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Updated: Aug 12, 2025

High Resolution Quantitative Synaptic Proteome Profiling of Mouse Brain Regions After Auditory Discrimination Learning
Published on: December 15, 2016
Synaptome.db: a bioconductor package for synaptic proteomics data
Oksana Sorokina1, Anatoly Sorokin2,3, J Douglas Armstrong1,4
1School of informatics, University of Edinburgh, Edinburgh EH8 9AB, UK.
Summary:
The neuronal synapse is underpinned by a large and diverse proteome but the molecular evidence is spread across many primary datasets. These data were recently curated into a single dataset describing a landscape of ∼8000 proteins found in studies of mammalian synapses. Here, we describe programmatic access to the dataset via the R/Bioconductor package Synaptome.db, which enables convenient and in-depth data analysis from within the Bioconductor environment. Synaptome.db allows users to obtain the respective gene information, e.g. subcellular localization, brain region, gene ontology, disease association and construct custom protein-protein interaction network models for gene sets and entire subcellular compartments.
Availability And Implementation:
The package Synaptome.db is part of Bioconductor since release 3.14, https://bioconductor.org/packages/release/data/annotation/html/synaptome.db.html, it is open source and available under the Artistic license 2.0. The development version is maintained on GitHub (https://github.com/lptolik/synaptome.db). Full documentation including examples is provided in the form of vignettes on the package webpage.
Supplementary Information:
Supplementary data are available at Bioinformatics Advances online.
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