Rapidly developing single cell-omics technologies have revolutionized modern biological research. Among them, single-cell proteomics provides the ultimate resolution to reveal cellular heterogeneity underlying many biological processes. In the presentation, I would like to share our recent effort in developing an integrated strategy combining custom chips and data-independent acquisition (DIA) mass spectrometry for sensitive proteomics profiling down to single cell level. These proteomics chips provide built-in functions to perform cell isolation, imaging and quantification, cell lysis and protein digestion as well as peptides clean-up in a streamlined manner. By mapping to project-specific spectra libraries, this workflow enables profiling of an average of ~1,500 protein groups from individual single mammalian cells. Additionally, analytical performances of chip-DIA workflows are demonstrated using adherent and non-adherent malignant cells. The result reveals 5 orders of proteome coverage, consistent ~100-fold protein quantification across 1-100 cells, and good reproducibility with low missing values. With the demonstrated cell manipulation and characterization, good proteomic sensitivity and assay reproducibility, chip-DIA workflow may offer general utility to realize advanced proteomics analysis at single cell level.

Streamlined single-cell proteomics by integrated chip and data-independent acquisition mass spectrometry

ACS Spring 2022

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