Hi Oded,
I think the old 5.2.0 might be under estimating the error rate as compared
to the new release candidate. You cannot see the decoys here because of
the settings you used. However your database has two independent sets of
decoys available DECOY0 and DECOY1. Can you use one of the set
You can convert the sptxt format to msp with:
rename mylibrary.sptxt mylibrary.msp
sptxt and msp are effectively the same thing. There is no specification on
exactly what msp is and it has evolved a little over time, and sptxt is
essentially the same as one of the variations.
Eric
Hi Ben,
I think you can convert a spectral library in the format of sptxt into msp.
However, you may need to write your own simple script to perform this
text-based conversion.
Best regards,
Wenguang
On Friday, February 12, 2021 at 6:09:37 PM UTC+1 benoit@gmail.com wrote:
>
> Hello,
>
>
Dear David,
This is PeptideProphet issue (we don't use iProphet for this analysis).
With the search parameters that I sent you followed by running the
PeptideProphet command of *xinteract -Ninteract.pep.xml -p0.05 -l7 -PPM
-OANEp -dDECOY Seq69478_QE2.pep.xml,*
and lastly using a cutoff of 1%
