Hello Alastair,
I downloaded the file you shared with me, however, there were no mzML files
to match the pepXML files so I couldn't actually try the analysis. I will
make another attempt if you can provide the mass spec data.
Thanks,
-David
On Mon, Aug 17, 2020 at 11:21 AM 'Alastair Skeffingto
Hi Alastair,
If your search results are either all heavy or all light (not variable mod
searched) then you should also use option -S.
1). You cannot specify anything but single amino acids in this string.
Your quantitation will be based on peptides without PTMs in this dataset.
2). -r8 is a MUCH
Hello and welcome!
You are correct! That is the model-estimated error/sensitivity table for
ProteinProphet, in this case. A table of this sort is generated for
PeptideProphet model estimates, iProphet based model estimates or
ProteinProphet model estimates depending on the file being considered.
Hi Carlos,
The TPP is statistical software that takes advantage of statistical trends
in data and requires many data points to work well. Do you have a dataset
of reasonable size with maybe dozens or hundreds of spectra? Also can you
post the file somewhere I can download it? Sending files as e
Dear Carlos,
There is probably some bug exposed by the modeling of this type of data
with the specific set of options you enabled. If you are able to share a
part of your dataset that can replicate the issue, I am able to
troubleshoot this further.
Thanks,
David
On Sat, Jul 18, 2020, 12:10 PM
Great! Although when you set MINPROB=0 the software is spending a lot of
time evaluating PSMs you will never use, and some of them might have many
mods causing a combinatorial expansion of peptide candidates the must be
evaluated (although this is less of an issue for MASSDIFFMODE.) If you set
thi
Hi Alex,
PTMProphet by default will ignore any spectrum with less than 90%
probability (iProphet is used when available.) You can change this 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 Zelt
Thanks Alex. I suspect it is a possible bug in PTMProphet. Can you see
what step of your analysis 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!
>
Hi Alex,
This seems like a bug that should be fixed. Are you running PTMProphet at
any point in your analysis 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 (MSFragge
This seems to be a permissions issue. Did you install this as admin on
your system?
On Sun, Mar 15, 2020, 3:47 PM RUI XU wrote:
> After installing TPP and restarting, I clicked the shortcut, but reported
> a 403 error.
> [image: 403.png]
>
> I don't know how to solve.
>
> --
> You received this
Hello Alastair,
When you ran PeptideProphet as follows:
PeptideProphetParser H1_EhN_cm2.pep.xml RT DECOY=XXX_ NONPARAM
Here is what happened:
You gave PeptideProphet the names of your decoys but without the flag
DECOYPROBS the decoy hits are all incorrect as far as PeptideProphet is
concerned a
It appears that you are trying to view the results on a Windows machine but
the data was processed on Linux with absolute paths to the mzML data
files. Unless the files are properly referenced at their correct locations
on your computer, this will not work. You might consider running the TPP
Too
Hello Cindy,
The error message says that the program cannot find your tmt10 conditions
file. Does the file exist on your computer and have necessary permission
to allow the program to read the contents? Please check and try again.
You can always generate a new conditions file using the TPP web in
Hi Alex,
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 combin
Hi Alex,
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 Alex Zelter wrote:
> I'm run
Hi Alex,
It looks like you are running an unofficial version of the code that
obviously has a few issues with this data and has aged by this point. If
you can share your input data I can try the latest version of the code and
see if that works or provide a solution in the near future?
Cheers,
-D
Your current version of the TPP doesn't have this feature. You will have
to upgrade to a more recent release. Try 5.2.0 and let us know if that
works.
David
On Mon, Jan 27, 2020, 9:49 AM Mehar Un Nissa
wrote:
> Hello Sir/Madam,
> We used TPP and PTMprophet for PTM analysis.
> PTM taken (Ph
The error message refers to the M[147] modification, which is oxidation of
Methionine. Please specify this modification and rerun the tool.
Thanks for using the TPP!
-David
On Sun, Jan 5, 2020 at 3:13 PM Mehar Un Nissa
wrote:
> Dear Sir/Madam,
>
>
> I have query related to PTMprophet.
>
>
> I
No it is not correct for xl peptides. There are two peptides in every
match thus id you assume the database contains half decoys and half
targets, then there are 3/4 chance to match a decoy peptide randomly and
only 1/4 chance to match a target. So the random xl matches will be 3/4
decoy and 1/4
Yes you can. You can cd to the extern directory and type "make all" that
should build all external libraries, including boost.
On Mon, Sep 30, 2019 at 10:05 AM Jai Ganesh wrote:
> Hi David ,
>
> We are using latest version of gcc "gcc-4.8.5-36.el7_6.2.x86_64" , Could
> you please advice whet
Hello Arun,
This is a problem with compiling boost a C++ library used with in the TPP
and PWIZ.
Can you tell us which version of gcc you are using? I think you might need
to upgrade to 4.8.0 or higher.
Thanks,
-David
On Mon, Sep 30, 2019 at 7:13 AM arun kumar wrote:
>
> Hello All,
>
> we hav
Hi Mike and Thomas,
I am not sure where Kojak search went wrong, but somehow the 1.6.1 search
contains 0 decoys ("REVERSE") tagged hits and the 1.5.5 search has many.
Can you check your database and search parameters? Also is there any
reason your are not enabling the ACCMASS option that will hel
Hi Thomas,
The tables for each type of linked peptide is in the pepXML file (near the
top of the file), listed separately for each type of link.
Thanks,
-David
On Thu, Sep 19, 2019 at 2:54 AM Thomas Gossenreiter <
thomas.gossenrei...@gmail.com> wrote:
> Dear all,
>
> I would like to filter my
It would be very helpful to see your Kojak pepxml results.
Thanks,
David
On Fri, Sep 13, 2019, 12:01 AM Thomas Gossenreiter <
thomas.gossenrei...@gmail.com> wrote:
> Hi David,
>
> thanks for your quick response. Here is the link to the zipped pep.xml
> files. Is this enough or do you also need
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