TPP:Mascot and the TPP

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Contents

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What is Mascot?

Mascot is a commercial, closed-source search engine sold by Matrix Science.

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Using Mascot and the TPP

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Mascot and the TPP GUI (Petunia)

Mascot is fully supported by the TPP GUI (Petunia.)

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Mascot processing on the command line

How to run MASCOT searches through the TPP:

  • On your TPP computer, convert your mzXML files of interest to mgf (Mascot generic format) files by "MzXML2Search -mgf file.mzXML" (Note that the old mzxml2other is retired)
  • Search MASCOT with this mgf file
  • When the search is complete, move the MASCOT output file (*.dat) back to the directory where the original file.mzXML file is.
  • Make sure you have the same database used my MASCOT on your TPP computer.
  • Rename the *.dat file so that it has the same name as the mzXML but with the *.dat extension (file.dat).
  • Convert MASCOT search results to pepXML with "Mascot2XML <file.dat> -D<full/path/to/database>"
  • Run xinteract as usual
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