s by
> setting the option MINPROB= when you run the tool. Let me know if that
> still fails for you.
>
> Thanks,
> -David
>
>
>
> On Mon, Apr 6, 2020 at 3:27 PM Alex Zelter >
> wrote:
>
>> I am running into a situation where MSFragger ret
I am running into a situation where MSFragger returns a massdiff but
PTMProphet seems to ignore it. No modification_info or mod_aminoacid_mass
position is reported by PTMProphet for some results, while for others
things work as expected.
Here are 2 PSMs as examples. I've included both MSFragger
s created these additional mods on C? I would
> help me narrow down the places to look.
>
> Cheers,
> David
>
> On Wed, Mar 18, 2020 at 11:56 AM Alex Zelter >
> wrote:
>
>> Hi David,
>> Thanks for the fast response!
>>
>> My list of comm
pipeline?
>
> Thanks,
> -David
>
> On Wed, Mar 18, 2020 at 11:38 AM Alex Zelter >
> wrote:
>
>> I am running PTMProphet (TPP v5.2.1-dev Flammagenitus, Build
>> 202003100907-8034) on MSFragger (MSFragger version MSFragger-2.3) output
>> and ending up with strang
I am running PTMProphet (TPP v5.2.1-dev Flammagenitus, Build
202003100907-8034) on MSFragger (MSFragger version MSFragger-2.3) output
and ending up with strange results in specific cases.
For example, for a specific PSM, 52782, MSFragger outputs:
This would indicate that C9 is +57
>
>
> The automated model invalidator seems to be getting triggered by this
> dataset. I will adjust the settings for Kojak analysis as this should not
> be happening on this data. In the meanwhile, fou can override this problem
> by using the PeptideProphetParser option FORCEDISTR (possibly
Hi.
I'm running into an issue with the TPP/Kojak pipeline. I am running a
crosslinking analysis using Kojak. As you know, Kojak also reports unlinked
PSMs. I'm finding that PeptideProphet is filtering out ALL the unlinked
PSMs in my analysis.
If I process the dataset with Kojak/Percolator I get
; Thanks for sharing your file. I have confirmed that the latest version of
> the code (SVN revision 8004) has corrected this problem. Please update
> your TPP software to latest SVN revision (or official release.)
>
> Cheers,
> David
>
> On Tue, Jan 28, 2020 at 8:57 AM
I'm running into the following error when trying to use xinteract to
process Kojak 2.0 results.
The command I'm running is:
/usr/local/tpp/bin/xinteract -Ninteract.pep.xml -p0 -l1 -eT
-D/path/to/database.fasta -PPM -OAPdp -drandom_ -ip ./kojak-output.pep.xml
INFO: Processing xl MixtureModel ...
/bin:$PATH
>
> Let me know if it still gives the same message after changing the PATH.
>
> -David
>
>
> On Tue, Oct 2, 2018 at 9:24 AM Alex Zelter >
> wrote:
>
>> Hi there,
>>
>> I am using TPP v5.2.0-b1 Flammagenitus Pre-release Beta, Build
>&g
Hi there,
I am using TPP v5.2.0-b1 Flammagenitus Pre-release Beta, Build
201809101205-7809 (Linux-x86_64) with Kojak pep.xml data running the
following command:
/usr/local/tpp/bin/xinteract -Ninteract.pep.xml -p0 -l1 -eT -PPM -OAPdp
-drandom_ -ip file1.pep.xml file3.pep.xml file3.pep.xml
Thi
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