Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline

Motivation: The quest for high-throughput proteomics has revealeda number of challenges in recent years. Whilst substantial improvementsin automated protein separation with liquid chromatography andmass spectrometry (LC/MS), aka ‘shotgun’ proteomics,have been achieved, large-scale open initiatives such as theHuman Proteome Organization (HUPO) Brain Proteome Project haveshown that maximal proteome coverage is only possible when LC/MSis complemented by 2D gel electrophoresis (2-DE) studies. Moreover,both separation methods require automated alignment and differentialanalysis to relieve the bioinformatics bottleneck and so makehigh-throughput protein biomarker discovery a reality. The purposeof this article is to describe a fully automatic image alignmentframework for the integration of 2-DE into a high-throughputdifferential expression proteomics pipeline. Results: The proposed method is based on robust automated imagenormalization (RAIN) to circumvent the drawbacks of traditionalapproaches. These use symbolic representation at the very earlystages of the analysis, which introduces persistent errors dueto inaccuracies in modelling and alignment. In RAIN, a third-ordervolume-invariant B-spline model is incorporated into a multi-resolutionschema to correct for geometric and expression inhomogeneityat multiple scales. The normalized images can then be compareddirectly in the image domain for quantitative differential analysis.Through evaluation against an existing state-of-the-art methodon real and synthetically warped 2D gels, the proposed analysisframework demonstrates substantial improvements in matchingaccuracy and differential sensitivity. High-throughput analysisis established through an accelerated GPGPU (general purposecomputation on graphics cards) implementation. Availability: Supplementary material, software and images usedin the validation are available at http://www.proteomegrid.org/rain/ Contact: g.z.yang{at}imperial.ac.uk Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: David Rocke