Hello SunSun, Libra does indeed need access to the spectra in mzML (or mzXML) format to carry out the quantitation, as you pointed out from the error message: "Failed to open input file 'c:/Inetpub/wwwroot/ISB/data/2ndhospital/1/F003158.mzXML'"
It would be best if you could track down the original raw files for your 3 runs and convert them to mzXML. Cheers, --Luis On Wed, Oct 31, 2012 at 7:04 PM, zeyu sun <[email protected]> wrote: > Erik, > I tried this before, but the libraproteinratioparser keep crashing all the > time: > here is the error message I got when I try to use it to process the > prot.xml: > > This application has requested the Runtime to terminate it in an unusual > way. Please contact the application's support team for more information. > > any quick remedy to this problem? > thanks! > > SunSun > > > On Wed, Oct 31, 2012 at 1:13 AM, ChargedPeptide <[email protected]> wrote: >> >> Oh, that's much easier :) >> In this case you would need to do the following: >> Run your mascot->pep.xml with libra quantities and also X!tandem -> >> pep.xml (If this is the same data ran with different search engines, if it >> is different data as well you need to process each batch separatley and set >> an experiment ID for each set, let me know if this applies and I'll give you >> som detail) >> >> Run iprophet on both your output pep.xmls to get a pep.xml with combined >> spectral matches and iProbabilities. >> Run protein-prophet on the iProphet output pep.xml. >> Now you will have a prot.xml with no quantities displayed. >> Manually run libraproteinratioparser (or similiar name, can't check now , >> on train) as this: >> libraproteinratioparser <your prot.xml> -c<your libra condition file> >> >> Voila. Enjoy your final prot.xml. >> >> Let me know if this works out for you. >> >> Den måndagen den 29:e oktober 2012 kl. 19:35:06 UTC+1 skrev sunsun: >>> >>> 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 >>>>> >>>>> >>>>> >>>>> 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 view this discussion on the web visit >> https://groups.google.com/d/msg/spctools-discuss/-/HefPZZmaIk4J. >> >> 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. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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