construct a self-made library from CSV output format

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construct a self-made library from CSV output format haidi yin  2018-06-18
 

Dear Brendan,

I am trying to use skyline to quantify glycoproteins. I am using pGlyco2.0 for glycoprotein identification. The output file is in txt file format, which can be easily transformed to csv file format for easy reading. The CSV file is shown in the attachment. My question is how I can construct a library from this CSV file? Thank you very much.

Haidi

 
 
Brian Pratt responded:  2018-06-19
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
 
Brian Pratt responded:  2018-06-25
Did you get this working, in the end?

Best,

Brian
 
haidi yin responded:  2018-06-25
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
 
haidi yin responded:  2019-03-06
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
 
Brendan MacLean responded:  2019-03-06
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
 
haidi yin responded:  2019-03-13
Dear Brendan,

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