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Small molecule method export

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Small molecule method export mcarey17  2018-12-03 08:55
 

Hi all,

Relatively new to Skyline but could use a great deal the method export feature. That's the one where based on a transition list/retention time and an existing *.exp file (which is the MAsslynx MS method details file) Skyline creates an MS method file ( *.exp file), which would be otherwise really clumsy with MAsslynx when more than 100 compounds are involved.

Re-create the error:
Open Skyline; Import transition list; Change setting to XEVO-TQS; Export MEthod

Operating system: Windows 7; Skyline version: latest; MAsslynx version: 4.2

Error message, see it on 'error support 3.PNG'
System.IO.IOException: Error no known instrument type found.
ERROR: Error no known instrument type found.
---> System.IO.IOException: Error no known instrument type found.
ERROR: Error no known instrument type found.

System.IO.IOException: Error no known instrument type found.
ERROR: Error no known instrument type found.
---> System.IO.IOException: Error no known instrument type found.
ERROR: Error no known instrument type found.

at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) in c:\proj\skyline_4_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 59
at pwiz.Skyline.Util.Extensions.UtilProcess.RunProcess(ProcessStartInfo psi, String stdin, String messagePrefix, IProgressMonitor progress, IProgressStatus& status) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Util\Extensions\UtilProcess.cs:line 45
at pwiz.Skyline.Model.MethodExporter.ExportMethod(String exeName, List1 argv, String fileName, String templateName, Dictionary2 dictTranLists, IProgressMonitor progressMonitor) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Export.cs:line 3772
at pwiz.Skyline.Model.WatersMethodExporter.ExportMethod(String fileName, String templateName, IProgressMonitor progressMonitor) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Model\Export.cs:line 3571
at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action1 performWork) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 228 --- End of inner exception stack trace --- at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1835 at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action1 performWork) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 176
at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action1 performWork) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 131 at pwiz.Skyline.FileUI.ExportDlgProperties.PerformLongExport(Action1 performExport) in c:\proj\skyline_4_1_x64\pwiz_tools\Skyline\FileUI\ExportMethodDlg.cs:line 1885
 
 
Brian Pratt responded:  2018-12-03 09:52
Hi,

Thanks for taking the time to report this. I'd like to investigate, may I ask for a couple more things?

In Skyline, use the menu item File | Share | Complete to create a .sky.zip file. Upload that file, and the method template file, to http://skyline.ms/files.url . If privacy is a concern we can work out some other transfer.

With those items in hand I should be able to work this out.

Best Regards,

Brian Pratt
 
Brendan MacLean responded:  2018-12-03 21:29
Hi Matt,
This has to do with the MassLynx setup on the computer you are using. You must not be running Skyline on the computer that is running the instrument you are creating the method for. Otherwise, I would not expect you to get that error. You can install MassLynx for method export on a stand-alone computer, but you need to install the instrument software as if you were going to run the instrument with your stand-alone computer.

I think you are best off either transferring your Skyline document to your instrument control PC or you should seek help in the MassLynx documentation or from Waters to get your stand-alone computer set up to mimic your instrument PC. I have done this before myself when I was testing the method export, but I am not now familiar enough with the steps to be able to guide you through them.

Maybe start by proving to yourself that you can export a method on the instrument PC for the instrument you intend to run it on. Then expand to other PCs after you have that working.

Hope this helps. Good luck with your methods.

--Brendan
 
mcarey17 responded:  2018-12-05 07:44
Hi both,

Thank you for your prompt responses, I have done as Brian asked and uploaded the files to the repository. There are only a few compounds as I am just trying to get the system to work.
In the meantime I will try and get my system set up correctly on the stand alone PC as Brendan has outlined. Just to clarify, I have Masslynx installed as though I were going to connect it to the instrument I am hoping to export the method to, with instrument control and Targetlynx etc, but did you mean any additional instrument software? Apologies for the confusion.

Thank you again for your help,
Matt

Edit:
For clarity, I am not running Skyline on the computer that is running the instrument.

Skyline installation runs into a Windows related problem when we try installation on the control computer, we are currently working on this.
 
Brendan MacLean responded:  2018-12-05 08:43
To clarify my advice:
1. Try it on the instrument control PC. (Just transfer your Skyline document to that PC.)
2. Seek support from Waters on how to set up your MassLynx software on the stand-alone PC to allow method export there. (This is not our area of expertise.)
 
Brendan MacLean responded:  2018-12-05 09:01
I should also point out this recent thread on method export issues with MassLynx 4.2

https://skyline.ms/announcements/home/support/thread.view?rowId=38266

Summary of advice from that thread: Seek support from Waters
 
hans_vissers responded:  2018-12-07 03:21
The following MassLynx 4.2 versions are supported. Please note that these are tandem/triple quadrupole releases. If the instrument type is not listed, please contact the local service support organization for advise.

SCN 977 (Xevo TQ-S micro)
SCN 978 (Xevo TQ-GC)
SCN 982 (Xevo TQ-XS)
SCN 989 (Xevo TQD/SQD/3100)

During installation, also specify the instrument and TargetLynx. The former is required to create a method template and the latter to populate the newly created method with the SRM/MRM transitions.
 
viragsagikiss responded:  2019-05-02 04:06
Hi Brendan,

I would like to report that we finally worked this out! It is brilliant, we are so happy with it! and using it for CE optimisation!


some details:
1; "This has to do with the MassLynx setup on the computer you are using. You must not be running Skyline on the computer that is running the instrument you are creating the method for. Otherwise, I would not expect you to get that error. You can install MassLynx for method export on a stand-alone computer, but you need to install the instrument software as if you were going to run the instrument with your stand-alone computer."

After several trials to install Masslynx(SCN 978) on different computers/different Windows op.system - even with Waters advice - we have failed to create an environment where it would export a transition list to a *.exp file. i have been running stand-alone Masslynx for years on different windows/masslynx versions and haven't seen one yet where the MS experiment files can be viewed or edited.

2; "I think you are best off either transferring your Skyline document to your instrument control PC .... Maybe start by proving to yourself that you can export a method on the instrument PC for the instrument you intend to run it on."

This worked! It just took relatively long time, because at first attempt Skyline couldn't be installed due to 'Windows Framework type of error', so first had to establish internet connection (secure way) to the instrument control, and after install Windows updates in Win7 and then finally install Skyline. But now we have skyline on the instrument control PC, so anyone out there who runs into this problem let you know that it will work on updated Windows7.

Thanks a lot for the help!
Virag
 
Brendan MacLean responded:  2019-05-02 16:02
Hi Virag,
Great news. Thanks for posting this report back.

Now you are all also set to try Panorama AutoQC on your Waters instrument PC:

https://panoramaweb.org/wiki/home/page.view?name=qc_with_panorama

Good luck with your research.

--Brendan