DDA settings for untargeted metabolomics and database searching
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Hi everyone,
I'm doing an untargeted metabolomics project using a Xevo G2-QToF. The samples are fractions of bacterial supernatant and pellet extract. The growth medium is quite rich, so many of the analytes - at least for the crude extract - are due to the media (probably due to it including peptone). Don't have Progenesis, just Masslynx.
I want to use DDA to get MS/MS results for everything *not* contained in the blank, and then search spectral databases like GNPS to check compound novelty. So far though the DDA chromatograms have just been literal straight lines with no good spectra, bearing little relation to the LC/MS chromatogram.
Does anyone have any suggestions about which settings to use for DDA, or any of the other MS/MS functions to do this? Would be happy with a good DDA result that included the blank masses too.
Thanks,
Josh
I'm doing an untargeted metabolomics project using a Xevo G2-QToF. The samples are fractions of bacterial supernatant and pellet extract. The growth medium is quite rich, so many of the analytes - at least for the crude extract - are due to the media (probably due to it including peptone). Don't have Progenesis, just Masslynx.
I want to use DDA to get MS/MS results for everything *not* contained in the blank, and then search spectral databases like GNPS to check compound novelty. So far though the DDA chromatograms have just been literal straight lines with no good spectra, bearing little relation to the LC/MS chromatogram.
Does anyone have any suggestions about which settings to use for DDA, or any of the other MS/MS functions to do this? Would be happy with a good DDA result that included the blank masses too.
Thanks,
Josh
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Answers
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Has anyone got any thoughts on this?0