comet search parameters for TMT labeled tryptic peptides

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sudarshan kumar

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Dec 21, 2020, 12:30:16 AM12/21/20
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Can anyone please hare with me The "comet search parameters for TMT 6plex labeled tryptic peptides???
It will be a great help.
Regards,
Sud

Phillip Wilmarth

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Dec 21, 2020, 1:25:54 AM12/21/20
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Hi Sud,
Here is a Comet parameters file with the TMT tags set as static modifications (see bottom of the file):
The tags are +229.1629 Da on the peptide N-term and on lysine residues. I have an open source pipeline that uses Comet and supports TMT labeling:
There are also many other resources at my GitHub site for TMT analyses.
Cheers,
Phil

sudarshan kumar

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Dec 21, 2020, 5:56:50 AM12/21/20
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Dear Phillip,
Thank you so much. It helped me a lot. Please be benevolent to help in future as well.
Regards,
Sudarshan

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--
-------------------------------------------------------------------
The real voyage of discovery consists not in seeking new lands but seeing with new eyes. — Marcel Proust

Dr. Sudarshan Kumar
(B.V.Sc.& A.H., M.V.Sc., PhD.)
Scientist
Animal Biotechnology Center
(Proteomics and Cell Biology Lab.)
National Dairy Research Institute Karnal, 132001
Haryana, India
Contact No 09254912456
URL www.ndri.res.in

sudarshan kumar

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Dec 21, 2020, 6:40:05 AM12/21/20
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Dear Phillip,
Can you please explain why I am getting this message during Xintreact processing. although its hase in the last processed all data.
running: "C:/TPP/bin/InteractParser "/tmp/a04564/params/Arvind/interact.pep.xml" "SF2.mzML.gz.pep.xml" -L"7""
 file 1: SF2.mzML.gz.pep.xml
Unknown .gz file. Only .mzML.gz and .mzXML.gz allowed. No file loaded.
WARNING: cannot open data file c:\TPP\data\Arvind\TMT_saliva_6plex\SF2.gz in msms_run_summary tag... unrecognized extension .gz, trying .mzML ...
WARNING: CANNOT correct data file c:\TPP\data\Arvind\TMT_saliva_6plex\SF2.mzML in msms_run_summary tag...
Unknown .gz file. Only .mzML.gz and .mzXML.gz allowed. No file loaded.
WARNING: cannot open data file c:\TPP\data\Arvind\TMT_saliva_6plex\SF2.gz in msms_run_summary tag... unrecognized extension .gz, trying .mzML ...
WARNING: CANNOT correct data file c:\TPP\data\Arvind\TMT_saliva_6plex\SF2.mzML in msms_run_summary tag...
 processed altogether 28219 results

On Mon, Dec 21, 2020 at 11:55 AM Phillip Wilmarth <pwil...@gmail.com> wrote:
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Phillip Wilmarth

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Dec 21, 2020, 9:33:59 AM12/21/20
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Hi Sudarshan,
I don't use the TPP much. It looks like InteractParser is trying to read a file it can't understand or a file that does not look like a valid type of file. mzML are converted RAW instrument files. Comet reads those and creates pep xml files with the search results. Those are usually the base name of the mzML file with the .pep.xml extensions (i.e. SF2.pep.xml). The command line is trying to read a file called SF2.mxML.gz.pep.xml. That looks odd to me. Maybe one of the TPP experts can help?
Cheers,
Phil
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