Failed Importing Results... Failed to Centroid Scan

Failed Importing Results... Failed to Centroid Scan bwidner  2019-10-02

Hello Skyline Team!

I tried to import a batch of ~30 files and got the following error for three of them

At 2:35 PM:
Failed importing results file 'C:\Filepath\mtab_BCderiv_BC43_092619_69.raw'.
[SpectrumList_Thermo::spectrum()] Error retrieving spectrum "controllerType=0 controllerNumber=1 scan=3119": [RawFileThreadImpl::getMassList()] failed to centroid scan

I opened each file in XCalibur and looked at the scan indicated in the error message (1972 for the example given above). The scan is for an MS2, and it appears to be completely empty of data (see attachment). I guess this is why it could not be centroided! Is there any way around this problem so I can import the files, as it seems to be just one bad scan?


Nick Shulman responded:  2019-10-02
Someone else ran into this error last month. The conclusion was that the .raw file was corrupted.

You can use MSConvert to create a .mzML file with that particular scan removed from it. There is a description of how to do that somewhere in this thread here:

The commandline arguments that you would use with msconvert would be something like:
msconvert.exe mtab_BCderiv_BC43_092619_69.raw --filter "peakPicking vendor" --filter "index 0-3117,3119-"

If you would like, you can send us your Skyline document and your .raw file.

In Skyline, you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file and the .raw file are less than 50MB you can attach them to this support request.
Otherwise, you can upload them here:

-- Nick
bwidner responded:  2019-10-03
Thanks, Nick.

I am familiar with msconvert and had planned to try importing the file as mzml. In the meantime, I found a work around in skyline. I had been using 'centroid' in the Transition Settings->Full-Scan->MS1 filtering->Precursor Mass Analyzer and MS/MS filtering->Product Mass Analyzer. My data is from an orbitrap, but after a previous issue I had, Brendan had recommended using 'centroid'. When I changed it back to 'Orbitrap' I was able to import the files no problem and proceed as normal.

The previous issue:

Brendan MacLean responded:  2019-10-03
I do still recommend centroiding Orbitrap data, but if it is failing, then extracting from the profile spectra is a reasonable workaround. Thanks for keeping us posted. I will release a Skyline-daily soon with our recent fixes and we would really appreciate if you could try again with that version to see if it fixes your issue.
bwidner responded:  2019-10-03
Will do!