The aim of our study was to investigate cerebrospinal fluid (CSF) tryptic
peptide profiles as potential diagnostic
biomarkers for the discrimination of
parkinsonian disorders. CSF samples were collected from individuals with
parkinsonism, who had an uncertain diagnosis at the time of inclusion and who were followed for up to 12 years in a longitudinal study. We performed shotgun proteomics to identify tryptic
peptides in CSF of
Parkinson's disease (PD, n = 10),
multiple system atrophy patients (MSA, n = 5) and non-neurological controls (n = 10). We validated tryptic
peptides with differential levels between PD and MSA using a newly developed selected reaction monitoring (SRM) assay in CSF of PD (n = 46), atypical
parkinsonism patients (AP; MSA, n = 17;
Progressive supranuclear palsy; n = 8) and non-neurological controls (n = 39). We identified 191 tryptic
peptides that differed significantly between PD and MSA, of which 34 met our criteria for SRM development. For 14/34
peptides we confirmed differences between PD and AP. These tryptic
peptides discriminated PD from AP with moderate-to-high accuracy. Random forest modelling including tryptic
peptides plus either clinical assessments or other CSF parameters (neurofilament light chain, phosphorylated
tau protein) and age improved the discrimination of PD vs. AP. Our results show that the discovery of tryptic
peptides by untargeted and subsequent validation by targeted proteomics is a suitable strategy to identify potential CSF
biomarkers for PD versus AP. Furthermore, the tryptic
peptides, and corresponding
proteins, that we identified as differential
biomarkers may increase our current knowledge about the disease-specific pathophysiological mechanisms of
parkinsonism.