TAR DNA binding protein 43 (TDP-43) accumulates in the cytoplasm of neurons in most people with the neurodegenerative diseases amyotrophic lateral sclerosis (ALS)/motor neuron disease (MND) and frontotemporal dementia (FTD). However, the drivers of TDP-43 dysfunction and the biological factors and pathways that modify these processes remain unclear. We therefore sought to determine the time course of global change in abundance of proteins across the disease course of TDP-43 proteinopathy, and to compare these changes to transcriptional and proteomic alterations in autopsy-derived tissues from people with ALS and/or FTD. We studied the rNLS8 (NEFH-tTA/tetO-TDP-43ΔNLS) mouse model using quantitative tandem mass tag mass spectrometry of cortex samples collected prior to motor phenotype onset and throughout disease progression. Weighted correlation network and cell type enrichment analyses identified subsets of proteins with correlated changes in abundance across the disease course, highlighting proteins particularly increased in the earliest stages of disease. Several distinct protein groups were characterized by differential longitudinal abundance changes, representing diverse biological pathways such as protein folding (neuronal), myelination (oligodendrocytic), and synaptic function. Notably, rNLS8 mice showed a transient protein-folding response, including post-transcriptional increase in abundance of chaperones, including the heat shock protein 40 family member DNAJB5, in neurons in the earliest stages of disease. Interestingly, over-expression of DNAJB5 increased TDP-43 solubility and decreased inclusion formation in cell and neuron culture models. Likewise, Dnajb5-/- mice developed exacerbated motor impairments upon adeno-associated virus-mediated neuronal cytoplasmic TDP-43 expression. Further, the late-disease proteomic signatures of rNLS8 mice correlated closely with those of human TDP-43 proteinopathy autopsy-derived samples, suggesting commonality of disease signatures in rNLS8 mice and human disease. We also developed an easy-to-use online webtool, TDP-map (https://shiny.rcc.uq.edu.au/TDP-map/), to allow users to search and visualise changes in any proteins of interest within these datasets to help guide future studies. Together, this work reveals involvement of distinct and overlapping biochemical pathways in formation of TDP-43 pathology and associated neurotoxicity, which may guide development of targeted therapeutics for intractable neurodegenerative diseases.