Thank you Luis, Yes, now I use the mzXML and the problem seems solved. SunSun
On Wed, Dec 5, 2012 at 5:49 AM, Luis Mendoza < [email protected]> wrote: > 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. > 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. 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