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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Get FDR #1666

Closed amingson closed 2 months ago

amingson commented 3 months ago

- Describe the feature:

Dear author,

Could you please advise where or how I can obtain the FDR information corresponding to each peptide? Also, how can I obtain all unfiltered peptide information?

Best regards,

Anler

fcyu commented 3 months ago

Could you please advise where or how I can obtain the FDR information corresponding to each peptide?

Reported peptides have been filtered with the pre-definded FDR threshold. There is no FDR information in the report.

Also, how can I obtain all unfiltered peptide information?

There are several layers of filtering: Percolator or PeptideProphet has min prob filter, and Philosopher has psm, ion, pep, prot FDR, and also min prob: https://github.com/Nesvilab/philosopher/wiki/Filter. To get unfiltered result, please change each of them.

Best,

Fengchao