HiQuant: Rapid postquantification analysis of large-scale MS-generated proteomics data

Kenneth Bryan, Mohamed-Ali Jarboui, Raso Cinzia, Manuel Bernal-Llinares, Bredan McCann, Jens Rauch, Karsten Bodlt, David Lynn

    Research output: Contribution to journalArticlepeer-review

    4 Citations (Scopus)

    Abstract

    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.

    Original languageEnglish
    Pages (from-to)2072-2079
    Number of pages8
    JournalJournal of Proteome Research
    Volume15
    Issue number6
    Early online date2016
    DOIs
    Publication statusPublished - 3 Jun 2016

    Keywords

    • bioinformatics
    • data analysis
    • high-dimensional data
    • mass spectrometry
    • network analysis
    • protein quantification
    • proteomics
    • software
    • visualization

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