PTMProphetParser on Linux

[Maik Boehmer]

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

[Joseph Slagel]

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

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[Maik Boehmer]

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

[David Shteynberg]

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

To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/DEjyYXgNFg0J.

[Maik Boehmer]

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

[Maik Boehmer]

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

[David Shteynberg]

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

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