I would suggest you run these in separate directories maintaining the same basename of your spectrum files, this way iProphet will be able to recognized multiple searches of the same spectra. Run xinteract on each search combining all fractions from each search into a single analysis at the PeptideProphet level. Something like:
cd sequest xinteract Band*.pep.xml cd xtandem xinteract Band*.pep.xml cd ../iprophet InterProphetParser ../sequest/interact.pep.xml ../xtandem/interact.pep.xml interact.iprophet.pep.xml Write back if you need further clarification. -David On Wed, Aug 3, 2011 at 3:06 PM, Kinfai Au <[email protected]> wrote: > Hi, > I have a data with 8 factions. I searched them in SEQUEST and X!tandem > respectively. The output files after PeptideProphet are: > > Band1.sequest.pep.xml > Band2.sequest.pep.xml > Band3.sequest.pep.xml > Band4.sequest.pep.xml > Band5.sequest.pep.xml > Band6.sequest.pep.xml > Band7.sequest.pep.xml > Band8.sequest.pep.xml > > Band1.xtandem.pep.xml > Band2.xtandem.pep.xml > Band3.xtandem.pep.xml > Band4.xtandem.pep.xml > Band5.xtandem.pep.xml > Band6.xtandem.pep.xml > Band7.xtandem.pep.xml > Band8.xtandem.pep.xml > > How can I merge them in InterProphet? I asked this question in the > workshop. I work on Linux. Could you write me an example of the > command line that I should use? > > Yours, > Kinfai > > -- > 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.
