TPP:Mascot and the TPP

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Revision as of 18:45, 20 June 2007 Jtasman (Talk | contribs) ← Previous diff		Current revision Jtasman (Talk | contribs) (adding Johan's command-line mascot recipe)
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	==What is Mascot?==		==What is Mascot?==
-	Mascot is a search engine sold by Matrix Science.	+	Mascot is a commercial, closed-source search engine sold by Matrix Science.
	==Using Mascot and the TPP==		==Using Mascot and the TPP==
-	This page is intended to give instructions for various ways of working with Mascot and the TPP. For example, someone could write instructions for working with the GUI, on the command-line, etc.	+
		+	===Mascot and the TPP GUI (Petunia)===
		+	Mascot is fully supported by the TPP GUI (Petunia.)
		+
		+	===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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Current revision

Contents 1 What is Mascot? 2 Using Mascot and the TPP 2.1 Mascot and the TPP GUI (Petunia) 2.2 Mascot processing on the command line

What is Mascot?

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

Using Mascot and the TPP

Mascot and the TPP GUI (Petunia)

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

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