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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
90 stars 45 forks source link

FDR control #2357

Open ShadoWyyyy opened 2 months ago

ShadoWyyyy commented 2 months ago

hello, good software, easy to use until I can not find q value settings, there is no option for setting q value or FDR threshold for final quality control of the results, or did I miss it ? I check every option in the XLSearch task because usually 0.05 is set for cross-linking.

trishorts commented 2 months ago

you are correct. for now you have to simply ignore anything in the output with a q-value greater than your desired tolerance.

I will create an issue and try to add this feature to a future release of MetaMorpheus. Please track this issue.

https://github.com/smith-chem-wisc/MetaMorpheus/issues/2358