title: HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.
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 .
authors.affiliation: EMBL Australia Biomedical Informatics Group, Infection & Immunity Theme, South Australian Health and Medical Research Institute , North Terrace, Adelaide, South Australia 5000, Australia.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Bryan
authors.affiliation: Medical Proteome Center Institute for Ophthalmic Research, Eberhard-Karls Universität Tübingen , Nägelestrasse 5, D-72074 Tübingen, Germany.
authors.forename: Mohamed-Ali
authors.initials: MA
authors.lastname: Jarboui
authors.affiliation: Systems Biology Ireland, University College Dublin , Belfield, Dublin 4, Ireland.
authors.forename: Cinzia
authors.initials: C
authors.lastname: Raso
authors.affiliation: EMBL Australia Biomedical Informatics Group, Infection & Immunity Theme, South Australian Health and Medical Research Institute , North Terrace, Adelaide, South Australia 5000, Australia.
authors.forename: Manuel
authors.initials: M
authors.lastname: Bernal-Llinares
authors.affiliation: Systems Biology Ireland, University College Dublin , Belfield, Dublin 4, Ireland.
authors.forename: Brendan
authors.initials: B
authors.lastname: McCann
authors.affiliation: Systems Biology Ireland, University College Dublin , Belfield, Dublin 4, Ireland.
authors.forename: Jens
authors.initials: J
authors.lastname: Rauch
authors.affiliation: Medical Proteome Center Institute for Ophthalmic Research, Eberhard-Karls Universität Tübingen , Nägelestrasse 5, D-72074 Tübingen, Germany.
authors.forename: Karsten
authors.initials: K
authors.lastname: Boldt
authors.affiliation: EMBL Australia Biomedical Informatics Group, Infection & Immunity Theme, South Australian Health and Medical Research Institute , North Terrace, Adelaide, South Australia 5000, Australia.|School of Medicine, Flinders University , Bedford Park, South Australia 5042, Australia.
authors.forename: David J
authors.initials: DJ
authors.lastname: Lynn
mesh_terms: D000818:Animals; D019295:Computational Biology; D003627:Data Interpretation, Statistical; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D025941:Protein Interaction Mapping; D011494:Protein Kinases; D017346:Protein Serine-Threonine Kinases; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D012984:Software; D057188:Workflow
chemical_list: D020543:Proteome; D011494:Protein Kinases; C097199:KSR-1 protein kinase; C557409:KSR2 protein, human; D017346:Protein Serine-Threonine Kinases
keywords: bioinformatics; data analysis; high-dimensional data; mass spectrometry; network analysis; protein quantification; proteomics; software; visualization