DIA samples

DIA samples geweigang  2019-06-16

I have used the skyline to run DIA. After exporting the results, why is the number of proteins detected in each sample the same?
What can I do to make the number of proteins or peptides detected in each DIA sample different?

Brendan MacLean responded:  2019-06-16

We need a bit more information on how you have decided which proteins were detected. Did you build an mProphet model and use a cut-off on Detection Q Value?

Screenshots of what you are seeing often help.


geweigang responded:  2019-06-16

Can you tell me where to set qvalue?

Brendan MacLean responded:  2019-06-17

Please give us a bit more information on what you are doing. It would be great if you could post PowerPoint slides with screenshots of what you are doing and seeing. Thanks.

Otherwise, if you want a good intro to using Skyline for DIA, I recommend the ETH tutorial (Tutorial 2 on this page):

And this webinar: