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Using the Object-Oriented PowerShell for Simple Proteomics Data Analysis

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Mass Spectrometry Data Analysis in Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2051))

Abstract

Scripting languages such as Python and Bash are appreciated for solving simple, everyday tasks in bioinformatics. A more recent, object-oriented command shell and scripting language, PowerShell, has many attractive features: an object-oriented interactive command line, fluent navigation and manipulation of XML files, ability to explore and consume Web services from the command line, consistent syntax and grammar, rich regular expressions, and advanced output formatting. The key difference between classical command shells and scripting languages, such as bash, and object-oriented ones, such as PowerShell, is that in the latter the result of a command is a structured object with inherited properties and methods rather than a simple stream of characters. Conveniently, PowerShell is included in all new releases of Microsoft Windows and is available for Linux and macOS, making any data processing script portable. In this chapter we demonstrate how PowerShell in particular allows easy interaction with mass spectrometry data in XML formats, connection to Web services for tools such as BLAST, and presentation of results as formatted text or graphics. These features make PowerShell much more than “yet another scripting language.”

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Author information

Authors and Affiliations

  1. Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands

    Yassene Mohammed & Magnus Palmblad

  2. University of Victoria–Genome British Columbia Proteomics Centre, Victoria, BC, Canada

    Yassene Mohammed

Authors
  1. Yassene Mohammed
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  2. Magnus Palmblad
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Corresponding author

Correspondence to Yassene Mohammed .

Editor information

Editors and Affiliations

  1. Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal

    Rune Matthiesen

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Mohammed, Y., Palmblad, M. (2020). Using the Object-Oriented PowerShell for Simple Proteomics Data Analysis. In: Matthiesen, R. (eds) Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology, vol 2051. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9744-2_17

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  • DOI: https://doi.org/10.1007/978-1-4939-9744-2_17

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9743-5

  • Online ISBN: 978-1-4939-9744-2

  • eBook Packages: Springer Protocols

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