Optimizing the Identification Results

[amingson]

Dear respected author, hello! I am currently conducting the database search work of immune peptidomics. May I ask, apart from simply setting the threshold of peptide false discovery rate (pep FDR), if I aim to enhance the authenticity of the identification results, what kind of filtering measures should I adopt? I wonder if you have any excellent suggestions? Thank you very much!

Best, Anler

[fcyu]

You could try out group FDR (https://fragpipe.nesvilab.org/docs/tutorial_group_fdr.html) and two-pass search (https://fragpipe.nesvilab.org/docs/tutorial_two_pass_search.html) approach.

Best,

Fengchao

[amingson]

You could try out group FDR (https://fragpipe.nesvilab.org/docs/tutorial_group_fdr.html) and two-pass search (https://fragpipe.nesvilab.org/docs/tutorial_two_pass_search.html) approach.

Best,

Fengchao

Thank you for your assistance. I deeply apologize for not providing you with a response promptly!

Best, Anler