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Chromatogram information unavailable VP13  2018-01-25 08:48
 
Dear Skyline team,
I have problem with chromatogram information unavailable. Every time I import wiff results, some of the analytes show chromatogram information unavailable. For some time I was creating new transition lists only with the analytes which were not processed and repeated inserting new transition lists and importing results until I obtained chromatograms for all the missing analytes. But this procedure is a little bit inconvenient and does not longer help anymore. Can you give me a piece of advice?
I am using version 4.1.0.1174, Windows 10 and working with MRM data.
Thank you in advance,
Veronika
 
 
Nick Shulman responded:  2018-01-25 11:32
Can you send us your files?
I will try to figure out what is going wrong.

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

You can upload that .zip file here:
https://skyline.ms/files.url

Can you also upload at least one of your .wiff files (as well as the .wiff.scan file that goes with it).
 
VP13 responded:  2018-01-29 01:04
Hello Nick,

I need to delete the uploaded file from File Sharing Folder for Skyline Support. Can you tell me how to do it or can you delete it by yourself?

Thank you,
Veronika
 
Brendan MacLean responded:  2018-01-29 02:27
Hi Veronika,
I deleted your ZIP file after downloading it. When I open the WIFF file in it with the ProteoWizard tool SeeMS, the closest chromatogram I see in it to the one you highlight as missing is:

- SRM SIC Q1=321 Q3=221 sample=1 period=1 experiment=1 transition=40

In the Skyline document transition list, however, the Q1 and Q3 m/z values are listed as:

Eicosanoids    321.2    -1    221.2    -1    8.60    15-HETrE _RT=8.6_min

You would have to make you "Method match tolerance m/z" in your Transition Settings - Instrument tab at least 0.2 in order for Skyline to match the document m/z values with the m/z values found in the WIFF file.

I guess I would suggest you change the m/z values in your transition list to match the ones in the WIFF file, if you want them to match in Skyline. If you don't have a good tool for looking at the values in the WIFF file, then I would suggest installing ProteoWizard and using SeeMS as I have done, but I would expect SCIEX to provide something that allows this also.

I hope this helps. Let us know if we are misunderstanding your intent, but so far I am not seeing a better m/z match for what you are showing in your Skyline document.

--Brendan