MSDA, a proteomics software suite for in-depth Mass Spectrometry Data Analysis using grid computing

Authors

  • Christine Carapito,

    Corresponding author
    1. Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
    • Correspondence: Dr. Christine Carapito, Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, ECPM Bât.R5 Niv.0, 25 rue Becquerel, 67087 Strasbourg, France

      E-mail: ccarapito@unistra.fr

      Fax: +33368852781

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  • Alexandre Burel,

    1. Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
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  • Patrick Guterl,

    1. Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
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  • Alexandre Walter,

    1. Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
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  • Fabrice Varrier,

    1. Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
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  • Fabrice Bertile,

    1. Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
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  • Alain Van Dorsselaer

    1. Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
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Abstract

One of the major bottlenecks in the proteomics field today resides in the computational interpretation of the massive data generated by the latest generation of high-throughput MS instruments. MS/MS datasets are constantly increasing in size and complexity and it becomes challenging to comprehensively process such huge datasets and afterwards deduce most relevant biological information. The Mass Spectrometry Data Analysis (MSDA, https://msda.unistra.fr) online software suite provides a series of modules for in-depth MS/MS data analysis. It includes a custom databases generation toolbox, modules for filtering and extracting high-quality spectra, for running high-performance database and de novo searches, and for extracting modified peptides spectra and functional annotations. Additionally, MSDA enables running the most computationally intensive steps, namely database and de novo searches, on a computer grid thus providing a net time gain of up to 99% for data processing.

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