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. > > -- 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.
