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Variants at the GBA locus, encoding glucocerebrosidase, are the strongest common genetic risk factor for Parkinson's disease (PD). To understand GBA -related disease mechanisms, we use a multi-part-enrichment proteomics and post-translational modification (PTM) workflow, identifying large numbers of dysregulated proteins and PTMs in heterozygous GBA - N370S PD patient induced pluripotent stem cell (iPSC) dopamine neurons. Alterations in glycosylation status show disturbances in the autophagy-lysosomal pathway, which concur with upstream perturbations in mammalian target of rapamycin (mTOR) activation in GBA -PD neurons. Several native and modified proteins encoded by PD-associated genes are dysregulated in GBA -PD neurons. Integrated pathway analysis reveals impaired neuritogenesis in GBA -PD neurons and identify tau as a key pathway mediator. Functional assays confirm neurite outgrowth deficits and identify impaired mitochondrial movement in GBA -PD neurons. Furthermore, pharmacological rescue of glucocerebrosidase activity in GBA -PD neurons improves the neurite outgrowth deficit. Overall, this study demonstrates the potential of PTMomics to elucidate neurodegeneration-associated pathways and potential drug targets in complex disease models. [Display omitted] • Proteomic/PTMomic analysis of GBA patient iPSC neurons identify disease phenotypes • PTM changes are highly abundant on lysosomal proteins and PD GWAS-related proteins • mTOR activation and mitochondrial movement perturbations are identified • GBA patient neurons show neuritogenesis defects that are rescued by a GCase chaperone Bogetofte et al. apply a post-translational proteomics pipeline to iPSC-dopaminergic neurons from patients with Parkinson's with a GBA-N370S mutation. This workflow simultaneously quantifies changes in protein phosphorylation, sialylation, and cysteine modifications, identifying affected pathways and phenotypes including impaired neurite outgrowth in GBA-N370S patient dopaminergic neurons that can be rescued by a GBA chaperone. [ABSTRACT FROM AUTHOR]