How is a precursor confidently identified?

[hxxhust163]

Hi Vadim

Hope this finds you well. Thanks for your work in DiaNN. I get a library for DDA data. Based on the intensity, I get two libraries, one is the top 12 ions and another is top 15. I run diann using the two libraries separately with same parameters. By comparing the results I found that 45 precursors only found by top 12 library and 47 precursors only found by top 15 library, while there were 2719 precursors overlap.

I have two questions: Q1. Though 45 is smaller than 2719, I wonder why this happens. It means the 45 and the 47 precursor are correct, but they will be lost if using different library.

I guess it is probably due to the FDR. The 45 precursors did not pass the FDR threshold when using the top 15 library. Q2. I wonder how the FDR calculated or how the decoy implemented.

Btw, I use diann 1.8.1 version in linux.

Best wishes Xiaoxiang