Hello Haidi,

Converting to the .ssl format should give you what you need:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BiblioSpec%20input%20and%20output%20file%20formats

Thanks for using the Skyline support board!

Brian Pratt

Did you get this working, in the end?

Best,

Brian

Dear Brian,

I could construct the library now. But I have another problem. Let me figure it out first. I will ask you again if I could not solve the problem. Thank you very much.

Haidi

Dear Brian,

I managed to build a self-made library from SSL file. However, I have another problem. The transition ion I try to use for quantification is not any b or y ion. They are b or y ion with modifications.

Is it possible that I can manually decide which transition ions I use for quantification?

Thank you very much,
Best regards,

Haidi

Hi Haidi,
Skyline does have a Quantitative property on transitions, which you can turn off (it is on by default). We intend to make this easier in the future, but you can use View > Document View to get access to this property. You just need to create a custom report with the property Transitions->Quantitative exposed in a column, and then you just uncheck it for the transitions you want to make qualitative.

Here is an image showing what this looks like:

https://skyline.ms/wiki/home/software/Skyline/download.view?entityId=79611505-d8fa-1035-b3d9-e465a39397c8&name=Quantitative%20Transitions.png

Sorry this isn't easier and we don't yet have better documentation for it.

--Brendan

Dear Brendan,

Thank you for your help. This problem is solved.
 
Best regards,
Haidi