Here is the best reference describing iProphet in detail:
https://pubmed.ncbi.nlm.nih.gov/21876204/
iProphet starts with PeptideProphet probabilities at the "PSM-level"
(always model-based) and computes the probabilities at the
"peptide-level." It always produces one result per spectrum (whether
One more question. I am using COMET prior to the peptide prophet steps.
COMET is already generating decoy database (concatenated search), do I need
to turn the decoy search off in COMET?
On Tuesday, May 14, 2024 at 2:38:00 PM UTC+5:30 Debojyoti Pal wrote:
> Thank you Dr David! That is really gr
Thank you Dr David! That is really great help.
I have a couple of follow-up queries:
1) If I use iProphet on these results, does that now use Decoy based FDR
estimates or the PeptideProphet statisitcal model only estimates.
2) If I combine multiple PeptideProphet outputs (from fractions of sa
