Hi Kshitiz, Thanks for your prompt response. Actually I dont have the mzXML files. I just have the mgf files using which I ran Mascot and got the .dat files. Now i want to convert the .dat files to pepxml. I was wondering if it is possible for me to convert the .dat files to pepxml with the mgfs. Right now, I have to separately convert the .raw files to mzXML to get TPP to convert .dat to .pepxml. I was wondering if I could do so without actually having the mzXMLs.
Thanks Vidya On Wednesday, July 25, 2012 11:43:25 AM UTC-4, kshitiz wrote: > > 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/-/qsN6kQf6_ycJ. 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.
