Quantification for small molecules by using C of IS without cal. curve

support
Quantification for small molecules by using C of IS without cal. curve ismailovadh  2025-03-18 02:50
 

Hello, dear Skyline support!

Is it possible to arrange quantification of concentration, using only the concentration of IS that is structurally relative to the target molecule? I need the concentration that is calculated according to the formula: C(tm)=Int(tm)*C(IS)/Int(IS), where tm -- target molecule, IS -- internal standart, Int -- intensity of the signal.

I have already tried labeling IS as heavy (it really is an isotoped molecule), but I can only calculate the ratio and the normalized area.

Maybe it is not quite accurate to ignore the external standart calibration curve, but to I need the calculation, I mentioned.

I would be very grateful for your help!

Best regards,
Ismailova Diana

 
 
Nick Shulman responded:  2025-03-18 13:03
You should use the Document Grid to create a report that includes the column "Internal Standard Concentration" and then set the values in the column to the concentration that your internal standard was spiked in at.
You can learn about the custom reports and the Document Grid here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

There is a binoculars button at the top of the Report Editor which will allow you to search for any column by name.

After you have specified the Internal Standard Concentration of your molecule, you can add the "Calculated Concentration" column to a report and that will contain the Internal Standard Concentration multiplied by the light to heavy peak area ratio.

If you have trouble getting this to work you can send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
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
 
ismailovadh responded:  2025-03-19 02:32
Thank you, Nick!
I already tried this before, but there was always N/A in the calculated concentration.

I attach here the zip documents.

Thanks a lot!!!
-Diane
 
Nick Shulman responded:  2025-03-19 07:16
Thank you for attaching that .sky.zip file.
You should go to the "Quantification" tab at "Settings > Molecule Settings" and do the following:
1. Change "Regression Fit" to "None"
It is currently set to "Linear" which makes Skyline think that you want to have a calibration curve with external standards. If you just want to multiply by the Internal Standard Concentration then the Regression Fit should be set to "None".
2. Change "Normalization Method" to "Ratio to Heavy"
Skyline only multiplies by the Internal Standard Concentration when the normalization method is "Ratio to Xxx".

By the way, Skyline seems to have done something wrong with the name of the Skyline document file when it created the .sky.zip file.
When I tried to open that .sky.zip file in Skyline, Skyline gave me the error "Illegal characters in path".
I was able to successfully extract the contents of the .zip file using 7-zip.exe but the name of the Skyline document file was changed to "______(_____ ________).sky".
What was the name of the file supposed to be?
It looks like Skyline might be doing something wrong in terms of using Unicode to encode the names of the files in the .zip file.
-- Nick
 
ismailovadh responded:  2025-03-20 02:58
Nick, thank you! The instruction you gave have worked!

Sorry for the name of the file, it was a special spell... Just joking, it was just written in another language. Something like "1001tries(once more)".

I wish you and your team prosperity and luck!
-Diane
 
Nick Shulman responded:  2025-03-20 07:46
Thank you for the info.
I believe that if you had been using Skyline-daily instead of Skyline 24.1 the filename in the .zip file would not have been a problem.
It looks like we fixed a bug last summer where the filenames were not being correctly encoded, but Skyline 24.1 does not include that fix:
https://github.com/ProteoWizard/pwiz/pull/3117

There are still limitations on what some of the other files associated with a Skyline document can be called, such as .blib spectral library files or some of the vendor mass spec raw files, but the .sky file itself is supposed to be able have any combination of foreign characters in its name.
In the current Skyline-daily I believe this is true, and it will also be true in Skyline 25.1 which will be released in a month or two.
-- Nick