Automated semiquantitative analysis of protein macroarrays

Protein arrays are systematically arranged, large collections of annotated proteins on planar surfaces commonly used for the characterisation of protein binding events against a wide range of possible probes. These may include analyses of protein-protein, peptide-protein, enzyme-substrate or antibody-antigen interactions from simple reagents to complex mixtures. Absence of appropriate image analysis and data processing software may bestow a substantial hurdle limiting the uptake of protein arrays in research. We developed a first, automated semiquantitative open source software package for the analysis of widely used protein macroarrays. The software allows accurate single array and inter-array comparative studies through the tackling of intra-array inconsistencies arising from experimental disparities. The innovative and automated image analysis process includes adaptive positioning, background identification and subtraction, removal of null signals, robust statistical analysis, and protein pair validation. The normalized values allow a convenient semiquantitative data analysis of different samples or timepoints, enabling accurate characterisation of sample series to identify relative changes for instance in clinical samples in response to diseases and treatment.