Hi Maik I am glad you got it to work. The reason it wasn't before is the mass you used in the search should match the mass you input for PTMProphet so my algorithm can identify the ids that contain your modification.
I will have to improve the information PTMProphet prints to the screen to help troubleshoot similar issues. Thanks, David On Sep 10, 2012 6:56 AM, "Maik Boehmer" <[email protected]> wrote: > OK, > > it looks that my mistake was to use 80 Daltons as the modification mass > for phosphorylations instead of 79.966. If I type the command: > /usr/local/tpp/bin/PTMProphetParser STY,79.966 MZTOL=0.1 > c:/Inetpub/wwwroot/ISB/data/MB_myprotein_21092011.pep.xml > interact.ptm.pep.xml > everything works as expected. I am still not sure why though, but as long > as it works, thats fine with me :). > > Thanks, > > Maik* > > > * > On Monday, 10 September 2012 10:48:24 UTC+2, Maik Boehmer wrote: >> >> Hi David, >> >> I was on vacation the last two weeks. So here's a late reply. The command >> line functions I tried for PTMProphet were: >> >> /usr/local/tpp/bin/**PTMProphetParser MB_myprotein_21092011.pep.xml or >> /usr/local/tpp/bin/**PTMProphetParser STY,80 >> MB_myprotein_21092011.pep.xml >> >> In both cases PTMProphet did not update the probabbilities for each >> tyrosine, serine or threonine being phosphorylated in the pep.xml file as >> expected, but it removed the entries for the phosphopeptides from the >> pep.xml files completely. The file size gets smaller and I no longer see >> any phosphopeptides in the pep.xml file. It seems that PTMProphet finds the >> phosphopeptides, removes the entries but is then not able to write a new >> entry including the phosphorylation probabilities. >> >> Any help would be greatly appreciated. >> >> Thanks, >> >> Maik >> >> >> On Monday, 27 August 2012 19:57:36 UTC+2, David Shteynberg wrote: >>> >>> Hello Maik, >>> >>> I am not sure what you mean that it removed phospho peptides. The >>> default function for PTMProphet updates the modifications to the most >>> probable positions, unless you used the NOUPDATE flag. Can you send the >>> commandline you used for PTMProphet? >>> >>> Thanks, >>> -David >>> >>> On Thu, Aug 23, 2012 at 1:43 AM, Maik Boehmer <[email protected]>wrote: >>> >>>> Hi Joe, >>>> >>>> thanks a lot for your help. I wasn't sure whether the copying of the >>>> PTMProphetParser file was the reason for its behavior, so I added the >>>> missing line in the makefile and installed it again. Unfortunately the >>>> behavior of PTMPropeht to remove phosphopeptides is still the same. I hope >>>> David can shed some light on what might be going wrong. >>>> >>>> Maik >>>> >>>> >>>> On Thursday, 23 August 2012 01:19:41 UTC+2, [email protected]: >>>> >>>>> Maik, >>>>> >>>>> PTMProphet should be available on both Linux and Windows. It appears >>>>> that we left out a line in the makefile for installing the executable >>>>> under >>>>> Llinux. I'll make sure this gets corrected in 4.6.1. In the meantime you >>>>> can just copy the executable from the build into your bin directory. As >>>>> to >>>>> the removal of the peptides I'll let David S. take a stab at answering >>>>> that. >>>>> >>>>> -Joe >>>>> >>>>> >>>>> On Wed, Aug 22, 2012 at 7:05 AM, Maik Boehmer <[email protected]>wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I installed TPP 4.6.0 on Ubuntu 10.04 for a Labkey server we are >>>>>> running on that machine. As requested in the Labkey installation >>>>>> instructions for TPP, I added XML_ONLY=1 to the TPP MAKEFILE.incl. >>>>>> >>>>>> I was hoping that the new release of the TPP would give us PTMProphet >>>>>> support also on Linux. So far it was only working on our windows >>>>>> machines. >>>>>> Unfortunately PTMProphetParser is not available in the TPP root directory >>>>>> after install. There is a PTMProphetParser available in the /build folder >>>>>> that seems to work but it acts quite peculiar. It recognizes petides with >>>>>> phosphorylations but then removes these peptides from the pep.xml file >>>>>> instead of adding probabilities to them. >>>>>> >>>>>> So my questions is: Should PTMProphet be available also on Linux or >>>>>> is it only available on Windows machines? or Did I miss something that >>>>>> would explain the peculiar behavior of PTMProphetParser on our machine? >>>>>> >>>>>> Thanks >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "spctools-discuss" group. >>>>>> To view this discussion on the web visit https://groups.google.com/d/ >>>>>> **ms**g/spctools-discuss/-/**TISCBRJtm**XkJ<https://groups.google.com/d/msg/spctools-discuss/-/TISCBRJtmXkJ> >>>>>> . >>>>>> To post to this group, send email to spctools...@googlegroups.**com. >>>>>> To unsubscribe from this group, send email to spctools-discu...@** >>>>>> googlegroups**.com. >>>>>> >>>>>> For more options, visit this group at http://groups.google.com/** >>>>>> group**/spctools-discuss?hl=en<http://groups.google.com/group/spctools-discuss?hl=en> >>>>>> . >>>>>> >>>>> >>>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To view this discussion on the web visit https://groups.google.com/d/** >>>> msg/spctools-discuss/-/**DEjyYXgNFg0J<https://groups.google.com/d/msg/spctools-discuss/-/DEjyYXgNFg0J> >>>> . >>>> >>>> To post to this group, send email to [email protected]. >>>> To unsubscribe from this group, send email to spctools-discu...@** >>>> googlegroups.com. >>>> For more options, visit this group at http://groups.google.com/** >>>> group/spctools-discuss?hl=en<http://groups.google.com/group/spctools-discuss?hl=en> >>>> . >>>> >>> >>> -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/2nm9BVJ1OrAJ. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
