Table 2.
Summary of available databases for plant metabolites identification and pathway analysis.
| Database | Compatibility | Link | Description | Reference |
|---|---|---|---|---|
| NIST | LC-MS, GC-MS | https://www.sisweb.com/software/ms/nist.htm | a most widely used mass spectral reference library, in which MS/MS spectra, mass spectra for multiple ion adducts, compound name, formula, CAS number, etc., are all included | – |
| METLIN | LC-MS | http://metlin.scripps.edu | including nearly one million molecular standards with MS/MS data, and supporting multiple retrieval modes | Smith et al. (2005) |
| BinBase | GC-TOF-MS | http://fiehnlab.ucdavis.edu/staff/wohlgemuth/binbase/ | peak filtering and annotation using a mass spectral metadata-based filtering algorithm | Fiehn et al. (2005) |
| MMCD | NMR, LC-MS | http://mmcd.nmrfam.wisc.edu/ | compatible for identifying metabolites from both NMR and MS data | Cui et al. (2008) |
| SIRIUS | LC-MS | https://bio.informatik.uni-jena.de/sirius/ | comprehensive assessment of molecular structure using MS/MS data |
Böcker et al. (2009); Dührkop et al. (2019) |
| MassBank | LC-MS, GC-MS | https://massbank.eu/MassBank/ | a distributed database and ESI-MS2 data, under different experimental conditions, are included | Horai et al. (2010) |
| ReSpect | LC-MS | http://spectra.psc.riken.jp/ | plant-specific MS/MS-based data resource and database | Sawada et al. (2012) |
| CSI:FingerID | LC-MS/MS | https://www.csi-fingerid.uni-jena.de/ | combining fragmentation tree computation and machine learning for molecular structure searching | Dührkop et al. (2015) |
| LC-MS/MS library | LC-MS/MS | http://www.noble.org/apps/Scientific/WebDownloadManager/DownloadArea.aspx | ultra-high-performance liquid chromatography-tandem mass spectral library of plant natural products | Lei et al. (2015) |
| MS2LDA | LC-MS | http://ms2lda.org/ | Mass2Motifs-based method is used to annotate metabolites without the necessary of existing reference spectra; establishing biochemical relationships between molecules | van der Hooft et al. (2016) |
| GNPS | LC-MS | https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp | a natural product and metabolomics analysis platform using molecular networks | Wang et al. (2016) |
| NAP | LC-MS | https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp | a re-ranking system is used to increase the annotation rates | da Silva et al. (2018) |
| MetDNA | LC-MS | http://metdna.zhulab.cn/ | large-scale and ambiguous identification of metabolites from LC-MS/MS datasets without the need of a standard spectral library | Shen et al. (2019) |
| MMN | LC-MS | / | MicroTom metabolome and transcriptome dataset | Li et al. (2020) |
| KEGG | – | https://www.genome.jp/kegg/ | one of the most complete and widely used databases; containing metabolic pathways from a wide variety of organisms | Ogata et al. (1999) |
| MetaCyc | – | https://metacyc.org/ | experimentally elucidated metabolic pathway database | Caspi et al. (2020) |
| WikiPathways | – | https://www.wikipathways.org | a biological pathway database, including pathways from more than 30 species | Martens et al. (2021) |
| PMN15 | – | https://plantcyc.org/ | genome-wide metabolic pathway databases for 126 plants | Hawkins et al. (2021) |