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This tutorial will give you a brief overview of the most important TOPP tools. First, we explain some basics that you will need for every TOPP tool, then we show several example pipelines.
The TOPP tools use the HUPO-PSI standard format mzData 1.05 as input format. In order to convert other open formats (DTA, mzXML, ANDI/MS) to mzData, a file converter is provided by TOPP.
Proprietary MS machine formats are not supported. If you need to convert these formats to mzData or mzXML, please have a look at the SASHIMI project page or contact your MS machine vendor.
mzData covers only the output of a mass spectrometry experiment. For further analysis of this data several other file formats are needed. The main file formats used by TOPP are:
- mzData The HUPO-PSI standard format for mass spectrometry data.
- featureXML The OpenMS format for quantitation results.
- consensusXML The OpenMS format for alignment of peak and feature data.
- featurePairsXML The OpenMS format for feature pairs.
- idXML The OpenMS format for protein and peptide identification.
Documented schemas of the OpenMS formats can be found at http://open-ms.sourceforge.net/schemas/
.
For identification results in idXML format, there is an XSLT-script that you can use to visualize the identifications in a web browser. Direct your browser to http://open-ms.sourceforge.net/schemas/IdXML.xsl
and store the XSLT-script in a directory of your choice, say, C:\scripts\IdXML.xsl
. Add a line of the form
<?xml-stylesheet type="text/xsl" href="*PATH*IdXML.xsl"?>
after the first line of the idXML file you want to inspect. This can be done using a standard text editor. Replace *PATH* with the path to the directory which contains the XSLT script IdXML.xsl. For example, if the directory is C:\scripts\ just exchange *PATH* with
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OpenMS / TOPP 1.1 |