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Updated: Sep 4, 2025

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

Published on: April 18, 2025

SimPLIT: Simplified Sample Preparation for Large-Scale Isobaric Tagging Proteomics.

Fernando J Sialana^1,2, Theodoros I Roumeliotis¹, Habib Bouguenina²

¹Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.

Journal of Proteome Research

|July 18, 2022

Summary

This summary is machine-generated.

We developed SimPLIT, a simplified, cost-effective proteomic workflow for large-scale cell line analysis. This method streamlines sample preparation, improving reproducibility for proteogenomic studies and drug target discovery.

Keywords:

CELMoDs IMiDs TMTpro cancer cell lines isobaric labeling targeted protein degradation

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

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Last Updated: Sep 4, 2025

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

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Published on: April 18, 2025

Enhanced Sample Multiplexing of Tissues Using Combined Precursor Isotopic Labeling and Isobaric Tagging cPILOT

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Published on: May 1, 2017

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Area of Science:

Proteomics
Cell Biology
Pharmacology

Background:

Large-scale proteomic profiling aids in understanding cellular mechanisms and drug actions.
Existing isobaric labeling workflows are often time-consuming and expensive, hindering scalability.

Purpose of the Study:

To present a simplified, cost-effective, and reproducible proteomic workflow for medium-to-large scale studies.
To demonstrate the workflow's utility in colorectal cancer cell line profiling and molecular glue degrader target discovery.

Main Methods:

A one-pot reaction workflow (SimPLIT) in a 96-well plate format.
Utilizes sodium deoxycholate lysis, a single detergent cleanup post-peptide labeling, and off-line fractionation.
Mass spectrometry (MS2) analysis for deep profiling.

Main Results:

SimPLIT minimizes processing steps and enhances reproducibility compared to other methods.
Successfully profiled colorectal cancer cell lines and identified dysregulated proteins.
Uncovered cell-dependent protein degradation profiles for seven CRL4^CRBN molecular glue degraders.

Conclusions:

SimPLIT is a robust and easily implementable method for TMT-based proteomic studies.
Facilitates deep profiling of cell lines and target discovery in drug development.
Enables efficient proteogenomic associations and pharmacological mechanism elucidation.