Dataset Information

MsSIM for single-cell proteomic analysis

ABSTRACT: We report the development of the spectral library-based multiplex segmented Selected Ion Monitoring (SLB-msSIM) method, a novel approach that significantly improves sensitivity and robustness for single-cell analysis. Single-cell MS data is acquired using the msSIM technique, which sequentially applies multiple isolation cycles with the quadrupole, utilizing a wide isolation window in each cycle to accumulate and store precursor ions in the C-trap for a single scan in the Orbitrap. Proteomic identification is achieved through spectral matching with a well-defined spectral library. We employed the SLB-msSIM method to explore cellular heterogeneity across multiple cell lines and to analyze cellular trajectories during epithelial-mesenchymal transition.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Pancreas

DISEASE(S): Pancreatic Cancer

SUBMITTER: Lakmini Senavirathna

LAB HEAD: Seng pan

PROVIDER: PXD055915 | Pride | 2025-10-13

REPOSITORIES: Pride

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			Action	DRS
	20230406_PNAC1_single_cells_TGFb_D3_1.raw	Raw
	20230406_PNAC1_single_cells_TGFb_D3_10.raw	Raw
	20230406_PNAC1_single_cells_TGFb_D3_11.raw	Raw
	20230406_PNAC1_single_cells_TGFb_D3_12.raw	Raw
	20230406_PNAC1_single_cells_TGFb_D3_13.raw	Raw

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Publications

SLB-msSIM: A Spectral Library-Based Multiplex Segmented SIM Platform for Single-Cell Proteomic Analysis.

Senavirathna Lakmini L Ma Cheng C Duong Van-An VA Tsai Hong-Yuan HY Chen Ru R Pan Sheng S

Proteomics 20250904 19

Mass spectrometry (MS)-based single-cell proteomics, while highly challenging, offers unique potential for a wide range of applications to interrogate cellular heterogeneity, trajectories, and phenotypes at a functional level. We report here the development of the spectral library-based multiplex segmented selected ion monitoring (SLB-msSIM) method, a conceptually unique approach with significantly enhanced sensitivity and robustness for single-cell analysis. The single-cell MS data is acquired ...[more]

PMID: 40904101

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