Development of Targeted Mass Spectrometry-Based Approaches for Quantitation of Proteins Enriched in the Postsynaptic Density (PSD)
by
Rashaun S. Wilson 1,2,3, Navin Rauniyar 4, Fumika Sakaue 5,6, TuKiet T. Lam 1,2,3
, Kenneth R. Williams 1,3 and Angus C. Nairn 1,6,*
Rashaun S. Wilson 1,2,3, Navin Rauniyar 4, Fumika Sakaue 5,6, TuKiet T. Lam 1,2,3, Kenneth R. Williams 1,3 and Angus C. Nairn 1,6,*
1
Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA
2
W.M Keck Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, CT 06511, USA
3
Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA
4
Tanvex BioPharma Inc., San Diego, CA 92121, USA
5
Department of Neurology and Neurological Science, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
6
Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA
*
Author to whom correspondence should be addressed.
Proteomes 2019, 7(2), 12; https://doi.org/10.3390/proteomes7020012
Received: 11 March 2019 / Revised: 27 March 2019 / Accepted: 28 March 2019 / Published: 2 April 2019
(This article belongs to the Special Issue Neuroproteomics)
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.
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Keywords:
postsynaptic density; PSD; parallel reaction monitoring; PRM; targeted proteomics; data-independent acquisition; DIA; quantitative mass spectrometry
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MDPI and ACS Style
Wilson, R.S.; Rauniyar, N.; Sakaue, F.; Lam, T.T.; Williams, K.R.; Nairn, A.C. Development of Targeted Mass Spectrometry-Based Approaches for Quantitation of Proteins Enriched in the Postsynaptic Density (PSD). Proteomes 2019, 7, 12.
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