Issue 577: Failed to import MassLynx (centered) Q-TOF raw data

issues
Status:resolved
Assigned To:matt.chambers42@gmail.com
Type:Defect
Area:Skyline
Priority:3
Milestone:4.1
Opened:2018-05-29 by melechco
Changed:2018-10-16 by Brendan MacLean
Resolved:2018-10-16 by Brendan MacLean
Resolution:Fixed
Closed:
2018-05-29 melechco
Title»Failed to import MassLynx (centered) Q-TOF raw data
Assigned ToGuest»Brendan MacLean
Type»Defect
Area»Skyline
Priority»3
Milestone»4.1
Dear Developers,
Skyline is failing to importing a Waters Synapt raw data (centered).
I attached the Skyline document but it does not contain any data.
Thanks!

At 6:51 PM:
Failed importing results file 'E:\20180522_Otimizacao_HILIC_005.raw'.
[pwiz::CLI::msdata::SpectrumList::spectrum] Unhandled exception: Unknown Code


Inner exceptions:
Exception type: System.Exception
Error message: [pwiz::CLI::msdata::SpectrumList::spectrum] Unhandled exception: Unknown Code
[pwiz::CLI::msdata::SpectrumList::spectrum] Unhandled exception: Unknown Code
   em pwiz.CLI.msdata.SpectrumList.spectrum(Int32 index, DetailLevel detailLevel)
   em pwiz.ProteowizardWrapper.MsDataFileImpl.get_SpectrumList() na c:\proj\pwiz_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:linha 510
   em pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() na c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:linha 197
 
 metabolomica.sky.zip

2018-05-29 matt.chambers42
Hi, can you upload the RAW file so we can take a look? If you need a place to upload it (keep in mind that it's not secure though): https://skyline.ms/project/home/support/file%20sharing/begin.view?

2018-05-30 matt.chambers42
Deja vu: https://skyline.ms/announcements/home/support/thread.view?rowId=35787

Apparently the previous fix didn't make it into the main code. But now it has and the fixed build of the core pwiz apps should be ready in a few hours. And presumably will be included in the next Skyline daily release. In the meantime, you can convert your file to mzML first with MSConvert and then import that to Skyline.

2018-10-16 Brendan MacLean
resolve as Fixed
Statusopen»resolved
Assigned ToBrendan MacLean»matt.chambers42@gmail.com
Please holler if this isn't fixed in Skyline. Otherwise, let's close this.