Hi There, Very few spectra below that score 15-20 only. Yes, that's my own data. I will surely familiarize myself with X!Tandem usage. Will update you very soon. Thanks for help
On Thursday, 18 January 2018 12:02:01 UTC+5:30, Luis wrote: > Hello, > > How did you determine the quality of the XTandem results? How many > spectra do you get below an Expect score of 0.01? Is this your own data? > > As for the parameters, you very likely will want to change the default > values that are included in TPP, and that may be the reason for the > observed discrepancies with Comet. I suggest that you familiarize yourself > with XTandem usage by going to the XTandem/GPM website. > > Cheers, > --Luis > > > On Wed, Jan 17, 2018 at 8:00 PM, Vipul Batra <[email protected] > <javascript:>> wrote: > >> Hello Luis, >> >> Thank you so much for your reply. The results from X!Tandem search seem >> fine to me. I understand that the quality may be poor, however, I have just >> changed the pipeline to TANDEM. I have used the same RAW files on Comet and >> got good results. The PARAMS file is the one by default. I have not changed >> it. Is TANDEM more sensitive than COMET? I mean that It sees the same data >> as bad which Comet had no problem in processing. >> >> >> On Wednesday, 17 January 2018 01:14:46 UTC+5:30, Luis wrote: >> >>> Hello, >>> >>> Can you verify if you are getting any decent results from your XTandem >>> search? (i.e. open SAMPLE1.tandem.pep.xml in the PepXMLViewer and >>> examine.) The warnings that you see are indicative of either poor data >>> quality, or bad search parameters, so you will want to check those as well. >>> >>> Cheers, >>> --Luis >>> >>> >>> On Mon, Jan 15, 2018 at 7:48 PM, Vipul Batra <[email protected]> >>> wrote: >>> >>>> >>>> On Saturday, 13 January 2018 19:59:06 UTC+5:30, Vipul Batra wrote: >>>>> >>>>> I am getting this error : "*Command FAILED * RETURN CODE:65280" every >>>>> time I am using X!tandem. I have used the same database and mzml files >>>>> with >>>>> comet and the commands were successfully run, however, there seems to be >>>>> an >>>>> issue with X! TANDEM. I have even tried with different databases e.g. >>>>> bovine, human, bubalis but no go . Please guide. >>>>> >>>> >>>> Iterations: .........10.........20...... >>>> WARNING: Mixture model quality test failed for charge (2+). >>>> WARNING: Mixture model quality test failed for charge (3+). >>>> WARNING: Mixture model quality test failed for charge (4+). >>>> WARNING: Mixture model quality test failed for charge (5+). >>>> model complete after 27 iterations >>>> command completed in 2 sec >>>> >>>> running: "E:/TPP/bin/ProphetModels.pl -i >>>> /tmp/a06808/params/interact.pep.xml" >>>> Analyzing /tmp/a06808/params/interact.pep.xml ... >>>> Parsing search results "e:/TPP/data/raw/SAMPLE1 (X! Tandem >>>> (k-score))"... >>>> => Found 0 hits. (0 decoys, 0 excluded) >>>> => Total so far: 0 hits. (0 decoys, 0 excluded) >>>> command completed in 0 sec >>>> moving tempfile /tmp/a06808/params/interact.pep.xml to interact.pep.xml >>>> >>>> running: "E:/TPP/cgi-bin/PepXMLViewer.cgi -I /tmp/a06808/params/ >>>> interact.pep.xml.a06808" >>>> command "E:/TPP/cgi-bin/PepXMLViewer.cgi -I /tmp/a06808/params/ >>>> interact.pep.xml.a06808" failed: Unknown error >>>> >>>> command "E:/TPP/cgi-bin/PepXMLViewer.cgi -I /tmp/a06808/params/ >>>> interact.pep.xml.a06808" exited with non-zero exit code: 255 >>>> QUIT - the job is incomplete >>>> >>>> >>>> >>>> -- >>>> 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 [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >> 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 [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
