MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment.
This module summarises the results generated by MetFrag. It takes the (sometimes very large) output tabular file, parses the file and enriches it with images of the spectra showing the extracted and matched peaks and putative structures of the compound candidates. The module supports limiting the results per compound (default 10 candidates). Results can be enriched with further information from PubChem and ClassyFire to make it easier to select candidates. The information is summarised in a HTML5 file which can be viewed directly in Galaxy.
Website: http://ipb-halle.github.io/MetFrag/
1. Tabular file
Tabular file created using the MetFrag tool.
2. MetFrag Hits Limit
Defines the limit of candidates returned per compound.
3. Synonyms
If set to True, synonyms for each candidate are fetched from PubChem.
4. ClassyFire
If set to True, compound classes are fetched for each candidate using ClassyFire.
The output is similar to the MetFrag results tabular, but enriched with additional images of spectra, compound candidates and (if enabled) compound classes, alternative names and links to online services.
adduct | name | ... |
[M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; | ... |
[M-H]- | D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; | ... |
... | ... | ... |
Table continued (these columns are derived from the MetFrag result):
... | sample_name | ExplPeaks | FormulasOfExplPeaks | ... |
... | 1_metfrag_result | 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 | 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- | ... |
... | 1_metfrag_result | 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 | 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- | ... |
... | ... | ... | ... | ... |
Table continued (columns are derived from the MetFrag result):
... | FragmenterScore | FragmenterScore_Values | FormulasOfExplPeaks | Identifier | InChI | ... |
... | 105.844569063138 | 696.0;1156.0;696.0;1156.0 | 6-(hydroxymethyl)oxane-2,3,4,5-tetrol | 206 | InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H | ... |
... | 105.844569063138 | 696.0;1156.0;696.0;1156.0 | (3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol | 5793 | InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1 | ... |
... | ... | ... | ... | ... | ... | ... |
Table continued (columns are derived from the MetFrag result):
... | NoExplPeaks | NumberPeaksUsed | OfflineMetFusionScore | SMILES | Score | SuspectListScore | XlogP3 |
... | 4 | 5 | 2.84566828424078 | C(C1C(C(C(C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 |
... | 4 | 5 | 2.84566828424078 | C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O | 1.82678219603441 | 1 | -2.6 |
... | ... | ... | ... | ... | ... | ... | ... |
This module queries the online services PubChem and ClassyFire.
Feunang YD, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, Wishart DS (2016): ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. J Cheminform 8:61. doi: 10.1186/s13321-016-0174-y
Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE (2019): PubChem 2019 update: improved access to chemical data. Nucleic Acids Res. 8;47(D1):D1102-D1109. doi: 10.1093/nar/gky1033