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?
thanks！
Brendan MacLean responded:
2019-06-16 06:38
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.
—Brendan
geweigang responded:
2019-06-16 19:09
Can you tell me where to set qvalue?
Brendan MacLean responded:
2019-06-17 09:28
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.