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Messages - ML

2
XCMS Online / Re: Processing IMS data on a short gradient with XCMS
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
3
XCMS Online / Re: Processing IMS data on a short gradient with XCMS
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 

4
XCMS Online / 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