Even though the cysteine mod is variable, I was able to successfully run
PTMprophet by entering the cysteine mod as one of the PTMs for
PTMprophet. Do you think this will cause problems? Also, what
localization score should be used as a cutoff for correct localization?
Thanks,
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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Jesse G. Meyer
Ph. D. Candidate
Department of Chemistry and Biochemistry
University of California, San Diego
[email protected]
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