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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
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Setting different FDR values? #1743

Open Dmorgen opened 4 years ago

Dmorgen commented 4 years ago

Is it possible to set different FDR values (peptide/protein)?

Thanks! D.

rmillikin commented 4 years ago

can you clarify? the q-value is reported in one of the text columns and you can go down the list to whatever you want. there is a setting in the Output Options of the search task to filter output to a given q-value.

only PSMs <1% FDR are used for parsimony. same with quantification. do you want to change that?

Dmorgen commented 4 years ago

yes - I'd like to try several FDR setting for certain searches I'm running (various proteases and native peptides). is that possible?

rmillikin commented 4 years ago

this is not a currently user-alterable setting, but it should be pretty easy to make it one. maybe not the next release, but probably the one after that