Introduction

Recent advances in mass-spectrometry-based proteomics are now facilitating ambitious large-scale investigations of the spatial and temporal dynamics of the proteome; however, the increasing size and complexity of these data sets is overwhelming current downstream computational methods, specifically those that support the postquantification analysis pipeline. Here we present HiQuant, a novel application that enables the design and execution of a postquantification workflow, including common data-processing steps, such as assay normalization and grouping, and experimental replicate quality control and statistical analysis. HiQuant also enables the interpretation of results generated from large-scale data sets by supporting interactive heatmap analysis and also the direct export to Cytoscape and Gephi, two leading network analysis platforms. HiQuant may be run via a user-friendly graphical interface and also supports complete one-touch automation via a command-line mode. We evaluate HiQuant's performance by analyzing a large-scale, complex interactome mapping data set and demonstrate a 200-fold improvement in the execution time over current methods. We also demonstrate HiQuant's general utility by analyzing proteome-wide quantification data generated from both a large-scale public tyrosine kinase siRNA knock-down study and an in-house investigation into the temporal dynamics of the KSR1 and KSR2 interactomes. Download HiQuant, sample data sets, and supporting documentation at http://hiquant.primesdb.eu .

Publications

  1. HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.
    Cite this
    Bryan K, Jarboui MA, Raso C, Bernal-Llinares M, McCann B, Rauch J, Boldt K, Lynn DJ, 2016-06-01 - Journal of proteome research

Credits

  1. Kenneth Bryan
    Developer

    EMBL Australia Biomedical Informatics Group, Infection & Immunity Theme, Australia

  2. Mohamed-Ali Jarboui
    Developer

    Medical Proteome Center Institute for Ophthalmic Research, Eberhard-Karls Universität Tübingen, Germany

  3. Cinzia Raso
    Developer

    Systems Biology Ireland, University College Dublin, Ireland

  4. Manuel Bernal-Llinares
    Developer

    EMBL Australia Biomedical Informatics Group, Infection & Immunity Theme, Australia

  5. Brendan McCann
    Developer

    Systems Biology Ireland, University College Dublin, Ireland

  6. Jens Rauch
    Developer

    Systems Biology Ireland, University College Dublin, Ireland

  7. Karsten Boldt
    Developer

    Medical Proteome Center Institute for Ophthalmic Research, Eberhard-Karls Universität Tübingen, Germany

  8. David J Lynn
    Investigator

    School of Medicine, Flinders University, Australia

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Summary
AccessionBT006832
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionAustralia
Submitted ByDavid J Lynn