The problem I find most often with peak picking is that it picks random low intensity peaks within a certain retention time. And the other issue I seem to find are separated mzs, where you get essentially the same or very similar mz for the same RT.
Yes, I did think NH4 to Na made sense, but it would occur at least three times in a row.
The 26 difference is 26.0225, also at least 3 times in a row...
And why would it all be shifted by 5 mz between MS1 and MS2?
Given that the peak picking went well and didn't merge several masses it shouldn't have, yes that is my experience. If you see big differences you know something is not going right.
4.9554 could be a Na+<-> NH4+ difference. https://github.com/stanstrup/commonMZ/blob/master/inst/extdata/adducts_fragments.tsv
26 I don't have a good idea for. What is it accurately?
Dear Forum members,
My MS1 files are showing multiple fragments at 26 mz apart with a strong base peak in between them. The more fragmented MS2 (I mean MSe here since this isn't MSMS) files are then showing the same peaks shifted by 4.9 mz each backwards.
Any idea what this may be?
Yes, I mean mz values. So the peaktable mz has a better accuracy than the peak mz shown in an actual spectrum at the same retention time?
Are you talking about which m/z value to use? The one from the peaktable or from the raw data?
In xcms the m/z for each feature in individual samples is the intensity weighted mean across the peak. Then when you group features across samples it uses the median m/z of those mean values.
Because of this averaging the m/z in your peaktable should have a bit better accuracy. That is under the assumption that the parameters were sane enough not to group things that are NOT the same compound. So using this value you should normally be able to restrict your m/z range more when you search.
I just wanted to double check the following approach is not incorrect. I may be overthinking, but better safe than sorry.
For metabolite identification, I am searching for the feature xcms spat out, but I predominantly search the peaks that turn up in my spectra. Occasionally, these may not perfectly match either Camera or Xcms features.
I guess the question is: what's deemed more reliable - the xcms feature detection or the spectrum in identifying molec ions for compound identification?
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