I have not seen that error before. That appears to be a bug in Skyline.
I can tell you that Skyline is looking at the "Explicit Retention Time" which was specified on your Molecule, and is checking whether the extracted chromatogram includes that explicit retention time, or if the extracted chromatogram should be discarded.
The error happens because the extracted chromatogram has no points in it.
One thing that you might be able to do to work around this bug would be to set the Explicit Retention Time of that molecule to blank.

It would be very helpful if you could send us your Skyline document and the .wiff file and .wiff.scan file.

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

It would be helpful if you could send us that .zip file as well as 20240507_Acylcamitines.wiff and 20240507_Acylcamitines.wiff.scan.
Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url
-- Nick

Dear Nick,

I send you what I can. I adapted all the time retentions in skylineand all transitions works now.
Unfortunately I will not be able to send you the wiff and wiff.scan file since there are patients data.
I am really sorry. Hope you will be able to find the problem without them.

Best, JC

Thank you for sending that Skyline document.
I see that this is an SRM experiment.

I wonder if you could have a look at "20240507_Acylcamitines.wiff" yourself using a program such as ProteoWizard SeeMS.exe and let me know whether you see a chromatogram in there which has no points in it at all.
-- Nick

The wiff has been imported in "SeeMS", but I was only able to see one blank.
When I imported the same wiff file with my skyline template for all Acylcarnitines, I was able to see all injections that were acquired for this sequence.

Thank you for posting that screenshot of SeeMS.exe.
Do you see the number "0" anywhere in the "Data Points" column in that grid?
-- Nick

Dear Nick,
Yuu still need an aswer from me. I do not see any "0" in the data point.
For your information, I tried yesterday to use the same skyline template for my folder Acylcarnitines in:

1_Thor/Acylcanritines Backup/SST
3_QQQ6500+/Acylcanritines/SST

I was able to sent them on the "1_Thor" but not on the "3_QQQ6500+" from the skyline file. I got always the same 404 error
I tried to send these measurements on the "2_Odin/FAO" and worked perfectly.

Did I setup something wrong on my "3_QQQ6500+" folder?
Again thank you for the help and wish you a nice weekend.

Kindregards
JC

Hi Jean-Christophe,

Uploads to the folder "3_QQQ6500+_SD" are failing because of the '+' character in the folder name. Sorry about that. We are looking into the problem and will have a fix as soon as possible.

The workaround until then would be to replace the '+' in the folder name with something else. You can rename a folder in Panorama by going through the Admin menu (gear icon in the top right corner) > Folder > Management. Click the "Rename" button in the toolbar.

Thanks,
Vagisha

Good Morning Vagisha,

Thank you so much for the tip. I removed the + and it works much better.

This morning i tried to automatically import our new SSTs (routine and Backup instrument), abd it worked automatically on the backup instrument folder activating AutoQC, but not for the routine folder (see LOGs in word file). When I opened the template skline file I made for the routine instrument, the new SST fils were there, but the automatic transfer to panorma did not worked. And then I could sent them manually with the button upload to panorama.

Are there any explanations for that?

Thank you for the support and wish you a nice day.
Jean-Christophe

Hi Jean-Christophe,

In your screenshot, for the "QQQ6500_SD Acylcarnitines SSD" configuration, the raw file had already been imported into the document, so it was not imported when you started the AutoQC configuration. You can see the message in the log - "The file has already been imported. Ignoring...".

AutoQC Loader will upload the Skyline document to Panorama only if a new raw file in successfully imported. In this case since nothing was imported, Panorama upload was skipped (log message: No results were imported. Skipping upload to Panorama). In the next version of AutoQC Loader there will be an option to upload the document to Panorama even if no new results are imported when the configuration starts.

Thanks,
Vagisha

Good Morning Vagisha,

Thank yo for your reply. I did a test this morning, where I removed from the skyline template and on panorama the three last SSTs that the routine measured on the 28.05. I started AutoQC again, the samples could be added to the skyline file, but then an unknown error occurs to upload to panorama.
I updated the importing issues word file with a new printscreen of the log.
Is the probelm that my skyline template file have a "+" character in his name?

Thanks for the support and sorry for all these questions

Have a nice weekend
JC

Hi Jean-Christophe,

Could you please send me the log file from AutoQC? That will make it easier to debug. In the "Log" tab there is a button to "Open Folder...". Clicking the button will open the folder that has an AutoQC.log file. Can you please send me that file?

I suspect the problem here is that you have renamed the folder on PanoramaWeb but not updated the folder name in the AutoQC configuration. In your screenshot I see the old folder path with the '+' character in the folder name. Can you please retry after correcting the folder path in your configuration?

Which version of Skyline are you using?

Thanks,
Vagisha

Good Morning Vagisha,
I will not have to send you the log file, since I removed all "+" charachters and the automatic import worked.
Thank you again for your help and I wish you a nice week.
Kind regards
JC