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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