Synaptic marker product focus

Synapses are highly important components of neural transmission in the brain, and much neuroscience research focuses on understanding the function of these specialized structures.

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Introduction to synapses

Synapses, the primary regulators of neuronal communication, and their plasticity defines learning and memory. Synapses commonly form between axons and dendrites, and consist of a pre-synaptic neuron, synaptic cleft, and dendrites. Each neuron can have between 1 to 100,000  synaptic connections.

Synaptic dysfunction in neurodegenerative diseases

In many central nervous system disorders, synaptic dysfunction is often the cause or consequence of many pathologies. Neuropsychiatric disorders such as schizophrenia, bipolar disorders and autism spectrum disorders have a developmental origin of synapse dysfunction. On the flip side, synaptic dysfunction can be the end point in various neurodegenerative diseases and plays a critical role in the pathophysiology of Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis (ALS). Synaptic dysfunction can lead to cognitive decline, motor deficits, and other neurological symptoms characteristic of these conditions.

Identifying synapses

 Synapses can be identified using electron microscopy to visualize the membrane and vesicles. This, however, is highly laborious, time consuming and expensive, with not every lab having access to this technology. A popular, more accessible alternative is to use antibodies to label and identify synapses. 

Being able to multiplex antibodies for immunofluorescence staining is highly important for co-localization studies. Proteintech’s FlexAble Antibody Labeling Kits enable easy multiplexing for primary antibodies. These kits allow you to multiplex same species antibodies by labeling as little as 0.5 μg of antibody with a high-affinity flex linker that works for any primary antibody, in any buffer condition. 

Proteintech has a wide range of top-cited synaptic marker antibodies that are all made in-house with expert validation.

Pre- synaptic marker antibodies

GAP43

Neuronal growth-associated protein (GAP43). GAP43 is one of the main substrates for protein kinase C in the brain. Contributes to neurotransmitter release, endocytosis, and synaptic vesicle recycling.

Immunofluorescence staining of (4% PFA) fixed mouse brain tissue using GAP43 antibody (16971-1-AP).

Neurexin 1

Synaptic cell-adhesion molecules that connect pre- synaptic neurons at synapses.

SNAP-25 

Highly popular pre-synaptic marker. Helps mediate exocytotic release at the synapse. Contributes to the SNARE complex with syntaxin and synaptobrevin.

Synapsin 1 / Synapsin 2

Phophso-proteins that reversibly tether vesicles to the actin cytoskeleton ready for release.

WB analysis of mouse brain using SYN1-Specific Antibody (20258-1-AP).

Synaptophysin

Integral membrane glycoprotein that regulates synaptic vesicle endocytosis and is the most abundant synaptic vesicle protein by mass.

Immunohistochemical analysis of paraffin-embedded rat cerebellum tissue slide using IHCeasy Synaptophysin Ready-to-Use IHC Kit (KHC0059).

Synaptotagmin-1 / Synaptotagmin-3 

Synaptotagmins are integral membrane proteins of synaptic vesicles thought to serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis.

HCT 116 (WT and SYT1 KO) lysates prepared with RIPA buffer, 50 μg protein loaded. 14511-1-AP  incubated at 1:500 at 4°C overnight in 5% BSA in TBST. Ponceau stained transfers shown on right. Data provided by YCharOS, an open science company with a mission to validate commercial antibodies to improve scientific reproducibility and transparency.

Syntaxin-1

Acts in concert with Synaptobrevin and SNAP-23 to fuse vesicles with the cell membrane.

VAMP2

VAMP2 (synonym: Synaptobrevin 2), is a member of the SNARE family of proteins.

VGAT

Vesicular GABA transporter.

Immunofluorescence staining of (4% PFA) fixed rat brain tissue using VGAT antibody (14471-1-AP) at dilution of 1:200 and CoraLite®488-Conjugated AffiniPure Goat Anti-Rabbit IgG(H+L).

VGLUT2

Glutamate transporter

VMAT

Monoamine transporter

Primary neurons from the mouse midbrain stained with VMAT2 polyclonal antibody (20873-1-AP). Data from Deng et al., 2026 Nature Genetics (PMID: 27270108). Open access.

Post- synaptic marker antibodies

Gephyrin

Gephyrin is a central element that anchors, clusters, and stabilizes glycine and GABA type A receptors at inhibitory synapses of the mammalian brain.

HOMER1 / HOMER2 / HOMER3

HOMERs are Postsynaptic density scaffolding protein.

Immunohistochemical analysis of paraffin-embedded human cerebellum tissue slide using HOMER3 polyclonal antibody (16624-1-AP) at dilution of 1:200 (under 10x lens).

Neuroligin 1 / Neuroligin 4

Neuroligins are cell adhesion molecules present at the postsynaptic side of the synapse.

PSD-95

PSD-95 is a scaffolding protein of the MAGUK protein family and engages in several vital protein-protein interactions in the brain with its PDZ domains. PSD-95 is a highly popular post-synaptic membrane marker.

Female mouse hippocampus tissue stained for Iba1 (white), CD68 (green) and Proteintech’s PSD-95-specific polyclonal antibody 20665-1-AP (red). Data from Wang et al., 2021 Neuron (PMID: 33831349). Open source.

SAP-102

Synapse-associated protein 102 (SAP102), also known as DLG3, highly expressed early in development and mediates receptor trafficking during synaptogenesis

SHANK1

Adapter protein in the postsynaptic density (PSD) of excitatory synapses. SHANK1 may play a role in the structural and functional organization of the dendritic spine and synaptic junction.

Immunofluorescence staining of (4% PFA) fixed mouse eye tissue using SHANK1 antibody (55059-1-AP) at dilution of 1:200 and CoraLite®488-Conjugated AffiniPure Goat Anti-Rabbit IgG(H+L).

Summary of synaptic markers

Pre- synaptic markers	Post- synaptic markers
GAP43	Gephyrin
SNAP-25	HOMER
Synapsin	Neuroligin
Synaptophysin	PSD-95
Synaptotagmin-1	SAP-102
Syntaxin-1	Shank
VAMP2
VGAT
VGLUT
VMAT