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Combination of imaging-based methods reveals the localization of hundreds of proteins in the cell

Published: 2013-03-03

In the first large systematic study of protein localization in the cell, 263 previously unlocalized proteins could be mapped to individual compartments in the cell and the existence of 65 proteins was shown for the very first time. In total, more than 500 proteins were analyzed with two well-established methods used in most laboratories for biological studies; immunofluorescence (IF) and fluorescence protein (FP) tagging.


‘This is the first time the two imaging methods IF and FP have been combined to study the location of a large number of proteins in the cell in an efficient and systematic way’, says Emma Lundberg, principal investigator and Director of the Subcellular Protein Atlas. ‘Knowing the subcellular location of a given protein is of great importance as it indicates the protein function and leads to a better understanding of how and why proteins interact in networks and signaling pathways.’

The Subcellular Protein Atlas is part of the Human Protein Atlas project (headed by Prof. Mathias Uhlen, Royal Institute of Technology, Sweden) and has together with the Fluorescence protein-cDNA localization project (headed by Prof. Rainer Pepperkok, European Molecular Biology Laboratory, Germany) joined forces in combining and comparing two well-established methods for biological research, IF and FP. From this large-scale study of protein expression and localization, systematic errors as well as similarities between the IF and FP methods could be found.

‘This study is useful for everyone in the field that use IF and FP in their work. Drawing conclusions from this large number of proteins analyzed we have put forward a scheme for systematic localization of uncharacterized proteins, pointing at potential pitfalls of each method and when and how you need to complement the methods or use other methods’, says Emma Lundberg.

Immunofluorescent and fluorescent-protein tagging show high correlation for protein localization in mammalian cells
Stadler, C., Rexhepaj, E., Singan, V.R., Murphy, R.F., Pepperkok, R., Uhlen, M., Simpson, J.C. and Lundberg, E.
Nature Methods, online 24 February
Journal website

Link to: The Human Protein Atlas

The Science for Life Laboratory is a joint effort between four Swedish universities, Karolinska Institute, The Royal Institute of Technology (KTH), Stockholm University and Uppsala University. The centre combines advanced technology with a broad knowledge in translational medicine and molecular biosciences. SciLifeLab is a new national strategic investment in life science research that demands large-scale and specialized infrastructure. SciLifeLab has the goal to become one of the leading research centres in the world within the areas of Health and Environment.