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

Show full item record

SCOPUSTM   
Citations 50

2
Last Week
0
Last month
checked on May 24, 2019

Google ScholarTM

Check

Altmetric


This item is available under the Attribution-NonCommercial-NoDerivs 3.0 Ireland. No item may be reproduced for commercial purposes. For other possible restrictions on use please refer to the publisher's URL where this is made available, or to notes contained in the item itself. Other terms may apply.