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MS Data Miner: A web-based software tool to analyze, compare, and share mass spectrometry protein identifications

Authors

  • Thomas F. Dyrlund,

    1. Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology, Aarhus University, Denmark
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  • Ebbe T. Poulsen,

    1. Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology, Aarhus University, Denmark
    2. Center for Insoluble Protein Structures (inSPIN), Aarhus University, Denmark
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  • Carsten Scavenius,

    1. Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology, Aarhus University, Denmark
    2. Center for Insoluble Protein Structures (inSPIN), Aarhus University, Denmark
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  • Kristian W. Sanggaard,

    1. Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology, Aarhus University, Denmark
    2. Center for Insoluble Protein Structures (inSPIN), Aarhus University, Denmark
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  • Jan J. Enghild

    Corresponding author
    1. Center for Insoluble Protein Structures (inSPIN), Aarhus University, Denmark
    • Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology, Aarhus University, Denmark
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Correspondence: Professor Jan J. Enghild, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C., Denmark

E-mail: jje@mb.au.dk

Fax: +45-89425063

Abstract

Data processing and analysis of proteomics data are challenging and time consuming. In this paper, we present MS Data Miner (MDM) (http://sourceforge.net/p/msdataminer), a freely available web-based software solution aimed at minimizing the time required for the analysis, validation, data comparison, and presentation of data files generated in MS software, including Mascot (Matrix Science), Mascot Distiller (Matrix Science), and ProteinPilot (AB Sciex). The program was developed to significantly decrease the time required to process large proteomic data sets for publication. This open sourced system includes a spectra validation system and an automatic screenshot generation tool for Mascot-assigned spectra. In addition, a Gene Ontology term analysis function and a tool for generating comparative Excel data reports are included. We illustrate the benefits of MDM during a proteomics study comprised of more than 200 LC-MS/MS analyses recorded on an AB Sciex TripleTOF 5600, identifying more than 3000 unique proteins and 3.5 million peptides.

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