STOCKHOLM—Although researchers have been able to catalogue many of the proteins that comprise the various proteomes, much of this characterization has been performed outside of the context of the cell where the proteins function. Advances in microscopy, however, have opened the possibility of high-throughput proteomic analysis within the subcellular milieu. Recently, researchers at the Royal Institute of Technology and Uppsala University performed a pilot study to develop a subcellular atlas of the human proteome.
As they report in Molecular and Cellular Proteomics, the researchers combined fluorescently tagged antibodies with tissue and cell arrays to characterize the subcellular localization of hundreds of proteins in three cancer cell lines. First, they used bioinformatics to identify protein epitopes that they then used to generate monospecific polyclonal antibodies. They then probed tissue and cell arrays with each antibody in combination with three probes identifying the nucleus, tubulin, and the endoplasmic reticulum, and had pathologists annotate the resulting confocal microscopy images manually.
The researchers compared their results with the Gene Ontology (GO) annotations for the same proteins to develop a score map. In more than 80% of the cases, the cellular annotation and GO results matched. When they looked at all three cell lines, however, the agreement with GO dropped to 60%, suggesting that events might be occurring within the cell lines that cannot be predicted strictly from GO terminology.
The researchers have added the images and annotation data to the open-access Human Protein Atlas where it can be analyzed in the context of other annotated information. Their goal is to include similar data for all the proteins in the atlas.