A high-resolution mass spectrometry based proteomic dataset of human regulatory T cells

Harshi Weerakoon; John J Miles; Ailin Lepletier; Michelle M Hill

doi:10.1016/j.dib.2021.107687

A high-resolution mass spectrometry based proteomic dataset of human regulatory T cells

Data Brief. 2021 Dec 6:40:107687. doi: 10.1016/j.dib.2021.107687. eCollection 2022 Feb.

Authors

Harshi Weerakoon^{1

2

3}, John J Miles^{4

5}, Ailin Lepletier^{4

6}, Michelle M Hill^{1

7}

Affiliations

¹ Precision and Systems Biomedicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.
² School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia.
³ Department of Biochemistry, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka.
⁴ Human Immunity Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.
⁵ Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.
⁶ Laboratory of Vaccines for the Developing World, Institute for Glycomics, Southport, QLD, Australia.
⁷ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.

Abstract

Regulatory T cells (Tregs) play a core role in maintaining immune tolerance, homeostasis, and host health. High-resolution analysis of the Treg proteome is required to identify enriched biological processes and pathways distinct to this important immune cell lineage. We present a comprehensive proteomic dataset of Tregs paired with conventional CD4⁺ (Conv CD4⁺) T cells in healthy individuals. Tregs and Conv CD4⁺ T cells were sorted to high purity using dual magnetic bead-based and flow cytometry-based methodologies. Proteins were trypsin-digested and analysed using label-free data-dependent acquisition mass spectrometry (DDA-MS) followed by label free quantitation (LFQ) proteomics analysis using MaxQuant software. Approximately 4,000 T cell proteins were identified with a 1% false discovery rate, of which approximately 2,800 proteins were consistently identified and quantified in all the samples. Finally, flow cytometry with a monoclonal antibody was used to validate the elevated abundance of the protein phosphatase CD148 in Tregs. This proteomic dataset serves as a reference point for future mechanistic and clinical T cell immunology and identifies receptors, processes, and pathways distinct to Tregs. Collectively, these data will lead to a better understanding of Treg immunophysiology and potentially reveal novel leads for therapeutics seeking Treg regulation.

Keywords: Conventional T cell; LC-MS/MS; Proteomics; Regulatory T cell; Tandem mass spectrometry.