Table 3 Comparison of the two approaches to collect and analyze samples obtained during DBS surgical procedure

Sample collection protocol

The brain tissue attached to the guide tube and microelectrode during standard DBS implantation procedure was used for sample preparation

A blunt stylet was inserted through the guide tube into the brain tissue during DBS implantation procedure for one minute to obtain material for analyses

Sample usage

Both RNA-seq and LC–MS analyses can be carried out from the same individual patients and their separate brain hemispheres (if patient is awake during the procedure)

Tissue sample was used either for RNA microarray analysis or pooled for Nano-LC–MS/MS. Samples were also alternatively used for immunocytochemistry or scanning electron microscopy

Transcriptomics

The tissue material was collected from the recording microelectrode targeted to the specific well-defined area in the deep brain region and was prepared for RNA-seq

RNA microarray for the tissue sample attached to the blunt stylet was carried out after application of double amplification protocol

Proteomics

No pooling of samples. Hemisphere-specific LC–MS data were obtained from the tissue collected from the guide tube

Six samples from different patients and brain hemispheres were pooled for in-gel fractionation and subsequent MS analysis