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MetFrag Vis (version 2.4.5+galaxy0)
Limit of candidate hits returned per compound
Fetch synonyms for each candidate from PubChem
Fetch compound classes for each candidate using ClassyFire

MetFrag Visualisation

Description

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/

Parameters

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.

Output

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
... ... ... ... ... ... ... ...

Additional notes

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

Developers and contributors

  • Kristian Peters (kpeters@ipb-halle.de) - IPB Halle (Germany)
  • Tom Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)
  • Christoph Ruttkies (christoph.ruttkies@ipb-halle.de) - IPB Halle (Germany)