Motor neurone disease (MND) is a fatal neurodegenerative disease resulting in the progressive loss of motor neurons in the brain and spine. More than 95% of cases are pathologically characterized by the cytoplasmic accumulation of hyperphosphorylated and ubiquitinated transactive response DNA-binding protein 43 (TDP-43). Multiple mouse models showing TDP-43 accumulation have been developed, however, whether they recapitulate molecular features of MND pathology is unclear. Given the lack of curative treatment for MND, there is an urgent need to identify the precise biological processes contributing to disease pathogenesis for the development of effective therapeutic treatments. To explore the complexity of MND, we employed label-based untargeted proteomics to quantify 7,946 proteins from the spinal cord and brain of TDP-43Q331K mice, a transgenic mouse model of MND. These findings were compared to the human sporadic MND proteome from the motor cortex, as well as the cervical, thoracic, and lumbar spinal cord regions. These data were analyzed for differentially expressed proteins (DEPs) and their associated biological processes. To identify mouse models that show higher concordance with our human dataset, we performed a meta-analysis of previously published proteomics datasets. In mice, we demonstrate unique and overlapping features in the brain and spinal cord, with a total of 76 DEPs identified in WT littermates versus TDP-43Q331K mice. These protein signatures were associated with a wide range of cellular processes including metabolism, mitochondrial function, muscle contraction, synaptic and neurotransmitter signaling. In humans, we observed highly overlapping responses across the four tissues examined, primarily related to the upregulation of immune processes and the downregulation of mitochondrial function. In contrast, in TDP-43Q331K mice we demonstrate a lack of enrichment for immune activation and the opposite regulation of mitochondrial processes. An examination of previously published mouse datasets identified the Ubqln2 knock-out mouse model as showing stronger parallels with our late-stage human MND. Overall, this study provides in-depth analysis of the site-specific dysregulated proteomes and their associated functional processes across species. Thereby, identifying potential therapeutic targets while emphasizing the limitations of specific mouse models in recapitulating certain MND-related processes for future model development.