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DDA file without target peptide

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DDA file without target peptide Winnie  2019-06-18 05:34
 
Hi all,

I have used skyline to analyzed low abundance peptides which were gathered by PRM mode. The low abundance of those peptides couldn't find in DDA mode either, even if the peptides have been set fractions. For those peptides, I have no library, no MS2 information. How are these peptides in PRM data analyzed with skyline?

Best regard!
 
 
Brian Pratt responded:  2019-06-18 09:57
Have you had a look at the Skyline PRM tutorial yet? That's a great place to start, it will show you how to proceed with or without library information.

Best regards,

Brian Pratt
 
Brendan MacLean responded:  2019-06-18 11:10

There are also some good Skyline Tutorial Webinars on PRM:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=webinars

Specifically:

https://skyline.ms/webinar17.url
https://skyline.ms/webinar09.url
https://skyline.ms/webinar03.url

These all come with datasets you can use for practice.