Hi David,
I am running the TPP v4.6 OCCUPY rev 3, Build 201307241109 (MinGW) version
of TPP. I have recently started exploring PTM prophet in TPP. I had a few
questions regarding the options and parameters within PTM Prophet.
Feel free to point me to any documentation or tutorial if there is one
already on these parameters. I can also send any input or result files if
needed.
1) The default residue mass shift of 79.96 on STY does not seem to work in
my case. Although, if i give the total mass change of 167 for S, 181 for T
and 243 for Y, it works. I noticed that my pep.xml files mention total
masses. Should total mass change be used?
This is the error I get:
running: "C:/Inetpub/tpp-bin/PTMProphetParser STY,79.966 MZTOL=0.1
interact.ipro.pep.xml interact.ptm.ipro.pep.xml"
INFO: Writing file interact.ptm.ipro.pep.xml ...
INFO: Reading file interact.ipro.pep.xml ...
WARNING: Unrecognized mod on peptide:
MAQPAWGLSASHRAPAPPPPPLLLPLPLLLPLLELPLLHRS[167]S
I also noticed that even if i use total mass change, for one peptide, I got
this warning
running: "C:/Inetpub/tpp-bin/PTMProphetParser S,167,T,181,Y,243 MZTOL=0.1
interact.ipro.pep.xml interact.ptm.ipro.pep.xml"
INFO: Writing file interact.ptm.ipro.pep.xml ...
INFO: Reading file interact.ipro.pep.xml ...
WARNING: Unrecognized mod on peptide: IPESLGLMTLPPESLQKT[181]
command completed in 1 sec
2) Should the m/z tolerance in the PTM prophet parameters be the same as
the fragment tolerance used during the search? If not, What does it exactly
represent?
3) What is the "Do not update modification_info tags in pepXML" option
meant for?
4) Within the interact.ptm.ipro.pep.xml, what does the tag
"ptmprophet_result prior="0.5" mean?
<analysis_result analysis="ptmprophet">
<ptmprophet_result prior="0.5" ptm="PTMProphet_T79.9663"
ptm_peptide="IPESLGLMT(0.916)LPPESLQKT(0.084)">
<mod_aminoacid_probability position="9" probability="0.916"/>
<mod_aminoacid_probability position="18" probability="0.084"/>
</ptmprophet_result>
5) The current TPP workflow seems to have options to run ProteinProphet
after PeptideProphet and/or after InterProphet. I was wondering if it was
possible to run ProteinProphet after PTMProphet? (i.e. can we run
ProteinProphet on the interact.ptm.ipro.pep.xml file created by
PTMProphet). Are there any reasons as to why that should not be done or
cannot be done after PTMProphet?
I would highly appreciate any inputs or suggestions from your end.
Thanks in advance,
Vidya
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