compomics-utilities

• What is compomics-utilities?
• Projects Using compomics-utilities
• Using compomics-utilities
• Download
• Maven Dependency

• Screenshots

• Bioinformatics for Proteomics Tutorial

compomics-utilities publication:

• Barsnes et al: BMC Bioinformatics. 2011 Mar 8;12(1):70.
• If you use compomics-utilities as part of a paper, please include the reference above.

What is compomics-utilities?

The Computational Omics and Systems Biology Group develops various bioinformatics tools for analyzing omics data.

compomics-utilities is a library containing code shared by many of our research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc. We believe that this library can be of use to other research groups doing computational proteomics, and have therefore made it available as open source.

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Projects using compomics-utilities

| Project | Description | Publication | |:------------|:----------------|:----------------| | PeptideShaker | interpretation of proteomics identification results|Vaudel et al: Nature Biotechnol. 2015 Jan;33(1):22–24.| | MetaProteomeAnalyzer | analyzing meta-proteomics data|Muth et al: J Proteome Res. 2015 (in press).| | DeNovoGUI | de novo sequencing of tandem mass spectra|Muth at al: J Proteome Res. 2014 Feb 7;13(2):1143-6.| | pride-asap | uniform annotation of identified spectra stored in PRIDE|Hulstaert et al: J Proteomics. 2013 Apr 17| | ProteoCloud | proteomics cloud computing pipeline|Muth et al: J Proteomics. 2013 Aug 2;88:104-8| | thermo-msf-parser | parser and viewer for thermo msf files|Colaert et al: J Proteome Res. 2011;10(8):3840-3| | SearchGUI | graphical user interface for proteomics identification search engines|Barsnes et al: J Proteome Res. 2018 (in press) Vaudel et al: Proteomics 2011;11(5):996-9| | XTandem Parser |java parser for X!Tandem output xml files|Muth et al: Proteomics 2010;10(7):1522-4| | jmzML |java implementation of the PSI-MS mzML specification|Côté et al: Proteomics 2010;10(7):1332-5| | Fragmentation Analyzer | analyzing MS/MS fragmentation data|Barsnes et al: Proteomics 2010;10(5):1087-90| | ms_lims | mass spectrometry based proteomics information management system|Helsens et al: Proteomics 2010;10(6):1261-4| | Rover | visualize and validate quantitative proteomics data|Colaert et al: Proteomics 2010;10(6):1226-9| | IceLogo | next-generation visualization of protein consensus sequences|Colaert et al: Nature Methods 2009;6(11):786-7| | OMSSA Parser | java parser for OMSSA omx files|Barsnes et al: Proteomics 2009;9(14):3772-4| | Peptizer | automating manual validation of MS/MS search results|Helsens et al: MCP 2008;7(12):2363-72| | MascotDatfile | java API for MS/MS search results by Mascot|Helsens et al: Proteomics 2007;7(3):364-6| | DBToolkit | manipulating fasta sequence databases|Martens et al: Bioinformatics 2005;21(17):3584-5| | MetaNovo | a probabilistic approach to peptide and polymorphism discovery in complex mass spectrometry datasets|Potgieter et al: BioRxiv 2019;605550|

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Using compomics-utilities

For example code and demos showing how the compomics-utilities library can be used in your project see Examples. Also check the JavaDoc.

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Download

We strongly recommend Maven when using compomics-utilities, as this makes sure that one gets all the dependencies right. See Maven Dependency below.

All compomics-utilities builds are available here.

See also the JavaDoc.

If you for some reason cannot use Maven and need a complete build of compomics-utilities, please let us know and we will send you the latest build as a zip file.

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Maven Dependency

compomics-utilities is available for use in Maven projects:

<dependency> <groupId>com.compomics</groupId> <artifactId>utilities</artifactId> <version>X.Y.Z</version> </dependency>

```

<!-- 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>

```

Update the version number to latest released version, see the Maven repository.

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Screenshots

(Click on figure to see the full size version)

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