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/* >>>>> *msg/spctools-discuss/-/**TISCBRJtmXkJ<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. >>> >>> 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 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.
