Brain Proteins

Measures of brain proteins


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
In most cases, the correlation was significant, and the peptide with the best signal-to-noise ratio was selected. However, some proteins were measured with multiple peptides. APP was measured with 4 peptides: 2 targeted at the core APP sequence, bA, and bA38. MAPT or tau was measured with 2 peptides targeted at tau_AT8 and tau_AT8_s202. Further details can be found in the data dictionary.

The dataset includes the following proteins:

AK4 Adenylate kinase 4
ANKRD40 Ankyrin repeat domain 40
AP2A2 Adaptor-related protein complex 2 alpha 2 subunit
APOE Apolipoprotein E
APP* Amyloid beta precursor protein
bA* Beta Amyloid (APP)
bA38* Beta Amyloid (APP)
BCL2L1 Bcl-2-like protein 1
BIN1 Bridging integrator 1
C1QA Complement C1q subcomponent subunit A
CD2AP CD2-associated protein
CD44 CD44 gene
CD47 CD47 gene
CPLX2 Complexin-2
DOCK2 Dedicator of cytokinesis 2
FBXO2 F-box protein 2
FCER1G Fc fragment of IgE receptor Ig
FYN Proto-oncogene, Src family tyrosine kinase
GSTP1 Glutathione S-transferase pi 1
HSPB2 Heat shock protein beta-2
IGFBP5 Insulin-like growth factor-binding protein 5
ITPK1 Inositol-tetrakisphosphate 1-kinase
KIF5B Kinesin family member 5B
MEF2C Myocyte enhancer factor 2C
PADI2 Peptidyl arginine deiminase 2
PICALM Phosphatidylinositol-binding clathrin assembly protein
PLXNB1 Plexin B1
PVALB Parvalbumin
SASH1 SAM and SH3 domain-containing protein 1
SLC6A12 Solute carrier family 6 member 12
SNAP25 Synaptosomal-associated protein 25
SNAP29 Synaptosomal-associated protein 29
SNAP47 Synaptosomal-assocaited protein 47
SNCA Alpha-synuclein
STX4 Syntaxin-4
STX5 Syntaxin-5
STX7 Syntaxin-7
STX12 Syntaxin-12
STX16 Syntaxin-16
STX18 Syntaxin-18
STX1A Syntaxin-1A
STX1B Syntaxin-1B
STXBP1 Syntaxin-binding protein 1
STXBP3 Syntaxin-binding protein 3
STXBP5 Syntaxin-binding protein 5
STXBP6 Syntaxin-binding protein 6
SV2B Synaptic vesicle glycoprotein 2B
SYN1 Synapsin I
SYN2 Synapsin II
SYN3 Synapsin III
SYT1 Synaptotagmin-1
SYT2 Synaptotagmin-2
SYT7 Synaptotagmin-7
SYT11 Synaptotagmin-11
SYT12 Synaptotagmin-12
TARDBP TAR DNA-binding protein
tau_AT8* Microtubule associated protein tau (MAPT) or tau
tau_AT8_s202* Microtubule associated protein tau (MAPT) or tau
TRIM28 Tripartite motif containing 28
UNC5C Unc-5 netrin receptor C
VAMP1 Vesicle-associated membrane protein 1
VAMP5 Vesicle-associated membrane protein 5
VAPB Vesicle-associated membrane protein B and C
VAT1 Vesicle amine transport 1
VGF VGF nerve growth factor inducible
VPS35 Retromer complex component
VSNL1 Visinin-like protein 1

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 dataset 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