Categories


Brain Proteins

Measures of brain proteins

See omics page to request data.

Subcategories

Presynaptic proteins (ELISA)

Measures of synaptic loss, pathology, and functionality are determined using ELISA tests performed at the Honer Lab at the University of British Columbia (Vancouver BC, Canada).

Click here for an overview of presynaptic protein variables

Complexin-I (inhibitory) Complexin-I protein density - Average of 6 regions (MAP only)
Complexin-II (excitatory) Complexin-II protein density - Average of 6 regions (MAP only)
SNAP-25 Synaptosomal-associated protein 25 (SNAP-25) density - Average of 6 regions (MAP only)
Synaptophysin Synaptophysin protein density - Average of 6 regions (MAP only)
Syntaxin-1 Synatxin-1 protein density - Average of 6 regions (MAP only)
VAMP Vesicle-associated membrane protein (VAMP) density - Average of 6 regions (MAP only)
Mean complexin density Mean complexin density - Average of 6 regions (MAP only)
Mean SNARE protein density Mean SNARE protein density - Average of 6 regions (MAP only)
Mean SNARE protein-protein interactions Mean SNARE protein-protein interactions - Average of 6 regions (MAP only)

SRM proteomics

Expression data
The abundance of endogenous peptides is quantified as a ratio to spiked-in synthetic peptides containing stable heavy isotopes and log2 transformed. During normalization, the “light/heavy” log2-ratios for each sample are shifted such that the median is set to zero.

Signal-to-noise assessment
After homogenization, small aliquots from each of the samples are pooled together and scattered throughout the study (8 samples per 96-well plate) to help capture variance that is due to sample preparation steps (except homogenization) and instrumental measurements. The standard deviation across controls indicates precision of the measurement. The signal-to-noise ratio is calculated as the ratio of variance across human subject samples vs. pooled controls. If the variance across the controls is equal to or higher than that across the human subject samples, the peptide is discarded from further consideration.

Handling redundancy
Proteins were measured with multiple peptides. Click here for further details.

Reference: Yu L, Petyuk VA, Gaiteri C, Mostafavi S, Young-Pearse T, Shah RC, Buchman AS, Schneider JA, Piehowski PD, Sontag RL, Fillmore TL, Shi T, Smith RD, De Jager PL, Bennett DA. Targeted brain proteomics uncover multiple pathways to Alzheimer’s dementia. Ann Neurol. 2018 Jul;84(1):78-88. PMID: 29908079; PMCID: PMC6119500.


TMT proteomics

Data are available for 160 ROS and MAP participants.

Tandem mass tags are chemical labels used in tandem mass spectrometry to identify and quantify proteins and other macromolecules.

This data set includes log2-transformed ratio for 160 proteins. See document for sample preparation, mass spectrometry, and normalization algorithm. See document for sample preparation, mass spectrometry, and normalization algorithm