The Mixed Lineage Leukaemia (MLL) gene located on chromosome 11q23 is a frequent site of translocation that results in a number of oncogenic fusion proteins. MLL-translocations are present in a variety of paediatric and adult leukaemias and are associated with poor survival outcome. Despite intense research efforts the mechanisms underlying the leukaemogenic activity of MLL-translocations are poorly understood. Our aim was to identify proteins involved in leukaemogenesis that are regulated by MLL fusion protein expression through quantitative proteome analysis using a murine leukaemia model. Our model of acute myeloid leukaemia (AML) involves the generation of leukaemic cells in vivo and is controlled by the regulated expression of a common MLL-translocation gene, MLL-AF9. Leukaemic cells were collected from mice before analysis of global protein expression using a SILAC quantitative proteomics workflow to generate a profile of proteins that are expressed in the presence or absence of MLL-AF9 expression. We extended this analysis by also profiling changes to the transcriptome using RNA-sequencing during MLL-AF9 regulation. These data underwent bioinformatic analysis to quantify and compare changes in protein and RNA expression before further comparison to human AML patient expression array and survival data to identify proteins and pathways of diagnostic and therapeutic interest. Our analysis has confirmed several known targets in AML and also highlighted novel pathways and targets that are regulated when MLL-AF9 is expressed. These pathways include epigenetic regulators, cell signaling and cell-cell or cell-extracellular matrix interactions. The results from this study not only identify mechanisms by which MLL-AF9 regulates leukaemogenesis, but also demonstrate the potential identification of clinical biomarkers and novel drug targets.