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schymane
commented
Oct 1, 2019
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Current thoughts after talking with @adelenelai is that option (1) is likely easiest, I can count at least 6 (and probably more) formats we'll need to work with, so that a new reader for each (option 2) seems impractical - and ideally we'd like to merge where possible and not have 1000s of libraries. |
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sneumann commentedOct 1, 2019
The class
de.ipbhalle.metfraglib.scoreinitialisation.OfflineMetFusionSpectralSimilarityScoreInitialiserat
MetFragRelaunched/MetFragLib/src/main/java/de/ipbhalle/metfraglib/scoreinitialisation/OfflineMetFusionSpectralSimilarityScoreInitialiser.java
Line 26 in c57f9d2
is used to initialize parameters for the MetFusion-like score which
includes the reading of the spectral file
MoNA-export-LC-MS.mb. If nothing else given in thesettings with
OfflineSpectralDatabaseFile = ...This class uses the file located at
https://github.com/ipb-halle/MetFragRelaunched/blob/master/MetFragLib/src/main/resources/MoNA-export-LC-MS.mb
As already declared this file is in non-standard format to only include a little information needed by the score. The class located at
de.ipbhalle.metfraglib.peaklistreader.MultipleTandemMassPeakListReade in https://github.com/ipb-halle/MetFragRelaunched/blob/c57f9d2b406350b2357ce9f7ce42a286cefcca13/MetFragLib/src/main/java/de/ipbhalle/metfraglib/peaklistreader/MultipleTandemMassPeakListReader.java is used to read this file. This creates ade.ipbhalle.metfraglib.collection.SpectralPeakListCollectionwhich is stored in the global MetFrag settings object later used by the score classde.ipbhalle.metfraglib.score.OfflineMetFusionSpectralSimilarityScore`uses this data to calculate the MetFusion-like score for each candidate.
There might be two possibilities now. First, you simply create a new
spectral file in the format I used. It's quite simple as it only needs
the parameters:
SampleName,InChI,InChIKey,IsPositiveIonMode,PrecursorIonMode,MassError,MSLevel,IonizedPrecursorMass,NumPeaks,MolecularFingerPrintfollowed by the spectral data. You can easily figure that out when looking in the default file. This file can then be used by defining its path with
OfflineSpectralDatabaseFile = ...The used fingerprint function is the MACCSFingerprint included in the CDK implementation.
The second possibility is to define it's own spectral file reader instead of the reader
de.ipbhalle.metfraglib.peaklistreader.MultipleTandemMassPeakListReadercurrently used. Here, you could implement a NIST or a MassBank file
reader which also needs to create a
de.ipbhalle.metfraglib.collection.SpectralPeakListCollectionobject. But you need to include the fingerprint of the underlying molecule for each spectrum.
Thanks @c-ruttkies for the information! Yours, Steffen