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Updated: Apr 12, 2026

TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis
Published on: June 8, 2020
Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein
Erik Ahrné1, Amalia Martinez-Segura2, Afzal Pasha Syed1
1Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
Abstract:
The generation of dynamic models of biological processes critically depends on the determination of precise cellular concentrations of biomolecules. Measurements of system-wide absolute protein levels are particularly valuable information in systems biology. Recently, mass spectrometry based proteomics approaches have been developed to estimate protein concentrations on a proteome-wide scale. However, for very complex proteomes, fractionation steps are required, increasing samples number and instrument analysis time. As a result, the number of full proteomes that can be routinely analyzed is limited. Here we combined absolute quantification strategies with the multiplexing capabilities of isobaric tandem mass tags to determine cellular protein abundances in a high throughput and proteome-wide scale even for highly complex biological systems, such as a whole human cell line. We generated two independent data sets to demonstrate the power of the approach regarding sample throughput, dynamic range, quantitative precision and accuracy as well as proteome coverage in comparison to existing mass spectrometry based strategies.
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