David,
I think I need to have some modifications added to the TPP code for
PTMprophet to work. I trying to combine two database searches that
specify either fixed light lysine or fixed heavy lysine (+8.0142), both
with variable modification of diGlycine (+114.0429). Therefore, lysine
in my datasets is found modified with +8.0142, +114.0429, or +122.0572.
If you add these to TPP, will I be able to combine these searches and
validate the mods with PTMprophet?
Any help would be appreciated.
Thank you,
Jesse
On 8/12/2014 1:16 PM, David Shteynberg wrote:
You need to only enter the variable mods for PTMProphet. However,
mods that are unknown will not be recognized without a change to the
code. A future version of PTMProphet will hopefully correct these
issues.
-David
On Tue, Aug 12, 2014 at 11:59 AM, Jesse Meyer <[email protected]> wrote:
I am also getting this error with a peptide containing a fixed modification
of cysteine (N-ethylmaleimide +125.047679). I am running PTMprophet to
localize a different variable modification on lysine. Do I need to enter
all mods including fixed mods under PTMprophet in the Petunia GUI?
Thanks,
Jesse
On Saturday, July 12, 2014 7:13:57 AM UTC-7, [email protected] wrote:
Sure. Let me know what you need and I will send you the data.
Best,
Oded
On Saturday, July 12, 2014 5:11:39 AM UTC+10, David Shteynberg wrote:
Hi Oded,
It is likely there is an issue with PTMProphet that doesn't recognize
the modifications in your dataset. If you can share a portion of your
data for testing purposes I can help troubleshoot further.
Thank you!
-David
On Tue, Jul 1, 2014 at 5:33 AM, Oded <[email protected]> wrote:
Hi all,
I am using TPP 4.7.1 on Win7 and currently trying to analyze data of
dimethylated phosphopeptides searched with X!tandem.
The searches were done by using 2 sets of fixed modifications for the
Cys
alkylation plus light or heavy dimethylation on N-term and K with STY
phosphorylation, Met-Ox and protein N-term acetylation as set as
variable
modifications.
When I try to run PTM prophet (following peptide prophet and iprophet
runs)
I getting the following error:
EXECUTING: run_in
c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014;
c:\Inetpub\tpp-bin\PTMProphetParser
STY,79.966,C,57.021464,n,34.063117,K,34.063117,M,15.99 MZTOL=0.1
c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014/interactNative1.ipro.pep.xml
interactNative
INFO: Writing file interactNative1.ptm.pep.xml ...
INFO: Reading file
c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014/interactNative1.ipro.pep.xml
...
WARNING: Cannot initialize for sequence: n[71]M[147]KDEPRSTNLFMK,
unknown
mods may exist in spectrum CHH20140618_M1HTiO2_100mM.03738.03738.2
WARNING: Cannot initialize for sequence: n[35]K[162]S[167]PAAAR,
unknown
mods may exist in spectrum CHH20140618_M1HTiO2_100mM.03900.03900.2
WARNING: Cannot initialize for sequence: n[35]VPS[167]RHINIGR, unknown
mods
may exist in spectrum CHH20140618_M1HTiO2_100mM.04358.04358.2
WARNING: Cannot initialize for sequence:
n[35]EGEEPT[181]VYSDEEEPK[162]DESAR, unknown mods may exist in spectrum
CHH20140618_M1HTiO2_100mM.04499.04499.3
WARNING: Cannot initialize for sequence: n[35]GTPGPAVR, unknown mods
may
exist in spectrum CHH20140618_M1HTiO2_100mM.05584.05584.2
WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162]
WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162]
WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162]
WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162]
WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162]
WARNING: Unrecognized mod on peptide: n[35]SCFESS[167]PDPELK[162]
{this appear 100-200 times}
This application has requested the Runtime to terminate it in an
unusual
way.
Please contact the application's support team for more information.
command "c:\Inetpub\tpp-bin\PTMProphetParser
STY,79.966,C,57.021464,n,34.063117,K,34.063117,M,15.99 MZTOL=0.1
c:/Inetpub/wwwroot/ISB/data/Oded/Enzo/Phospho_June2014/interactNative1.ipro.pep.xml
interactNative1.ptm.pep.xml" failed: No such process
I tried adding both heavy and light dimethylation (+28 and +34 on K and
N-term) just light and just heavy (as shown above), the the mass of the
DiMet N-term as it appear in the pepXML (+35 or +29) but the error is
still
the same...
Is there a way to sort this?
Many thanks,
Oded
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