CFCComplex fold change CV Coefficient of variation FARMS Factor Analysis for Robust Microarray Summarization FC Fold change FDR False discovery rate GO Gene ontology KEGG Kyoto Encyclopedia of Genes and Genomes LFQ Label-free quantitation LTQ Linear trap quadrupole ODR Orthogonal distance regression PCA Principal component analysis PPI Protein-protein interactionAbstract (300 words) We have developed ComplexBrowser, an open source, online platform for supervised analysis of quantitative proteomics data that focuses on protein complexes. The software uses information from CORUM and Complex Portal databases to identify protein complex components. Based on the expression changes of individual complex subunits across the proteomics experiment it calculates Complex Fold Change (CFC) factor that characterises the overall protein complex expression trend and the level of subunit co-regulation. Thus up-and down-regulated complexes can be identified. It provides interactive visualisation of protein complexes composition and expression for exploratory analysis. It also incorporates a quality control step that includes normalisation and statistical analysis based on Limma test. ComplexBrowser performance was tested on two previously published proteomics studies identifying changes in protein expression in human adenocarcinoma tissue and during activation of mouse T-cells. The analysis revealed 1519 and 332 protein complexes, of which 233 and 41 were found co-ordinately regulated in the respective studies. The adopted approach provided evidence for a shift to glucose-based metabolism and high proliferation in adenocarcinoma tissues and identification of chromatin remodelling complexes involved in mouse T-cell activation.The results correlate with the original interpretation of the experiments and also provide novel biological details about protein complexes affected. ComplexBrowser is, to our knowledge, the first tool to automate quantitative protein complex analysis for highthroughput studies, providing insights into protein complex regulation within minutes of analysis.A fully functional demo version of ComplexBrowser v1.0 is available online via
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