Hi Luis, I just had a question about using converting Mascot data to pepxml in TPP. I was able to successfully convert Mascot generated .dat files to pepxml using TPP gui. Though, i was wondering if having mzXML within the same folder structure is mandatory. Will the process work without mzXML? Also, can we use mgfs instead of mzXML within the same folder structure to convert .dat to pepxml.
Thanks Vidya 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. > > > > > > -- 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/-/GvxKt2ZwY3EJ. 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.
