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Messages - Jan Stanstrup

61
XCMS Online / Re: Issue with .cdf files
You will need to know what is in each function/scanEvent to know what is best to do. Analyzing different functions together probably doesn't make much sense. One could be a low energy scan and the other a high energy scan, or MSE.
If you open the _extern.inf file inside the raw folder each function is described at the bottom.

For conversion with proteowizard you have two problems:
1) Centroiding (if your files actually were recorded in profile mode). For waters data msconvert cannot use the Waters centroiding algorithm. It uses its own which is inferior. You can get around it by centroiding the files in masslynx to create centroided raw files that can then be converted
2) Accurate mass. It used to be that msconvert were not able to use the lockmass information to calibrate the masses. So you got uncalibrated data. Now it appears that the solution depends on how the files were recorded and the version of masslynx... So yes a big mess. Options are:
a) Some files will need the lockmassRefiner filter in msconvert. From my short tests it appears that some newer versions of masslynx will do the conversion correctly without this now.
b) Some files now seem to have the correction baked in.

You will need to check the masses masslynx is showing and comparing to the converted file to understand if things were converted correctly.
62
Other / Re: CDF chromatogram alignment
Would be possible with some hacking, yes. The CDF writer in XCMS is not compatible with any other software though. If you can use one of the XML based formats it is more feasible.

I think what you'd need to do is do peakpicking, feature grouping and retcor. Then use the results from retcor to modify and xmcsRAW object with the corrected retention times.
You will only change the scan times this way though. You won't get any fancy peak warping.

You might want to take a look at MSnbase for handling the raw data. The development version of XCMS uses MSnbase-based handling of the raw data.
63
XCMS / Re: Multiple features for narrow RT range
Are you talking about adducts and fragments? XCMS does not attempt to give you one feature per compound but one feature per ion.

CAMERA would be the standard tool to try to group ions originating from the same compound. There is however no consensus on how to statistically treat/merge those groups.
64
XCMS / Re: Spectra versus XCMS/Camera
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.
66
XCMS / Re: Spectra versus XCMS/Camera
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.
68
Compound identification / Re: Mzmed - mz of fragment or compound?
XCMS spits out "features" meaning all chromatographic peaks it can find for all masses (so think of it as XCMS doing extracted ion chromatograms for all possible masses and integrating all peaks it sees). Meaning that there might be many features in your list that come from the same compound. Some are pseudo moelcular ions, some are fragments, some are adducts, some are isotopes, some are noise, some are contaminants... You cannot even count on all compounds showing a pseudo molecular ion.

Probably the main challenge in metabolomics is exactly deciphering what is what. It is not a trivial task.
The typical first step to figuring what is what is to use the CAMERA package that try to group features according to which are likely to come from the same compound.
70
XCMS / Re: How to save xcmsSet object from workspace
To save your whole workspace use save.image(). To save only the xcmsSet object use save or saveRDS.

Probably what you want though is a peak table. For that you use peakTable and save that table for example with write.csv.
71
Mass spectrometers / Re: Internal Standards for LCMS
If you want to do real quantification then you need an internal standard for each compound you want to measure.
A weaker approach would be external calibration curves with non-labelled standards. This would not take into account the matrix effect. So unless you can validate that this makes some sense with your particular matrix by comparing to an approach with labelled standards first I would not give any validity to such an approach.

For untargeted metabolomics people disagree heavily. Some use a single standard, some try to use a standard for each compound group or possibly group by retention time.
I have yet to see anyone show that internal standards help anything in untargeted studies...


EDIT: I should clarify that my comments regarding untargeted was for the idea that you can use internal standards to quantify in an untargeted setting and the idea that you can use internal standards to correct analytical drifts.
As @stacey.reinke and @romanas chaleckis pointed out they can however be very useful to check the system.