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
On Monday, December 21, 2020 at 3:40:05 AM UTC-8 kumarsu...@gmail.com wrote: > 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: > >> Hi Sud, >> Here is a Comet parameters file with the TMT tags set as static >> modifications (see bottom of the file): >> >> https://github.com/pwilmart/Metaplastic-BC_PXD014414/blob/master/comet.params >> 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: >> https://github.com/pwilmart/PAW_pipeline >> There are also many other resources at my GitHub site for TMT analyses. >> Cheers, >> Phil >> >> On Sunday, December 20, 2020 at 9:30:16 PM UTC-8 kumarsu...@gmail.com >> wrote: >> >>> Can anyone please hare with me The *"comet search parameters for TMT >>> 6plex labeled tryptic peptides*??? >>> It will be a great help. >>> Regards, >>> Sud >>> >> -- >> > You received this message because you are subscribed to a topic in the >> Google Groups "spctools-discuss" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/spctools-discuss/JAH2WjPJmU0/unsubscribe >> . >> To unsubscribe from this group and all its topics, send an email to >> spctools-discu...@googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/af6d08ea-6eb3-475a-ae09-589b37ecd6fcn%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/af6d08ea-6eb3-475a-ae09-589b37ecd6fcn%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > > > -- > ------------------------------------------------------------------- > 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 > Orcid Id: https://orcid.org/0000-0002-9816-4307 > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/d1f004cc-3201-41d7-8d1d-cc25359bcdb5n%40googlegroups.com.
