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Updated: Sep 9, 2025

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells
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SLB-msSIM: A Spectral Library-Based Multiplex Segmented SIM Platform for Single-Cell Proteomic Analysis.

Lakmini Senavirathna1, Cheng Ma1, Van-An Duong1

  • 1The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA.

Proteomics
|September 4, 2025
PubMed
Summary
This summary is machine-generated.

We developed a new mass spectrometry method (SLB-msSIM) for highly sensitive single-cell proteomics. This approach reveals cellular heterogeneity and epithelial-mesenchymal transition trajectories in pancreatic cancer cells.

Keywords:
cancer cell heterogeneityepithelial‐mesenchymal transition (EMT)mass spectrometryproteomicssingle‐cell proteomicsspectral library‐based multiplex segmented selected ion monitoring (SLB‐msSIM)

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Cell Biology

Background:

  • Single-cell proteomics is crucial for understanding cellular heterogeneity and function.
  • Existing methods face challenges in sensitivity and robustness.
  • Interrogating cellular phenotypes requires advanced proteomic techniques.

Purpose of the Study:

  • To develop a highly sensitive and robust mass spectrometry-based method for single-cell proteomics.
  • To apply this novel method for analyzing cellular heterogeneity in pancreatic cancer.
  • To investigate single-cell trajectories during epithelial-mesenchymal transition (EMT).

Main Methods:

  • Development of the spectral library-based multiplex segmented selected ion monitoring (SLB-msSIM) method.
  • Acquisition of single-cell mass spectrometry data using multiplex segmented selected ion monitoring (msSIM).
  • Proteomic identification via spectral matching against a defined spectral library.

Main Results:

  • The SLB-msSIM method demonstrated significantly enhanced sensitivity and robustness for single-cell analysis.
  • Analysis of pancreatic cancer cell lines (PANC-1, MIA-PaCa2, AsPc-1, HPAF) and normal HPDE cells revealed common and distinct functional traits.
  • The study provided the first detailed insights into single-cell trajectories during EMT induction and reversal in PANC-1 cells.

Conclusions:

  • The SLB-msSIM method is a sensitive and robust platform for single-cell proteomic studies.
  • This approach is applicable across a wide range of mass spectrometry instruments.
  • The method enables detailed functional characterization of cellular heterogeneity and dynamic processes like EMT at the single-cell level.