Hi, I think you dont need to convert mascot .dat files to pepxml using Mascot2XML, you can directly run xinteract which takes care of the conversions. It should go something like:
xinteract -D/full/path/database -e(enzyme; T for Trypsin) (generaloptions) -O(prophetoptions) -Noutput.pep.xml summary1.dat summary2.dat.... I generally have the mzXML files in the same directory or I make a soft link in the search directory pointing to the original mzXML files. I dont think you can have mgf files because, if I am not wrong, mgf files dont store MS info. I am fairly new with TPP so apologies if I have said anything wrong. Also note that I use the linux version of TPP. Cheers, Kshitiz On Monday, June 27, 2011 10:45:37 PM UTC+1, Dhruti 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 view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/u7MZcosFn3gJ. 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.
