Synaptometry by time-of-flight (SynTOF) mass spectrometry data from NHP

Western and Mediterranean diets differentially affect cerebral cortical gene expression, brain structure, and socioemotional behavior in middle-aged, female nonhuman primates (Macaca fascicularis). Here we quantified the impact of these diets on the presynaptic proteome of approximately 3.6 million synapses isolated from the lateral temporal cortex with synaptometry time of flight (SynTOF) mass spectrometry, a powerful technology for quantifying the molecular diversity of single presynapses. Associations between the presynaptic proteome, adjacent cortex transcriptome, and multi-system phenotypes were assessed using a machine learning approach. Subjects were socially housed macaques (Macaca fascicularis) randomized to eat Mediterranean (n=17) or Western (n=19) diets for 31 months prior to brain retrieval. Six presynaptic proteins (DAT, Aβ42, calreticulin, LC3B, K48-Ubiquitin, SLC6A8) were elevated in the presynaptic proteome by the Mediterranean compared to the Western diet (p<0.05). ..., Synaptometry by time-of-flight (SynTOF) mass spectrometry. Following our established and published protocol for a SynTOF panel1,2, synaptosome samples were prepared, barcoded, and stained. Mass Synaptometry data were acquired, debarcoded, and sequentially gated for % negative and positive events. positive events were selected by CD56 and SNAP25, and nonpresynaptic events selected by CD11b, gephyrin, PSD95, and MBP. Nonpresynaptic events were removed from downstream analyses. Synaptosome processing and analysis pipelines were previously described by us at 2,3,4.
[1] Gajera CR, Fernandez R, Postupna N, et al. Mass synaptometry: High-dimensional multi parametric assay for single synapses. J Neurosci Methods 2019;312:73-83.
[2] Gajera CR, Fernandez R, Montine KS, et al. Mass-tag barcoding for multiplexed analysis of human synaptosomes and other anuclear events. Cytometry A 2021;99:939-945
[3] Berson E, Gajera CR, Phongpreecha T, et al. Cross-species comparative analysis of single presynapse..., , # SynTOF NHP

[https://doi.org/10.5061/dryad.stqjq2cc8](https://doi.org/10.5061/dryad.stqjq2cc8)

## Description of the data and file structure

Single-cell presynapse from NHP.

### Files and variables

#### File: single\_event\_data.zip

**Description:** Single-presynapse data from NHP.

This folder contains data files representing single events measured from individual specimens. Each file is formatted as a table with:

* The first column corresponds to the event number
* Other columns represent markers used in the study.

Code to read and process these data files is provided (see below).

#### File: Metadata.csv

**Description:** Metadata information linking specimen to their diet group and batch group.

This file provides metadata linking each specimen to its corresponding diet and batch groups. The columns in the file are as follows:

1. *File Name:* Matches the names of the files in the *single_**event*_*data* folder.
2. *Cohort (\"BC009\"=Cohort1, \"BC010\"=Cohort2):* Specifies the ...