Parkinson’s disease (PD) is the second most abundant neurodegenerative disease (after Alzheimer’s disease) with a prevalence of about 1% for over 60-year-olds. The Parkinson’s Progression Markers Initiative (PPMI) is an observational clinical study for the monitoring of PD progression and identification of new biomarkers. It comprises about 1500 patients in the initial cohort and close to 5000 patients scheduled for an expansion of the study. Previous studies using smaller cohorts have shown that urinary proteome profiling is a promising strategy for the detection of novel biomarkers and patient stratification. We employed our automated high-throughput mass spectrometry (MS)-based proteomics pipeline to the PPMI cohort to identify novel biomarkers for PD.