Dear Oded,
Sorry it has taken me this long to work the bugs out in this analysis.
The first problem I found was with your search parameters. Instead
of using two different static mods on K and n-terminus (which is not
supported by TPP in a single search), I used a static mod in
combination with a variable mod so instead of:
<parameter name="residue, modification mass"
value="+57.021464@C,+28.031300@K,+28.031300@["/>
<parameter name="residue, modification mass 1"
value="+57.021464@C,+34.063117@K,+34.063117@["/>
<parameter name="residue, potential modification mass"
value="15.994915@M,79.966331@Y,79.966331@S,79.966331@T"/>
we now have:
On Tue, Aug 12, 2014 at 1:19 PM, Jesse Meyer <[email protected]> wrote:
> 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
>>>>>>
>>>>>> --
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups
>>>>>> "spctools-discuss" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>>> an
>>>>>> email to [email protected].
>>>>>> To post to this group, send email to [email protected].
>>>>>> Visit this group at http://groups.google.com/group/spctools-discuss.
>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>> --
>>> You received this message because you are subscribed to the Google Groups
>>> "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send an
>>> email to [email protected].
>>> To post to this group, send email to [email protected].
>>> Visit this group at http://groups.google.com/group/spctools-discuss.
>>> For more options, visit https://groups.google.com/d/optout.
>
>
>
> --
> Jesse G. Meyer
> Ph. D. Candidate
> Department of Chemistry and Biochemistry
> University of California, San Diego
> [email protected]
>
>
> ---
> This email is free from viruses and malware because avast! Antivirus
> protection is active.
> http://www.avast.com
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to [email protected].
> To post to this group, send email to [email protected].
> Visit this group at http://groups.google.com/group/spctools-discuss.
> For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
To post to this group, send email to [email protected].
Visit this group at http://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.
