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README.md

XTandem Parser

XTandem Parser Publications:

SearchGUI and PeptideShaker:

  • To run X!Tandem searches we recommend the use of SearchGUI.
  • To visualize and analyze X!Tandem results we recommend the use of PeptideShaker.

download v1.13.0 - All platforms ReleaseNotes

Introduction

XTandem Parser is a Java project for extracting information from X!Tandem output xml files. X!Tandem software can match tandem mass spectra with peptide sequences and works as a search engine for protein identification.

The output xml format can be found here (PDF).

And the input xml format is explained here here.

If you need an example file to play with, one is provided as a zip file in the downloads section on the right.

The parser is developed by Thilo Muth under the guidance of Marc Vaudel, Prof. Dr. Albert Sickmann and Prof. Dr. Lennart Martens. Great help came from Harald Barsnes who was involved in the development of OMSSA Parser. Thanks to Steffi Wortelkamp for persistent testing.

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Libraries

The following libraries were used for the general user interface (spectrum viewer):

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Maven Dependency

XTandem Parser is available for use in Maven projects:

<dependencies>
    <dependency>
        <groupId>de.proteinms.xtandemparser</groupId>
        <artifactId>xtandem-parser</artifactId>
        <version>X.Y.Z</version>
    </dependency>
</dependencies>
<repositories>

    <!-- Compomics Genesis Maven 2 repository -->
    <repository>
        <id>genesis-maven2-repository</id>
        <name>Genesis maven2 repository</name>
        <url>http://genesis.UGent.be/maven2</url>
        <layout>default</layout>
    </repository>

    <!-- old EBI repository -->
    <repository>
        <id>ebi-repo</id> 
        <name>The EBI internal repository</name>
        <url>http://www.ebi.ac.uk/~maven/m2repo</url>
    </repository>

    <!-- EBI repository -->
    <repository>
        <id>pst-release</id>
        <name>EBI Nexus Repository</name>
        <url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
    </repository>
     
</repositories>

Update the version number to latest released version.

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Result Analysis

To visualize and analyze X!Tandem results we recommend the use of PeptideShaker. PeptideShaker is a search engine independent platform for visualization of peptide and protein identification results from multiple search engines.

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Screenshots

(Click on the screenshot to see the full size version)

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