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Topic: Processing IMS data on a short gradient with XCMS (Read 466 times) previous topic - next topic

  • ML
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Processing IMS data on a short gradient with XCMS
Hi there,

I am trying to process some ion-mobility data that I have acquired on a short gradient.

With the Centwave method, no chromatographic peaks are detected.

With Masspec wavelet, I have this error message:
Error: stop worker failed:
  'clear_cluster' receive data failed:
  reached elapsed time limit
I first thought it would be a memory problem from my computer but I have check that and it's all right, I have even added more RAM in case.

By consequence, I think it might be coming either from the IMS dimension of the dataset or from the short gradient that I am using.

Anyone would have any experience with XCMS to process IMS dataset, please? Or with a short gradient?

Many thanks in advance,
ML
  • Imperial College London

  • Jan Stanstrup
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Re: Processing IMS data on a short gradient with XCMS
Reply #1
How did you convert the files? Do they show something sensible in for example MzMine?
You might want to strip the IMS data. I have no experience with this but if you are converting with msconvert the scanEvent filter might be what you need.
With Waters files I have also had good luck simpy deleting the IMS data file (the masswolf converter I was using would crash otherwise)...

A short gradient should make no difference as long as there is still a sensible number of scans per peak.
  • University of Copenhagen, Denmark
Blog: stanstrup.github.io

  • ML
  • [*]
Re: Processing IMS data on a short gradient with XCMS
Reply #2
Hi Jan,
Many thanks for your answer! I am glad to know that the short gradient should not induce any difference.
I have converted my raw files using Proteowizard using this command:
inputCmd    <- c()
for (filePath in targetFiles){
  inputCmd    <- c(inputCmd,    paste('msconvert.exe', filePath, '-o', saveFolder, '--zlib --filter "scanEvent 1"', sep=' '))
}
The conversion seemed to be ok, I can open the spectra into MzMine and it seems fine.
The problem appears during the peak picking step.
Do you think that if I remove the IMS files into the raw folder of the samples (so by deleting the .cdt and .ind files right?), and reconvert them and re-try the peak picking afterwards, it might solve the problem?
Many thanks for your help, I really appreciate it!
Marine 

  • Imperial College London

  • Jan Stanstrup
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  • Administrator
Re: Processing IMS data on a short gradient with XCMS
Reply #3
No it doesn't sound like IMS is to blame to me.
Ideas to check:
1) decent number of scans per peak?
2) the data is centroided?
3) peak picking settings makes sense?
  • University of Copenhagen, Denmark
Blog: stanstrup.github.io

  • ML
  • [*]
Re: Processing IMS data on a short gradient with XCMS
Reply #4
Hi Jan,

Many thanks for those suggestions.

1) The number of scans per peak is small but enough I think (about 5 to 10 on average, the minimum for a well-defined peak is 7 right?).
2) Unfortunately, I have just realised that this dataset I have been acquired in continuum mode and not centroid. So I am assuming that's where the problem is coming from? Sorry, it might be really basic understanding but I am still at the beginning of the learning curve.
3) I have adapted the parameters to the dataset and playing with them quite a lot, but it might be coming from here too.

Many thanks for your help.
Marine
  • Imperial College London

  • Jan Stanstrup
  • [*][*][*][*][*]
  • Administrator
Re: Processing IMS data on a short gradient with XCMS
Reply #5
XCMS needs centroided data. If this is Waters data you can centroid your data in masslynx and then convert. See here: http://www.metabolomics-forum.com/index.php?topic=1247.msg3673#msg3673
  • University of Copenhagen, Denmark
Blog: stanstrup.github.io

  • ML
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Re: Processing IMS data on a short gradient with XCMS
Reply #6
Great! I will try that many thanks for your help!
  • Imperial College London