Updated project metadata. To identify molecular differences between closely related motor neurons relevant for understanding of neurodegenerative diseases, such as Amyotrophic Lateral Sclerosis (ALS), we exploited induced cranial and spinal motor neuron populations from mouse embryonic stem cells. We performed a large scale time-dependent TMT-based proteomics analysis in the presence and absence of protein misfolding stress. We profiled ~8,600 proteins from two different motor neuron cell lines, measured in two replicates and three time points.