Comprehensive immune cell spectral library for large-scale human primary T, B, and NK cell proteomics.

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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).", "claims": [{"id": "claim-method", "statement": "The filtered proteins were subjected to the Kruskal-Wallis test and Dunn’s test as post-hoc tests with Bonferroni adjustment using SPSS.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39127789", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "The filtered proteins were subjected to the Kruskal-Wallis test and Dunn’s test as post-hoc tests with Bonferroni adjustment using SPSS."}], "state": "complete"}, {"id": "claim-data-access", "statement": "A spectral library was generated using the commercial software Spectronaut and evaluated using DIALib-QC. 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