On Friday, July 22, 2011 3:33:09 PM UTC-4, Luis Mendoza wrote: > > Hello, > I am not sure if this is the source of the error, but the recommended > procedure to process MASCOT data with the TPP is the following: > > 1. Convert Thermo .raw file to mzML (or mzXML) ==> myRun.mzML > 2. Convert this file to mgf (using MzXML2Search) ==> myRun.mgf > 3. Use this file as an input to MASCOT; MASCOT then generates .dat > file ==> F0123456.dat > 4. Rename this to the original base name ==> myRun.dat > 5. Convert to pepXML ==> myRun.pep.xml > 6. Analyze with PeptideProphet, etc. > > Let us know if this does not work. Also, what version of the TPP are you > using? > > Cheers, > --Luis > > > On Mon, Jun 27, 2011 at 2:45 PM, Dhruti <[email protected]> wrote: > > I tried to convert Mascot DTA to pepXML using MASCOT2XML program > > without any success. I get following error > > > > c:/Inetpub/wwwroot/ISB/data/F002856.pep.xml [ Unreadable! ] > > c:/Inetpub/wwwroot/ISB/data/F002857.pep.xml [ Unreadable! ] > > > > un_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\Mascot2XML c:/ > > Inetpub/wwwroot/ISB/data/F002856.dat -Dc:/Inetpub/wwwroot/ISB/data/ > > dbase/uniprot_trembl.fasta -pI -Etrypsin -notgz -desc -shortid > > > > command "c:\Inetpub\tpp-bin\Mascot2XML c:/Inetpub/wwwroot/ISB/data/ > > F002856.dat -Dc:/Inetpub/wwwroot/ISB/data/dbase/uniprot_trembl.fasta - > > pI -Etrypsin -notgz -desc -shortid" failed: Unknown error > > > > Command FAILED > > > > THe Dta was generated by searching thermo raw files using MASCOT > > 2.3. > > > > THanks > > > > -- > > 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. > > > > > >
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