Protocol Archive

Procedure for On-bead/in-solution digestion and phosphopeptide enrichment used in "Serine-129 phosphorylation of α-synuclein is a trigger for physiologic protein-protein interactions and synaptic function."

Procedure for Liquid Chromatography with Tandem Mass Spectrometry (LC-MS/MS) used in "Serine-129 phosphorylation of α-synuclein is a trigger for physiologic protein-protein interactions and synaptic function."

Procedure for proteome analysis used in "Serine-129 phosphorylation of α-synuclein is a trigger for physiologic protein-protein interactions and synaptic function."

Procedure for multi-electrode array used in "Serine-129 phosphorylation of α-synuclein is a trigger for physiologic protein-protein interactions and synaptic function."

Procedure for ColabFold protein structure prediction and membrane interaction modeling used in "Serine-129 phosphorylation of α-synuclein is a trigger for physiologic protein-protein interactions and synaptic function."

Procedure for multiple sequence alignment used in "Serine-129 phosphorylation of α-synuclein is a trigger for physiologic protein-protein interactions and synaptic function."

Blood pressure measurement in mice.

Quantification of p62-positive inclusions in the rodent brain.

Heart rate measurement in mice.

Polysomnography in mice.

Magnetic resonance imaging (MRI) of mouse brain.

Passive avoidance (step-down test) for mice.

Open field mice.

QuPath is an open-source digital pathology analysis software. Here, it is used to quantify various misfolded proteins across anatomical regions. This protocol is appropriate for both human and mouse tissue, and will outline the methods of tissue preparation, digitisation, segmentation, and importing images into QuPath.

Beam test for mice.

Novel object recognition test for mice.

Habituation and dishabituation (olfaction test) for mice.

The protocol is optimized to detect SOX10, a nuclear oligodendrocyte marker, and alpha-synuclein inclusions, which are frequently retained at the perinucleus in MSA (the so-called Papp-Lantos inclusions). This protocol also describes its use in affected PD and MSA brain regions such as the putamen, substantia nigra (SN), and cerebellum.

This protocol details quality control of libraries and should be performed after Section 2: NGS library preparation for sequencing.

This protocol details NGS library preparation for sequencing and should be performed after Section 1: Enzymatic DNA Fragmentation (Manually).