Erik, Thanks for the reply. However, the problem you described is not what I have encountered. I did the search separately without merging them, so I have individual dat. files that corresponding to each mzXML.In my case, the Libra have no problem to read the data at all. I can do the Mascot-TPP-Libra successfully, and I can also do the Tandem-TPP-Libra successfully, but I just haven't find a way to combine both data into a prot.xml.
Despite of that, I think your Java script is very interesting and may help others if they want to try it out. Thanks for the help. SunSun On Sun, Oct 28, 2012 at 11:41 PM, ChargedPeptide <[email protected]>wrote: > Hey SunSun, I've had a number of problems running through mascot data. The > most usual error for me is that the > <msms_run_summary base_name= > in the pep.xml is set erroneously. This is especially true if you are > running Mascot2XML on a merged Mascot search where results from multiple > MGF files are in one .dat output file. > Libra reads the msms_run summary_base_name= and raw_data= to get the > location and extension of input data. > I've recently wrote a bit of Java to split the results from Mascot output > files into their own pep.xmls after Mascot2XML and I'm not really aware of > another way to do it, though I've missed something. > If this is your problem I'd need to adapt it a bit (right now it only runs > as part of our pipeline, not stand-alone) but I'd be happy to send it over > if you need it. > > Your first check should be if this: > c:/Inetpub/wwwroot/ISB/data/**2ndhospital/1/F003158.mzXML > is an actual data file. It looks like a mascot-search ID to me. > > Den söndagen den 14:e oktober 2012 kl. 02:45:19 UTC+2 skrev sunsun: > >> Dear TPP team, >> I'm running a 8plex iTRAQ data analysis using the Mascot-TPP-Libra >> pipeline. It went through peptideProphet and proteinProphet smoothly >> without Libra. However, when I add Libra option into the picture, it >> generate an error. It seems the Libra quantitation require the spectrum >> data in mzXML format, however, all I have is mg files. Do I really need to >> convert everything to mzXML? or is there something else going wrong that I >> really unaware off. Please help me out! >> thank you so much! >> SunSun >> >> >> here is the error message I got: >> >> *EXECUTING: run_in c:/Inetpub/wwwroot/ISB/data/2ndhospital/1; >> c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.95 -l7 -O >> -Lcondition_zeyuiTRAQtest1.xml-1 F003158.pep.xml F003159.pep.xml >> F003160.pep.xml * >> >> c:\Inetpub\tpp-bin\xinteract (TPP v4.6 OCCUPY rev 0, Build 201208170820 >> (MinGW)) >> >> running: "C:/Inetpub/tpp-bin/**InteractParser "interact.pep.xml" >> "F003158.pep.xml" "F003159.pep.xml" "F003160.pep.xml" -L"7"" >> file 1: F003158.pep.xml >> file 2: F003159.pep.xml >> file 3: F003160.pep.xml >> processed altogether 2737 results >> >> >> results written to file >> c:/Inetpub/wwwroot/ISB/data/**2ndhospital/1/interact.pep.xml >> >> direct your browser to >> http://localhost/ISB/data/**2ndhospital/1/interact.pep.**shtml >> <http://localhost/ISB/data/2ndhospital/1/interact.pep.shtml> >> >> >> >> command completed in 5 sec >> >> running: "C:/Inetpub/tpp-bin/**DatabaseParser "interact.pep.xml"" >> command completed in 1 sec >> >> running: "C:/Inetpub/tpp-bin/**RefreshParser "interact.pep.xml" >> "c:/Inetpub/wwwroot/ISB/data/**dbase/zeyu_human.1.fasta"" >> - Searching the tree... >> - Linking duplicate entries... - Printing results... >> >> - Building Commentz-Walter keyword tree...command completed in 18 sec >> >> running: "C:/Inetpub/tpp-bin/**PeptideProphetParser "interact.pep.xml" >> MINPROB=0.95" >> (MASCOT) >> results for charge 1: 9 id tot and 1 adj scores >> results for charge 2: 512 id tot and 16 adj scores >> results for charge 3: 903 id tot and 46 adj scores >> results for charge 3: 7.65044 adj_ion_mean and 23.2164 adj_ion_hom mean >> 37.4548id mean0.928281 correlation (r) >> 3+ ion - id = 1.02138*(ion - hom) + -16.0625 with error = 6.00641 >> mean ion - id: 7.65044, mean ion - hom: 23.2164 >> results for charge 4: 347 id tot and 1 adj scores >> results for charge 5: 966 id tot and 1 adj scores >> results for charge 6: 0 id tot and 0 adj scores >> results for charge 7: 0 id tot and 0 adj scores >> init with MASCOT trypsin >> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: >> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN >> >> PeptideProphet (TPP v4.6 OCCUPY rev 0, Build 201208170820 (MinGW)) >> AKeller@ISB >> read in 5 1+, 382 2+, 813 3+, 324 4+, 886 5+, 0 6+, and 0 7+ spectra. >> Initialising statistical models ... >> Iterations: .........10.........20.. >> WARNING: Mixture model quality test failed for charge (1+). >> WARNING: Mixture model quality test failed for charge (4+). >> WARNING: Mixture model quality test failed for charge (5+). >> model complete after 23 iterations >> command completed in 5 sec >> >> running: "C:/Inetpub/tpp-bin/**ProphetModels.pl -i interact.pep.xml" >> Analyzing interact.pep.xml ... >> Parsing search results "c:/Inetpub/wwwroot/ISB/data/**2ndhospital/1/F003158 >> (MASCOT)"... >> => Total of 12 hits. >> => Total of 0 decoy hits. >> => Total of 0 excluded hits. >> Parsing search results "c:/Inetpub/wwwroot/ISB/data/**2ndhospital/1/F003159 >> (MASCOT)"... >> => Total of 14 hits. >> => Total of 0 decoy hits. >> => Total of 0 excluded hits. >> Parsing search results "c:/Inetpub/wwwroot/ISB/data/**2ndhospital/1/F003160 >> (MASCOT)"... >> => Total of 45 hits. >> => Total of 0 decoy hits. >> => Total of 0 excluded hits. >> command completed in 5 sec >> >> running: "C:/Inetpub/tpp-bin/**LibraPeptideParser "interact.pep.xml" >> -ccondition_zeyuiTRAQtest1.**xml" >> Failed to open input file >> 'c:/Inetpub/wwwroot/ISB/data/**2ndhospital/1/F003158.mzXML'. >> could not open input file >> c:/Inetpub/wwwroot/ISB/data/**2ndhospital/1/F003158.mzXML >> >> command "C:/Inetpub/tpp-bin/**LibraPeptideParser "interact.pep.xml" >> -ccondition_zeyuiTRAQtest1.**xml" failed: Operation not permitted >> >> command "C:/Inetpub/tpp-bin/**LibraPeptideParser "interact.pep.xml" >> -ccondition_zeyuiTRAQtest1.**xml" exited with non-zero exit code: 1 >> QUIT - the job is incomplete >> >> command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.95 -l7 -O >> -Lcondition_zeyuiTRAQtest1.**xml-1 F003158.pep.xml F003159.pep.xml >> F003160.pep.xml" failed: Operation not permitted >> >> *Command FAILED* >> RETURN CODE:256 >> >> >> The Libra condition.xml was generated within TPP using the default 8plex >> setting. >> > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/YVdRAe93h40J. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- *Sun* -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
