Chromatogram information unavaliable

support
Chromatogram information unavaliable io  2018-01-19 01:09
 
Dear Skyline team,
Today I have problems to import wiff results, the chromatogram information is unavaliable.
I am using 4.1.0.11714 with windows 10.
Yesterday, I used the same Skyline file and I didn't have problems with the import
I have also checked the wiff files and theay are correct.
I attached a screenshot.
Thanks in advance
 
 
Brendan MacLean responded:  2018-01-19 02:32
Hi Irene,
Can you give us more information about what type of data this is? SRM, PRM, DIA, or DDA?

Maybe you could provide a screenshot of what you mean by "checked the wiff files and they are correct".

The screenshot you have provided indicates that Skyline was unable to find anything in your WIFF file to match the targets in your Targets view. If it is SRM, that would seem to indicate no Q1 and Q3 pairs were found to match the transitions in the document. If it is PRM, that would indicate no precursor m/z values were found to match the ones in the document. DIA and DDA would be harder to explain unless the settings are somehow problematic.

If you can provide a bit more information, hopefully, we can figure this out fairly quickly.

--Brendan
 
io responded:  2018-01-19 02:50
Hi Brendan,
Thank you for your fast response.
It is SRM.
I attached the screenshot with the wiff file in analyst.
I exported the SRM method from the same Skyline file I am now trying to import in.
Irene
 
Brendan MacLean responded:  2018-01-19 03:39
Hi Irene,
Unfortunately, that doesn't really tell me much. Exporting the method from Skyline should ensure the transitions match between your WIFF file and Skyline, but for some reason they are not matching.

If you know how in Analyst to show a list of the Q1 and Q3 pairs available in your WIFF file, it would be far more helpful to see that as proof the file contains the right transition m/z values that would be expected to match the targets in Skyline.

If you don't then, I would suggest installing ProteoWizard, if you haven't already, from here:

http://proteowizard.sourceforge.net/downloads.shtml

This might be useful anyway as it will allow you to see your WIFF file as Skyline sees it during import.

Once installed, you can just right-click on your WIFF file in the Windows Explorer and click Open with SeeMS. The SeeMS window that pops up should give you a list of transitions at the bottom.

Sending a screenshot that shows the file contains transition m/z values you expect to match with the ones you have shown in your first screenshot, like:

471.7358, 827.5734
471.7358, 730.4206
471.7358, 616.3777
471.7358, 488.3191
471.7358, 387.2714
476.7579, 837.4816
476.7579, 740.4289
476.7579, 626.3860
476.7579, 498.3274
476.7579, 397.2797
etc.

That would be a good place to start. If it does actually contain these values it will be difficult for me to come up with a reason why they are not matching, but we will get to that once you have shown that it does.

--Brendan
 
Brendan MacLean responded:  2018-01-19 03:41
If the WIFF file and Skyline document are reasonably small, you could also post them to this support board or if they are larger to:

http://skyline.ms/files.url

And I could have a look. Remember to use File > Share - Minimal to create a .sky.zip file from your Skyline document.

--Brendan
 
io responded:  2018-01-19 04:37
Hi Brendan,
I have solved the problem.
The list of the Q1 and Q3 pairs were right, but there was something wrong with the library that blocked the load of the wiff file.
When I`ve tried to share the Skyline file, an error pops up.
I attached the screenshot with the error.
Thanks a lot
Regards
Irene
 
io responded:  2018-01-19 04:37