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Updated: Jun 17, 2025
T and B Cell Receptor Immune Repertoire Analysis using Next-generation Sequencing
Published on: January 12, 2021
Comprehensive immune cell spectral library for large-scale human primary T, B, and NK cell proteomics
Hyeon-Jeong Lee1,2, Yoondam Seo1, Yoon Park3
1Doping Control Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea.
Insights
Researchers created a comprehensive spectral assay library for human immune cells, including primary cells like T and B lymphocytes. This resource enables deeper proteomic analysis of immune cell heterogeneity and function.
Area of Science:
- Immunology
- Proteomics
- Biochemistry
Background:
- Proteomics is vital in immune research, but a public spectral assay library for immune cells is lacking.
- Existing methods struggle to capture the comprehensive proteome of diverse immune cell types.
Purpose of the Study:
- To develop and provide a publicly accessible spectral assay library for human immune cells.
- To enable high-quality proteomic profiling of immune cell lines and primary cells.
Main Methods:
- Utilized data-dependent acquisition (DDA) on fractionated samples (>100 µg protein) for high-quality MS/MS spectral data.
- Employed data-independent acquisition (DIA) for analyzing proteomes from 10,000 primary immune cells (CD4 T, CD8 T, NK, B cells).
Main Results:
- Generated an immune cell spectral assay library containing 10,544 protein groups and 127,106 peptides.
- DIA analysis revealed significant heterogeneity in B cells and similarity between CD4 T and CD8 T cells.
- Data is publicly available in ProteomeXchange (PXD047742).
Conclusions:
- The created spectral library significantly advances immune cell proteomic research.
- This resource facilitates detailed investigation into immune cell diversity and function.
- The findings highlight distinct proteomic profiles among human immune cell types.
Abstract:
Although proteomics is extensively used in immune research, there is currently no publicly accessible spectral assay library for the comprehensive proteome of immune cells. This study generated spectral assay libraries for five human immune cell lines and four primary immune cells: CD4 T, CD8 T, natural killer (NK) cells, and B cells. This was achieved by utilizing data-dependent acquisition (DDA) and employing fractionated samples from over 100 µg of proteins, which was applied to acquire the highest-quality MS/MS spectral data. In addition, Data-indedendent acquisition (DIA) was used to obtain sufficient data points for analyzing proteins from 10,000 primary CD4 T, CD8 T, NK, and B cells. The immune cell spectral assay library generated included 10,544 protein groups and 127,106 peptides. The proteomic profiles of 10,000 primary human immune cells obtained from 15 healthy volunteers analyzed using DIA revealed the highest heterogeneity of B cells among other immune cell types and the similarity between CD4 T and CD8 T cells. All data and spectral library are deposited in ProteomeXchange (PXD047742).
