A primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics

Area of Science:

• Proteomics
• Immunology
• Mass Spectrometry

Background:

• Data-independent acquisition (DIA) mass spectrometry, such as SWATH-MS, offers robust quantitative proteomics.
• A significant gap exists in public spectral libraries for primary human T-cells, hindering proteomic analysis.
• T-cells play a crucial role in the immune system, making their proteomic profiling essential.

Purpose of the Study:

• To generate a high-quality, public spectral library for human T-cells.
• To improve protein identification and quantification in human T-cell proteomic studies.
• To address the resource gap in primary human T-cell proteomic data.

Main Methods:

• Generation of a spectral library from 4,833 distinct proteins in primary human T-cells.
• Utilized sequential window acquisition of all theoretical mass spectra (SWATH-MS) for data acquisition.
• Comparison of the new library against a larger Pan-human spectral library.

Main Results:

• The new human T-cell spectral library reliably identified and quantified 2,850 proteins at 1% FDR.
• Combining the new library with the Pan-human library enabled quantification of 4,078 human T-cell proteins.
• The generated library covers approximately 24% of the UniProt/SwissProt reviewed human proteome.

Conclusions:

• The developed human T-cell spectral library is a valuable public resource for proteomic research.
• This resource significantly enhances the depth and reliability of human T-cell proteomic profiling.
• The data archive supports future investigations into T-cell function and disease.