Skyline after upgrade 22_2 and update about AutoQC possibility to importe single injections from wiff file

Skyline after upgrade 22_2 and update about AutoQC possibility to importe single injections from wiff file jean-christophe prost  2023-07-17 03:27

Dar Skyline team,

I am sorry for that but we have a small problem. We observed big discrepancy between XEVO and Sciex measurements using skyline. And comparing the raw data processed with the their own software, the area obtain between TargetLynx and Sciex OS are really close.

In the attachement for exemple, I put in Skyline QTRAP and XEVO measurements of ERNDIM 1 and 2 controls used for our Acylcarnitine assay.
In skyline you have the feeling, we lost all sentibility with the sciex instrument, and when you compare the data in their process soft, you see, you are very close to each other.

I have the feeling, since we updated the new release of we have such problems. We are only able to install the unpluged version due to our firewall restrictions. When I go the mail from Brendan or Brian to install the new 22.2 release, I desinstall all the the skyline versions and install the new versions, and did not the "recovering from a broken Installation" workflow.

I really do not understand how it is possible to observe such area differences in skyline, which are not present at all in the respective processing softwares.

In advance thank you for your help.

Sorry I am coming back to you regarding questions I had in February abour AUtoQC (2023-02-22 01:41:18), since I never had any feedback from you. And I am no more able to sign in and ask again to these Email flow (QC trend report)
Vagisha told me it is not possible to implement in AutoQC single injections from wiff file. COuld you fix this issue? Since we have only Sciex instruments it would be really nice to be able to implement AutoQC without import always all data, and then exclude replicates you do not want.

In advance thank you for your help.
Kind regards,

Nick Shulman responded:  2023-07-17 03:50
In order for us to figure out what is going on, we would need you to send us a couple of "" files. I see that you attached a ".skyd" file to this support request. The ".skyd" file contains extracted chromatograms, but it is impossible for us to get any information out of it without the ".sky" file which goes with it.

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

Files which are less than 50MB can be attached to this support request. You can upload larger files here:

It would probably also be helpful if we could see at least one of your .wiff files. Can you also send us one or more of your .wiff files and the .wiff.scan files that go with them?

I am not sure that I understand the other part of your question.
It sounds like you are talking about the following support request on

Are you saying that you are having trouble signing in to the website?
-- Nick
jean-christophe prost responded:  2023-07-25 05:41
Dear Nick,
Please I want to appologize for my late answer, but I never got an email regarding your response to my first support request. Normally I always get a mail.
As you asked I put you a file. This time I processed the Recipe 1 and 2 we measured with both instruments. As you cold see in the word document I sen you 10 days aga, the area for these two samples more or less the same in TargetLynx and SciexOS. but not in Skyline.
Furthermore, I send you also the two XEVO TQ-S raw data for these samples and the complete wiff file from the QTRAP6500+, we acquired.

Sorry for thr panorama questions. I will contact them directly through the panorama support.
SOrry for that.

In advance thank you for your help and support.
Kind regards
Nick Shulman responded:  2023-07-25 12:32
I am not sure what numbers I am supposed to be looking at.

It sounds like you were saying that you were seeing different numbers with an older version of Skyline compared to a newer version. Could you send me a file with some numbers from the older version of Skyline? It is usually straightforward for me to figure out why two different versions of Skyline are producing different numbers.

-- Nick
jean-christophe prost responded:  2023-07-25 22:52
I do not have these numbers numbers with an old version, and I do not have instrument comparaison withl an old version of skyline.

I would have an input from skyline people, how it is possible to have so big discrepancies in area comparing instruments using skyline (see the zip file I sent you), compared to the area obtain using TargetLynx when measured with the Xevo and in SciexOS when measured with the Qtrap (see the word document I sent you in my first support request). If you look to recipe 1 and 2 area obtained with their respective processing software, for example C5 (as show in the example in the word file, the Xevo data in TargetLynx shows an area of 1'084'721 for C5 in Recipe 1 and the same sample in SciexOS present an area of 1'437'583. but when we take exactly these two samples in skyline, we observe an area of 1'393'389 for the C5 for the QTRAP sample and an area of 65'962'876 for the C5 with the Xevo sample. How it is possible to have a factor of 65 between both area in skyline and only a factor of 1.3 compring TargetLynx and SciexOS.

In advance thank you for oyur help.
Kind regards,
Mike MacCoss responded:  2023-07-26 01:25
It is not possible to compare a single run directly like that. The methods each tools uses to calculate the area, select transitions, background subtract are different. Even more important it isn't possible to compare the areas between instruments as they have different ion sources, ion detection systems, and signal processing.

What you can do is demonstrate that a set of known dilutions show the same linear response using a given instrument and tool. This paper from the Hoofnagle lab shows nicely how they demonstrated that Skyline performs as well TargetLynx ...

Hope this helps,