Thanks for your help. Updated to 5.1 solved the issue. Sorry it took me
awhile to set it up and try out.
All the best,
Emma
On 25 June 2018 at 12:39, David Shteynberg <
david.shteynb...@systemsbiology.org> wrote:
> Hi Emma,
>
> I think you are a version behind. Can you please try the latest ver
Hi Emma,
I think you are a version behind. Can you please try the latest version to
see if it fixes the issue you've observed?
Thank you,
-David
On Sat, Jun 23, 2018, 3:38 PM Emma Whittington wrote:
> Hi David,
>
> I am using TPP 5.0.0. The modifications I'm specifying are M,15.994915
> STY,7
Hi David,
I am using TPP 5.0.0. The modifications I'm specifying are M,15.994915
STY,79.9663 K,79.9663.
Thanks
On 22 June 2018 at 18:28, David Shteynberg <
david.shteynb...@systemsbiology.org> wrote:
> Hi Emma,
>
> Which version of the TPP are you running? Which modifications are you
> specifyi
Hi Emma,
Which version of the TPP are you running? Which modifications are you
specifying when you run the tool?
Thanks,
-David
On Fri, Jun 22, 2018 at 11:44 AM, Emma Whittington
wrote:
> Good afternoon,
>
> I've trying to use PTMprophet to analyse my data and keep getting the
> following erro
Good afternoon,
I've trying to use PTMprophet to analyse my data and keep getting the
following error. Do you have any idea what's happening?
INFO: Writing file bursa.ptmp.pep.xml ...
INFO: Reading file bursa.ptm.ipro.99.pep.xml ...
WARNING: Illegal peptide with unknown mod: WYNWGSYDASSGEC[16
Hi Maik
I am glad you got it to work. The reason it wasn't before is the mass you
used in the search should match the mass you input for PTMProphet so my
algorithm can identify the ids that contain your modification.
I will have to improve the information PTMProphet prints to the screen to
hel
OK,
it looks that my mistake was to use 80 Daltons as the modification mass for
phosphorylations instead of 79.966. If I type the command:
/usr/local/tpp/bin/PTMProphetParser STY,79.966 MZTOL=0.1
c:/Inetpub/wwwroot/ISB/data/MB_myprotein_21092011.pep.xml
interact.ptm.pep.xml
everything works as
Hi David,
I was on vacation the last two weeks. So here's a late reply. The command
line functions I tried for PTMProphet were:
/usr/local/tpp/bin/PTMProphetParser MB_myprotein_21092011.pep.xml or
/usr/local/tpp/bin/PTMProphetParser STY,80 MB_myprotein_21092011.pep.xml
In both cases PTMProphet
Hello Maik,
I am not sure what you mean that it removed phospho peptides. The default
function for PTMProphet updates the modifications to the most probable
positions, unless you used the NOUPDATE flag. Can you send the commandline
you used for PTMProphet?
Thanks,
-David
On Thu, Aug 23, 2012 a
Hi Joe,
thanks a lot for your help. I wasn't sure whether the copying of the
PTMProphetParser file was the reason for its behavior, so I added the
missing line in the makefile and installed it again. Unfortunately the
behavior of PTMPropeht to remove phosphopeptides is still the same. I hope
D
Maik,
PTMProphet should be available on both Linux and Windows. It appears that
we left out a line in the makefile for installing the executable under
Llinux. I'll make sure this gets corrected in 4.6.1. In the meantime you
can just copy the executable from the build into your bin directory. A
Hi,
I installed TPP 4.6.0 on Ubuntu 10.04 for a Labkey server we are running on
that machine. As requested in the Labkey installation instructions for TPP,
I added XML_ONLY=1 to the TPP MAKEFILE.incl.
I was hoping that the new release of the TPP would give us PTMProphet
support also on Linux.
Dear all,
I tried to run PTMProphetParser on available in the version 4.5.0 of
TPP installed on our server.
I got this error message
malessio@brutus3 test]$ PTMProphetParser
USAGE: PTMProphetParser
OPTIONS:
[malessio@brutus3 test]$ PTMProphetParser SDG_interact.pep.xml
Segmentation fault
I h
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