Hi Pavel,
The choice of peptide-level FDR or protein-level FDR depends on what
conclusions you hope to make. If you want to make conclusions about the
peptides you have identified, you can use peptide-level FDR. If you are
trying to identify proteins for biological reasons you should use
protein-level FDR. To accomplish this, you need to submit your pep.xml
to protein prophet, which you can read more about here:
http://tools.proteomecenter.org/wiki/index.php?title=Software:ProteinProphet
After ProteinProphet, you can determine what cutoff will give your
desired protein-level FDR.
Best,
Jesse
On 3/28/2013 9:14 PM, Pavel wrote:
Hi all,
I have a question about FDR estimation for protein identification
(using reversed decoy database together with target database in a
single file).
I can estimate the probability threshold for peptides to get for
example 1% FDR. My question is how to use this peptide probability
threshold for protein identification? Do I have to filter out peptides
below the probability threshold before ProteinProphet analysis(how?)?
Or do I have to run ProteinProphet, then filter out peptides below the
threshold and then estimate FDR for proteins? Or just etimate FDR on
the protein level? What is the right way ?
This is probably a silly question but I am confused about information
I found in different papers, sometimes there are FDR estimations on
the protein level only, sometimes there are FDR for peptides only and
sometimes one can found info like „FDRs for both peptides and proteins
were x%“.
Thank you
Pavel
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Jesse G. Meyer
Graduate Student
Department of Chemistry and Biochemistry
University of California, San Diego
[email protected]
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