mz).