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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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Updated: Jul 14, 2026

Extracellular Protein Microarray Technology for High Throughput Detection of Low Affinity Receptor-Ligand Interactions

Extracellular Protein Microarray Technology for High Throughput Detection of Low Affinity Receptor-Ligand Interactions

Published on: January 7, 2019

A high-throughput strategy for protein profiling in cell microarrays using automated image analysis.

Sara Strömberg¹, Marcus Gry Björklund, Caroline Asplund

¹Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.

|June 6, 2007

Summary

Automated image analysis of immunohistochemistry (IHC) on cell microarrays offers a high-throughput solution for protein profiling. This method accurately quantifies protein expression, enabling global comparisons with transcript levels.

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Published on: January 7, 2019

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Area of Science:

Biotechnology
Molecular Biology
Bioinformatics

Background:

Growing availability of affinity reagents for immunohistochemistry (IHC).
Tissue microarray (TMA) technology enables multiplexed tissue analysis.
Manual microscopic analysis of IHC data is a significant bottleneck.

Purpose of the Study:

To develop a high-throughput strategy for analyzing immunohistochemistry (IHC) data.
To introduce a novel automated image-analysis application (TMAx) for IHC data.
To assess the correlation between mRNA and protein levels using automated IHC analysis.

Main Methods:

Combined IHC on a cell microarray with the automated image-analysis application TMAx.
Evaluated TMAx performance on 200 digital images of IHC-stained cell spots.
Compared automated TMAx annotation with manual annotation by seven human experts.

Main Results:

High concordance observed between automated TMAx and manual annotation for staining intensity and positive cell fraction.
Demonstrated feasibility of correlating mRNA and protein levels using TMAx output and quantitative real-time PCR.
Automated analysis provides accurate protein quantification for high-throughput profiling.

Conclusions:

Automated analysis of IHC-stained cells in a microarray format enables high-throughput protein profiling.
TMAx software offers a validated, efficient alternative to manual IHC data analysis.
Integration with RNA extraction allows for global comparison of transcription and protein expression.