Hello Rene
Thanks for using the tools and double checking your work.
In my tests I have found that applying the NSP model at the iProphet step
greatly improves performance on peptide level. And applying the NSP model
at the ProteinProphet step improves performance on the protein level. The
two models are somewhat different since the ProteinProphet model considers
grouping information while the iProphet model doesnt. I have not found the
two to interfere.
A safe and conservative approach so would look at the conservative estimate
e.g. ProteinProphet probability cutoff to give me 1% error with decoys or
1% error with the model which ever is more conservative.
When the model tends to underestimate error on protein or peptide level
this is usually stemming from underestimation at the spectrum level by
PeptideProphet and can be controlled by the CLEVEL={value} option for
PeptideProphetParser -c{value} for xinteract. Setting this to a number
greater than zero like .5 or 1 or 2 will serve to make the model more
conservative overall, a negative value will have opposite effect which will
carry through to the peptide and protein levels.
Also I am curious why you set decoy rate to 0.25?
Best,
David
On Dec 18, 2013 7:29 AM, "Rene B" <[email protected]> wrote:
> Hi all,
>
> I am running PeptideProphet, iProphet and ProteinProphet (TPP 4.6.3) on Q
> Exactive data searched with Comet, Myrimatch and OMSSA. I wondered if the
> NSP model should be disabled in ProteinProphet when it is enabled in
> iProphet? I got confused because it seems Petunia enables the NSP model
> both in iprophet and proteinprophet by default (ie. when xinteract runs
> with the -ip option).
>
> Another question is that when I compare decoy estimated protein FDRs to
> ProteinProphet modelled FDRs, ProteinProphet seems a bit optimistic (decoy
> based FDR of 0.1% corresponds to ~0.02% model FDR). This is with NSP
> enabled in iProphet and disabled in ProteinProphet. How should I deal with
> discrepancy, ie. should I take the decoy or probability based FDR to select
> a probability cutoff?
>
> I have attached some examples for a search with myrimatch only. These are
> the commands I used to generate the graphs:
>
> xinteract -Nmyrimatch.pep.xml -OAP -p0 -a%ExperimentFolder% -dDECOY0
> -E%ExperimentTag% *.pep.xml
> InterProphetParser myrimatch.pep.xml myrimatch.ipro.pep.xml
> ProphetModels.pl -i myrimatch.ipro.pep.xml -k -r 0.25 -d "DECOY1"
> ProteinProphet myrimatch.ipro.pep.xml myrimatch.prot.xml IPROPHET NONSP
> ProtProphModels.pl -k -r 0.25 -d DECOY1 -i myrimatch.prot.xml
>
> The graphs are:
>
> myrimatch_all.ipro.pep_FDR_10pc: PeptideProphet/iProphet decoy vs model
> FDR, all models enabled
> myrimatch_nonsp.ipro.pep_FDR_10pc: PeptideProphet/iProphet decoy vs model
> FDR, NSP model disabled in iProphet
> myrimatch_nonsp.prot_FDR_5pc: ProteinProphet decoy vs model FDR, NSP model
> disabled in ProteinProphet
> myrimatch_all.prot_FDR_5pc: ProteinProphet decoy vs model FDR, NSP model
> enabled in iProphet and ProteinProphet
>
> Thanks in advance!
>
> Kind regards,
>
> Rene
>
>
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