Hi David,
This time I used
*xinteract -NinteractDecoyCount.pep.xml -p0.05 -l7 -PPM -OANEdp -dDECOY0
Seq69478_QE2.pep.xml. *
With TPP 5.2 the count of DECOY1 ids at 1% error rate is 84 and the total
count of DECOY ids is 151 (out of 7102 PSMs).
With TPP 6.0 the count of DECOY1 ids at 1% error
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
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%
Dear Oded,
Thanks for this. I ran a quick test and I actually observed a few more
PSMs for PeptideProphet 6.0.0-rc14 for the same PeptideProphet probability
cutoff for this dataset. Is the issue you see with PeptideProphet or
iProphet results? Which spectra were getting excluded in the your
And also the search results with the new vs the old version (although I
think they are more or less the same):
https://www.dropbox.com/t/8VyBVdeuoWdk982q
On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote:
> Hi David,
> You can find the mzML, Comet parameters and FASTA file here:
>
Hi David,
You can find the mzML, Comet parameters and FASTA file
here:https://www.dropbox.com/t/Yld0ZBWhsuFajeLj
The link is valid for 7 days.
Many thanks,
Oded
On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote:
> I don't mind taking a crack at it over vacation. Please let me
I don't mind taking a crack at it over vacation. Please let me know where
I can pull the data from. I might not have quick solution for you but I can
get started looking for the problem. Which search engine did you use
here? I would need mzML data search results and the fasta database to get
Hi David,
Thank you for the quick reply. We are using TPP v6.0.0-rc14 Noctilucent,
Build 202103031119-8400 (Windows_NT-x86_64).
As for the data let me know when you are back and I will transfer you
either the raw file or the search results.
Enjoy your vacation.
Thanks,
Oded
On Monday, 12 April
Hi Oded, Which release candidate are you referring to? The earlier
candidates may have a bug that is corrected in a later version. If you can
share some data and specifics about the missing PSMs I can run it here and
troubleshoot the problem.
Thanks!
David
P.S. I am on vacation this week so
Hi there,
We recently download the TPP 6.0 RC and while using it we noticed that we
obtain fewer peptides IDs than what we got for the same dataset and search
output with version 5.2.
Many of the missing peptides seem to have decent Expect value and MS/MS
following a visual inspection.
This
10 matches
Mail list logo
