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Proteomes. 2019 Apr 2;7(2). pii: E12. doi: 10.3390/proteomes7020012.

Development of Targeted Mass Spectrometry-Based Approaches for Quantitation of Proteins Enriched in the Postsynaptic Density (PSD).

Wilson RS1,2,3, Rauniyar N4, Sakaue F5,6, Lam TT7,8,9, Williams KR10,11, Nairn AC12,13.

Author information

1
Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA. rashaun.wilson@yale.edu.
2
W.M Keck Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, CT 06511, USA. rashaun.wilson@yale.edu.
3
Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA. rashaun.wilson@yale.edu.
4
Tanvex BioPharma Inc., San Diego, CA 92121, USA. navin.rauniyar@tanvex.com.
5
Department of Neurology and Neurological Science, Tokyo Medical and Dental University, Tokyo 113-8519, Japan. sakaue.nuro@tmd.ac.jp.
6
Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA. sakaue.nuro@tmd.ac.jp.
7
Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA. tukiet.lam@yale.edu.
8
W.M Keck Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, CT 06511, USA. tukiet.lam@yale.edu.
9
Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA. tukiet.lam@yale.edu.
10
Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA. kenneth.williams@yale.edu.
11
Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA. kenneth.williams@yale.edu.
12
Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA. angus.nairn@yale.edu.
13
Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA. angus.nairn@yale.edu.

Abstract

The postsynaptic density (PSD) is a structural, electron-dense region of excitatory glutamatergic synapses, which is involved in a variety of cellular and signaling processes in neurons. The PSD is comprised of a large network of proteins, many of which have been implicated in a wide variety of neuropsychiatric disorders. Biochemical fractionation combined with mass spectrometry analyses have enabled an in-depth understanding of the protein composition of the PSD. However, the PSD composition may change rapidly in response to stimuli, and robust and reproducible methods to thoroughly quantify changes in protein abundance are warranted. Here, we report on the development of two types of targeted mass spectrometry-based assays for quantitation of PSD-enriched proteins. In total, we quantified 50 PSD proteins in a targeted, parallel reaction monitoring (PRM) assay using heavy-labeled, synthetic internal peptide standards and identified and quantified over 2100 proteins through a pre-determined spectral library using a data-independent acquisition (DIA) approach in PSD fractions isolated from mouse cortical brain tissue.

KEYWORDS:

DIA; PRM; PSD; data-independent acquisition; parallel reaction monitoring; postsynaptic density; quantitative mass spectrometry; targeted proteomics

PMID:
30986977
DOI:
10.3390/proteomes7020012
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