Hello Paul,
The quickest way to greater understanding on the use of the tools is to execute
the binaries in question at the command line with no options specified. The
output will show information about their usage. For example on my old Linux
install of TPP 4.8, at the command line, I change directory to the …/tpp/bin
directory and type in e.g. ./xinteract. There is quite a bit of usage
information output for xinteract since it is a wrapper for many of the binaries
to execute them in succession to form the pipeline. If you page down (in my
version) after running the xinteract command there is this output which
references PTMProphet:
PTMProphet options [run PTMProphet on the iProphet result with options that
follow the '-M' (e.g. -M-STY,79.9663-MZTOL=0.4)]:
-{<amino acids, n, or c>,<mass_shift>,...} [specify mod
masses (e.g. -STY,79.9663,K,114.0429,M,15.9949)]
-MZTOL=<number> [Use specified +/-
mz tolerance on site specific ions (default=0.1 dalton)]
-NOUPDATE [Don't update
modification_info tags in pepXML]
Also running the binaries at the command line can sometimes aid in
troubleshooting since they tend to output more information about what is going
on than is displayed via the GUI web interface.
Aside from this, you can also look up the published papers on many of the
tools, attend the periodic TPP training courses, and ask questions to this
forum. I am personally not aware of any tutorials for PTMProphet or most of
the other tools for that matter.
It would be a wonderful thing were the TPP developer team to provide tutorials
(online not just the courses which you must attend in person) that cover the
breadth and depth of the TPP toolset much like what the developers of Skyline
and Maxquant have done. This would enable many more people to learn and use the
TPP tools at their own pace, in their own environment. I think that would
markedly increase TPP usage around the world.
Cheers,
Brian
On Jan 5, 2018, at 10:29 AM, Paul Abraham
<pabraham6...@gmail.com<mailto:pabraham6...@gmail.com>> wrote:
Hello,
I am having a difficult time locating documentation for several of the TPP
tools. For example, the PTMProphet tool referenced on the wiki page does not
have any supporting documentation. Am I missing some obscure landing page
somewhere? The only information I find for how to efficiently utilize this tool
is by scouring this forum and this is by no means a good use of time,
considering most posts highlight the issues.
Can anyone point to documentation for this tool particularly, but other TPP
tools as well?
Regards,
Paul
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