thank you Jimmy. I will try the search w/o refinement. I will let you know if the problem solved.
SunSun On Monday, October 6, 2014 1:13:01 AM UTC+8, Jimmy Eng wrote: > > I don't know what the issue is with X!Tandem but just wanted to comment on > an unrelated issue which is that you should think twice about using > X!Tandem's refinement mode, especially if you are going to push those > search results through PeptideProphet or even simple target-decoy FDR. All > proteins that make it to the refinement step (and their corresponding > peptides identified before or after refinement) will all have > distorted/high statistics. Here are two publications that discuss this > problem: > > http://www.ncbi.nlm.nih.gov/pubmed/19947654 > http://www.ncbi.nlm.nih.gov/pubmed/21288048 > > The simple solution is to not use refinement mode. > > On Sun, Oct 5, 2014 at 1:09 AM, zeyu sun <[email protected] <javascript:>> > wrote: > >> Hi, Dear SPC users and developers: >> I'm wondering if anyone have some clue or remedy to the problem I have >> with the X!tandem search in TPP(v4.7.1): >> I have some Orbitrap Velos data in RAW and converted them to mzXML files >> by MSconverter (ProteoWizard). >> I ran the Comet pipeline on them and everything was just fine. >> However, when I search the same mzXMLs by Tandem, some of those files >> gave error reports: >> _________________________________________ >> X! TANDEM Jackhammer TPP (2013.06.15.1 - LabKey, Insilicos, ISB) >> >> Loading spectra (mzParser)............................ loaded. >> Spectra matching criteria = 55267 >> Pluggable scoring enabled. >> Starting threads . started. >> Computing models: >> 12345678 >> ********* >> Warning: One or more sequences appear to contain invalid amino acid codes. >> >> ********* >> >> 9 sequences modelled = 9 ks >> Model refinement: >> partial cleavage .......... done. >> finishing refinement ... done. >> Creating report: >> initial calculations ..... done. >> sorting ..... done. >> finding repeats ..... done. >> evaluating results ..... done. >> calculating expectations ..... done. >> writing results ..... done. >> >> command "c:\Inetpub\tpp-bin\tandem >> c:/Inetpub/wwwroot/ISB/data/xxx.tandem.params" failed: Unknown error >> >> Command FAILED >> RETURN CODE:65280 >> _________________________________________ >> Despite this error message, the .tandem files were generated, >> When I use the command tandem2XML to convert the .tandem files to >> .pep.xml, as expected, it didn't work out: >> Operation not permitted >> Command FAILED >> RETURN CODE:256 >> >> It only happens in few mzXML files, not all of them. And Comet runs OK on >> all files, so I guess the mzXMLs should be fine. >> I further checked .tandem files, looks like they contain all necessary >> parts of Xtandem search results, and all spectra-peptide matches were >> listed there with scores. I just don't know why such files still gave error >> message and cannot go through tandem2XML. >> Please help! >> Thank you very much! >> >> SunSun >> >> -- >> 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 http://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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
