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 Wed, Jul 25, 2012 at 4:35 PM, Vidya Venkatraman <[email protected]>wrote: > 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 spctools-discuss@googlegroups.** >> com <[email protected]>. >> > To unsubscribe from this group, send email to >> spctools-discuss+unsubscribe@**googlegroups.com<spctools-discuss%[email protected]> >> . >> > For more options, visit this group at http://groups.google.com/** >> group/spctools-discuss?hl=en<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. > -- Kshitiz Tyagi -- 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.
