Hi Peter,
No, what happens is that multiple true peptides will map to the same
protein, but practically all false peptides will map singly to unique
proteins. As a result, the protein FDR will likely be greater than 1%.
Typically, if you do not perform some sort of protein level statistics,
you would say your protein IDs were inferred from peptides identified at
a 1% FDR threshold.
Cheers,
Mike
On 11/26/2013 8:52 PM, zion wrote:
Dear All:
If there are some confident peptide ids at FDR<=1% at the peptide level,
when inferring proteins by confident peptides and at least one unique
peptide, CAN i say that at the protein level, its FDR<=1%?
Many thanks,
-Peter
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