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

Title: HiQuant: Rapid postquantification analysis of large-scale MS-generated proteomics data
Authors: Bryan, Kenneth
Jarbou, Mohamed-Ali
Raso, Cinzia
McCann, Brendan
Rauch, Jens
et al.
Permanent link: http://hdl.handle.net/10197/9763
Date: 18-Apr-2016
Online since: 2019-04-02T08:03:44Z
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.
Funding Details: European Commission - Seventh Framework Programme (FP7)
Science Foundation Ireland
Type of material: Journal Article
Publisher: American Chemical Society
Journal: Journal of Proteome Research
Volume: 15
Issue: 6
Start page: 2072
End page: 2079
Copyright (published version): 2016 American Chemical Society
Keywords: BioinformaticsData analysisHigh-dimensional dataMass spectrometryNetwork analysisProtein quantificationProteomicsSoftwareVisualization
DOI: 10.1021/acs.jproteome.5b01008
Language: en
Status of Item: Peer reviewed
Appears in Collections:SBI Research Collection

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