search

vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
Other
237 stars 51 forks source link

Setting Precursor and Protein PEP in DIA-NN #1070

Open barny116 opened 2 days ago

barny116 commented 2 days ago

Hi Vadim, Hope this message finds you well. I am currently searching in DIA-NN using two proteomes- mouse and human, making the search space rather large. Do you have any advice on how to make the search more stringent? Is it possible to set a protein q-value cutoff by both experiment and run in DIA-NN? Currently, I use a 1% precursor and protein group FDR. Also, can I set a precursor and protein PEP (Posterior Error Probability) in DIA-NN? Thanks!

vdemichev commented 2 days ago

Hi Barny,

I assume you use MBR and search with the default FDR filtering set in the GUI (1%), in that case all you need to do is to filter the final report (in .parquet format) using Lib.PG.Q.Value <= 0.01 and PG.Q.Value <= 0.01.

Yes, you can use PEP and PG.PEP columns of the main report for extra stringency.

Best, Vadim