Hi, Please try using Protowizard's msconvert (which comes bundled with TPP) to do the conversion instead of ReAdW. The older ReAdW isn't being supported and doesn't automatically come bundled with TPP and has to be installed seperately, hence the error.
-Joe On Tue, Jan 31, 2012 at 10:02 AM, XC <[email protected]> wrote: > one thing I can think of is that last week, we didn't do the database > search through TPP. we did the search through Proteome discoverer as > interface. then copy the resulting .dat files and the .fasta file > into C:\Inetpub\wwwroot\ISB\data. but we didn't change the file > name. > So today, we tried to start from the raw data. but when we tried to > convert raw to mzXML, we got teh error message as shown below. > Thanks.. > > Attempting to run the following commands > > c:\Inetpub\tpp-bin\ReAdW -v --mzXML c:/Inetpub/wwwroot/ISB/data/ > 12032011_60min_PaG_XC_HP101_01.raw > > > > Output so far: > > # Commands for session 5EJFN64ZU on Tue Jan 31 12:33:25 2012 > # BEGIN COMMAND BLOCK > ###### BEGIN Command Execution ###### > [Tue Jan 31 12:33:25 2012] EXECUTING: c:\Inetpub\tpp-bin\ReAdW -v -- > mzXML c:/Inetpub/wwwroot/ISB/data/12032011_60min_PaG_XC_HP101_01.raw > OUTPUT: > The system cannot find message text for message number 0x2331 in the > message file for Application. > END OUTPUT > RETURN CODE:256 > ###### End Command Execution ###### > # All finished at Tue Jan 31 12:33:25 2012 > # END COMMAND BLOCK > > > > On Jan 27, 3:48 pm, Luis Mendoza <[email protected]> > wrote: > > Hello, > > There appears to be a couple of issues going on. > > > > The first is that Mascot2XML cannot find scan numbers in the .dat > > file. How did you do the Mascot search? For the TPP to support > > Mascot results, you must start with an mzML (or mzXML) file, convert > > that to an .mgf (using MzXML2Search), and search that file with > > Mascot. Once you retrieve the .dat file, you should rename it to the > > original base name of the mzML file (instead of Fxxxxxx.dat). Convert > > this to pepXML, and the scan numbers should be there! > > > > Second, you also need to specify the sequence database (in fasta > > format) that you used in the search. It seems that you selected the > > .dat file as that input, which is incorrect. > > > > Hope this helps, > > --Luis > > > > > > > > > > > > > > > > On Thu, Jan 26, 2012 at 2:29 PM, XC <[email protected]> wrote: > > > Hi there, > > > we are trying to run some Mascot search results through TPP. We copied > > > the .dat files and the .fasta file for database into C:\Inetpub\wwwroot > > > \ISB\data. in the TPP interface, we went to the "pepXML" tab under > > > "analysis pipeline(Mascot)", added the files, then hit the "convert to > > > pepXML" button. then we got something as shown at the end. Anyone know > > > why? Thanks a lot. > > > we use TPP v4.5 (rapture) rev 1, PERL 5.12.4.1205, winXP. > > > > > # Commands for session MUT6YN88F on Thu Jan 26 17:22:12 2012 > > > # BEGIN COMMAND BLOCK > > > ###### BEGIN Command Execution ###### > > > [Thu Jan 26 17:22:12 2012] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/ > > > data/4953; c:\Inetpub\tpp-bin\Mascot2XML c:/Inetpub/wwwroot/ISB/data/ > > > 4953/F004954.dat -Dc:/Inetpub/wwwroot/ISB/data/4953/F004954.dat - > > > Etrypsin > > > OUTPUT: > > > filepath: c:/Inetpub/wwwroot/ISB/data/4953/, extn: F004954 > > > A stored as 71.0371 > > > B stored as 114.535 > > > C stored as 103.009 > > > D stored as 115.027 > > > E stored as 129.043 > > > F stored as 147.068 > > > G stored as 57.0215 > > > H stored as 137.059 > > > I stored as 113.084 > > > J stored as 0 > > > K stored as 128.095 > > > L stored as 113.084 > > > M stored as 131.04 > > > N stored as 114.043 > > > O stored as 0 > > > P stored as 97.0528 > > > Q stored as 128.059 > > > R stored as 156.101 > > > S stored as 87.032 > > > T stored as 101.048 > > > U stored as 150.954 > > > V stored as 99.0684 > > > W stored as 186.079 > > > X stored as 111 > > > Y stored as 163.063 > > > Z stored as 128.551 > > > c stored as 17.0027 > > > n stored as 1.00782 > > > variable modification 1, delta mass 57.0215 for Carbamidomethyl (C): > > > residues: C > > > nterm: 0 > > > cterm: 0 > > > > > > -------------------------------------------------------------------------------- > > > ...skipping 8796 lines of output... [ view all ] > > > > -------------------------------------------------------------------------------- > > > > > Warning: could not find scan numbers of spectrum Spectrum3799scans: > > > 7221, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum4340scans: > > > 8033, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum4762scans: > > > 8683, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum4765scans: > > > 8688, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum5492scans: > > > 9762, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum5478scans: > > > 9744, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum2940scans: > > > 5953, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum2937scans: > > > 5949, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum2931scans: > > > 5940, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum4262scans: > > > 7902, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum5067scans: > > > 9157, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum5856scans: > > > 10228, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum5846scans: > > > 10216, > > > Set to 0000 > > > Warning: could not find scan numbers of spectrum Spectrum4395scans: > > > 8121, > > > Set to 0000 > > > trypsin : cut(KR) nocuts(P) sense(C) > > > prev_aa and next_aa have already been read from .dat file. > > > Replacing 35007 protein id with full ids by parsing through the > > > database... > > > searching c:/Inetpub/wwwroot/ISB/data/4953/F004954.datwarning, size of > > > protein exceeds 50000 > > > Sequence line exceeds 40000characters > > > > > command "c:\Inetpub\tpp-bin\Mascot2XML c:/Inetpub/wwwroot/ISB/data/ > > > 4953/F004954.dat -Dc:/Inetpub/wwwroot/ISB/data/4953/F004954.dat - > > > Etrypsin" failed: Operation not permitted > > > END OUTPUT > > > RETURN CODE:256 > > > ###### End Command Execution ###### > > > # All finished at Thu Jan 26 17:23:02 2012 > > > # END COMMAND BLOCK > > > > > -- > > > 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 athttp:// > 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. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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