David,
Yes I have multiple pepXML files from heavy and light. I tried your
suggestion of analyzing them separately, and PTMprophet works on the
light pepXML, but with the heavy pepXML, PTMprophet does not finish and
it returns many lines that look like this:
WARNING: Illegal peptide with unknown mod: KKQLQDEMLRRV
WARNING: Unrecognized mod on peptide: GGAPLSPQTHRFM[147]
WARNING: Cannot initialize for sequence: GGAPLSPQTHRFM[147], unknown mods may
exist in spectrum t02095_A.19205.19205.3
WARNING: Illegal peptide with unknown mod: HDQFKSTLPDADREREA
Warnings similar to the first and last line are reported during PTMprophet of
the light pepXML, but warnings like the middle two only occurred with the heavy
pepXML.
Thanks for your help,
Jesse
On 12/15/2014 2:47 PM, David Shteynberg wrote:
Hi Jesse,
I am not certain I fully understand the issue, but it sounds to me
like you have multiple searches and should therefore have multiple
pepXML files (from you heavy and light). I would suggest you modify
your pipeline slightly by analyzing the heavy and the light searches
separately and combining them only after PTMProphet has processed the
results. Is this feasible?
Thanks,
-David
On Mon, Dec 15, 2014 at 2:28 PM, Jesse <jgme...@ucsd.edu
<mailto:jgme...@ucsd.edu>> wrote:
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
<superhasht...@gmail.com <mailto:superhasht...@gmail.com>> 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,
2kl...@gmail.com <mailto:2kl...@gmail.com> 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
<oded.k...@gmail.com <mailto:oded.k...@gmail.com>>
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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