Efi Kontou
posted about 2 months ago
I am Efi and I am a PostDoc in DTU Biosustain, in Copenhagen. I specialize in MS based metabolomics, wet lab to computational processing.
MethodPaper discussion

How to claim that a compound is produced by your strain in a publication?

LC-MS data is often used in papers to confirm/show that a specific molecule is being biosynthesized by a strain. But how can you correctly support your claim and how should you present your data in a publication?

Non-novel metabolite identification: 1. If the compound of interest can be found as a commercial standard or is being produced by a model strain that you have in your collection, run both the standard and the sample that putatively contains the compound in the same sequence (LC-MS). If the retention time and mass spectrum (MS1) are identical (or any other orthogonal information e.g., retention time and fragmented mass spectrum (MS2). This is the most confident form of identification (MSI level 1). 2. If you do not have access to the compound of interest (standard), but the annotated MS2 spectrum is deposited to a public (e.g. GNPS, MassBank) or in-house MS2 library, spectral matching should be performed between the reference and the experimental MS2 data. This can be done manually, or by using algorithms/tools (e.g. through Library Search from GNPS or MetaboliteSpectralMatcher from OpenMS). MSI level 2 annotations are putatively annotated compounds and are based on the same principle as MSI level 1, but using an external library (non-identical experimental conditions). Unknown compounds: 3. If the compound of interest is structurally related to one deposited in a public library, there are several algorithms that can predict the structure based on spectral similarities. MSI level 3 annotations are putatively characterized compound classes. For example, CSI:FingerID structural predictions are classified as MSI level 3 annotations. 4. MSI level 4 corresponds to unknown compounds that can still be differentiated or classified through their MS2 data (e.g., MSNovelist, ClassyFier).

By this nomenclature, only through MSI level 1 can one declare the presence of a compound with absolute confidence in a publication.

The author should always publish the reference spectra (and when possible, also the experimental) (see example under data availability in paper https://www.mdpi.com/1420-3049/26/21/6580).

Login or Signup to leave a comment