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MS-DIAL / Features list containing duplicates
I need help to understand the feature list produced by MS-Dial.
I am processing over 200 samples analysed in GC/MS. The data has been acquired in several separate batches and unfortunately there is a RT shift of up to 3.6 seconds between the batches. I performed a processing with MS-Dial version 4.9 and the parameters in the attached text file.
By looking through the feature list from the alignment, I found features with the same RT, the same distribution profile across the samples but a different quant mass. When opening the files on AMDIS I find that there is a chromatographic peak at this retention time (hopefully!), and that the two m/z selected by MS-Dial line up perfectly with the same peak shape (see attached image).
I would say that these two features belong to the same molecule and therefore there should not be two lines in the feature list. I had two hypotheses to explain this:
(1) There is a problem during deconvolution. I tested sigma values between 0.5 and 0.8, which I understand should decrease the number of deconvolved peaks, but this had no effect. I also tried increasing the EI spectra cutoff from 10 to 100 amplitude and got even more features.
(2) There is a problem with the alignment. I tried to align according to the RI rather than the RT, as each sample has its own list of alkanes, but this also had no effect.
What parameters should I change to avoid these duplicates?
Is there a way to automatically remove these duplicates?
Side question: When I look at the "Raw vs. Purified" to see the difference between the deconvoluted spectra, it doesn't change no matter which feature I look at. Is this normal?
I look forward to your suggestions
Best,
Nathalie