Re: [spctools-discuss] PTM prophet and DiMethylation

Tue, 16 Dec 2014 11:34:30 -0800

Yes I am using 4.8. I forgot to set variable metOx for the heavy and PTM prophet now finishes, but none of the modifications are localized. I used the following to account for heavy K and diglycine (actual file structure removed):
*cd c:/FILESTRUCTURE& c:\Inetpub\tpp-bin\PTMProphetParser K,122.0572,M,15.995 MZTOL=0.1 NOUPDATE c:/FILESTRUCTURE/UV0h.interact.ipro.pep.xml UV0h.test122m16.interact.ptm.pep.xml 


I also tried running it with K,114.043,M,15.995 and neither result has 
localized diglycine modifications.  Do I need to specify fixed 
modification of lysine to account for silac?


Thanks,
Jesse


*On 12/16/2014 11:00 AM, David Shteynberg wrote:

Are you using version 4.8 of the TPP?  Can you send the commands 
(amino acids and modifications) you are using for both the light that 
works and heavy that doesn't?


Thanks,
-David


On Tue, Dec 16, 2014 at 10:29 AM, Jesse <[email protected] 
<mailto:[email protected]>> wrote:


    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 <[email protected]
    <mailto:[email protected]>> 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
            <[email protected]
            <mailto:[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] <mailto:[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]
                        <mailto:[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]
                            <mailto:[email protected]>.
                            To post to this group, send email to
                            [email protected]
                            <mailto:[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]
                <mailto:spctools-discuss%[email protected]>.
                To post to this group, send email to
                [email protected]
                <mailto:[email protected]>.
                Visit this group at
                http://groups.google.com/group/spctools-discuss.
                For more options, visit
                https://groups.google.com/d/optout.




        -- 
        Jesse Meyer

        Graduate Student
        Department of Chemistry and Biochemistry
        University of California, San Diego
        La Jolla, CA 92092


        ---
        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]
        <mailto:spctools-discuss%[email protected]>.
        To post to this group, send email to
        [email protected]
        <mailto:[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]
    <mailto:[email protected]>.
    To post to this group, send email to
    [email protected]
    <mailto:[email protected]>.
    Visit this group at http://groups.google.com/group/spctools-discuss.
    For more options, visit https://groups.google.com/d/optout.




    -- 
    Jesse Meyer

    Graduate Student
    Department of Chemistry and Biochemistry
    University of California, San Diego
    La Jolla, CA 92092



    ------------------------------------------------------------------------
    <http://www.avast.com/>       

    This email is free from viruses and malware because avast!
    Antivirus <http://www.avast.com/> protection is active.



    -- 
    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]
    <mailto:[email protected]>.
    To post to this group, send email to
    [email protected]
    <mailto:[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] 
<mailto:[email protected]>.
To post to this group, send email to [email protected] 
<mailto:[email protected]>.

Visit this group at http://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.



--
Jesse Meyer
Graduate Student
Department of Chemistry and Biochemistry
University of California, San Diego
La Jolla, CA 92092



---
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.

























					Reply via email to