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
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.
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
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?
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
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
Great! I will try that many thanks for your help!