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Unravelling the Web of Protein Interactions - Introducing ProHits-viz

July 19, 2017


ProHits-viz: a suite of web tools for visualizing interaction proteomics data

By Meghan Krizus

  ProHits-viz: a suite of web tools for visualizing interaction proteomics data:


The field of biochemistry – understanding the chemistry of life – began with reductionism. This reductionist approach provided a linear understanding of protein interaction: that one protein performs an action, which is then directly transmitted to another protein. However, thanks to the work of scientists like the late Dr. Tony Pawson, researchers in the fields of biochemistry and cell biology began to realise that proteins do not work in this merely linear fashion. Instead, they are often part of molecular machines comprised of many proteins, often with transient and variegated interactions. 

Now, we know that interaction between proteins forms the backbone of a vast array of cellular and biological processes. Remarkably, of the 20,000+ proteins possibly encoded by the human genome, we still only understand a minority of their functions; however, we have discovered that defects in protein-protein interaction are implicated in a whole host of human diseases. This makes the study of interaction proteomics (how proteins interact with one another) of interest to researchers investigating everything from cancer to mental illness.

The advent of methods such as protein mass spectrometry has enabled highly efficient and high throughput identification of which proteins interact with one another. Mass spectrometry is a powerful technology, but this power in turn presents a dilemma: often the volume of data it generates is difficult to analyze, and it can be even more challenging to visualize in a way understandable to fellow researchers. “[We need] tools to convey the key points of the message,” explains Dr. Anne-Claude Gingras. “To help scientists look at their data and make the conclusions that can be made from it.”

As outlined in a recent correspondence in Nature Methods, researchers from the Gingras lab have designed just such a tool: ProHits-viz. This software allows scientists to perform complex and nuanced analyses of proteomic data, and facilitates useful and understandable visualizations of these analyses. Spearheaded by Dr. James Knight, and designed with the input of Dr. Gingras and her research team, this tool was originally created to fulfill the Gingras lab’s need for more rigorous proteomic analysis than what was previously available to them.

However, its innovative design has made it appealing to anyone in the field of interaction proteomics. ProHits-viz is streamlined, elegant, and web-based, making it user-friendly and easily accessible for anyone in need of a tool to visualize and analyze their mass spectrometry data. ProHits-viz is also useful for integrating the analyzed data into manuscripts, as it allows users to export the images they create in scalable vector graphics (SVG) form.

ProHits-viz also allows not only for standard bait-prey comparisons, but prey-prey and bait-bait comparisons, too. This will help researchers to analyze not only how their proteins of interest interact with others, but also how these interactors relate to one another.

This analysis software tool is free to anyone who needs it, something that both Dr. Knight and Dr. Gingras say is crucially important. Not only does ProHits-viz’s open accessibility allow the Gingras lab to collaborate easily with other labs both within the LTRI and around the world, but it makes this tool available to anyone who has a web browser and data they need analyzed.

So what’s next for ProHits-viz and its designers? “It’s an ongoing process,” says Dr. Knight. “New features…are always in the planning stages.” He and his colleagues are always trying to improve ProHits-viz, to make it even more comprehensive and useful. It is his goal, in his own words, that ProHits-viz is “not just cool, but also functional.”


Mass spectrometry, proteomics, and more: learn what these terms mean and how they relate to you!

Learn more about our researchers and their work!

This work was supported by Genome Canada, Ontario Genomics Institute, CIHR and LTRI.




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