Institute at Mount Sinai Hospital in Toronto,. Anne-Claude Gingras studies protein-protein interactions using affin- ity purification coupled with mass spectrometry.
this month The Author File
Anne-Claude Gingras
npg
As a biochemist at Samuel Lunenfeld Research Institute at Mount Sinai Hospital in Toronto, Anne-Claude Gingras studies protein-protein interactions using affinity purification coupled with mass spectrometry (AP-MS). Background contaminants clutter the data collected in experiments to probe these interactions. The clutter makes it harder to study how proteins interact, for example, Anne-Claude Gingras when cells transition from healthy to diseased states. False positive information can even be found in protein-protein interaction data repositories. She and Alexey Nesvizhskii, a close collaborator at the University of Michigan, previously developed a software suite called significance analysis of interactome (SAINT) to give confidence scores to the interactions discovered in AP-MS experiments. But as Gingras characterized contaminants in her own AP-MS work, she discussed with colleagues the need for a new online resource to help others score their data against the backdrop of knowledge about contaminants. For the new resource, Gingras knew she needed to find laboratories willing to contribute hundreds of mass spectrometry runs and annotate them. “Piece of cake, right?” she jokes. The cake has been baked. She convinced 12 labs to participate, all of whom have been supportive of the project from the start in 2009, she says. She and her team call the new resource the contaminant repository for affinity purification, or CRAPome. It allows researchers to upload data and score them, using SAINT, for background contaminants. Gingras originally proposed to name it Total CRAP, which would have required subdivisions into human CRAP, mouse CRAP and rat CRAP, she says. “Sadly, my collaborators had a bit more class than me, and we came to a compromise.” Her lab has just deposited many files from a new protocol that uses in vivo biotinylation as a proximity labeling technology. People are interested in contributing data to the CRAPome, she says, particularly researchers working with different model organisms. Mount Sinai Hospital
© 2013 Nature America, Inc. All rights reserved.
Proteins are sociable and interact with other proteins. A new web resource helps to score experimental data about these relations.
The CRAPome’s data are currently from cell lines. As the resource grows, she hopes scientists will add data from experiments across different cancer lines and tissues, too. Gingras also knows she will have more users than contributors. The resource’s main users are likely to be experimentalists looking at hits from their own sample analysis or when checking a published paper’s results. The team designed the resource to be easy to use for those who are not experts in mass spectrometry or bioinformatics, she says. Nesvizhskii and Gingras met during their postdoctoral fellowships in Ruedi Aebersold’s proteomics lab when he was at the Institute for Systems Biology in Seattle. “Going to Ruedi’s lab was great,” she says. She had worked with him on projects during her graduate studies in biochemistry at McGill University and decided on his lab for her postdoc. For Gingras, CRAPome marks a milestone for her long-term collaborations, which require common research interests, mutual respect and the ability to communicate. She and Nesvizhskii are complementary, she says. Although his training is in math and physics and hers is in biochemistry, “we are somehow able to communicate well with each other and come up with projects that neither of us could do alone but that we are very well suited to do as a team.” When it comes to mass spectrometry, Gingras is “She cuts “a force of nature,” says cancer researcher Jim through Woodgett, director of the crap in research at the Lunenfeld Research Institute. In his everything she view, the new resource’s name says all: “she cuts does.” through the crap in everything she does,” he says. The institute lured her back to Canada from her postdoctoral fellowship. “When we recruited Anne-Claude from the Institute for Systems Biology, we lucked out, as she is a mash-up of Ruedi Aebersold’s mass spectrometry skills, Leroy Hood’s infectious enthusiasm and Nahum Sonenberg’s scientific drive.” As a native French speaker, Gingras admits that learning English has not come easily. “I made a fool of myself more than once during grad school, and am still hesitant in English to this day,” she says. In 2011, she was named one of Canada’s top 100 most powerful women. She says it affected her only for one day, during which she bossed others around. Gingras took public transportation to the award event, where she later realized most awardees had arrived with private chauffeurs. “And had way better shoes.”
Vivien Marx
Mellacheruvu, D. et al. The CRAPome: a contaminant repository for affinity purification– mass spectrometry data. Nat. Methods 10, 730–736 (2013). nature methods | VOL.10 NO.8 | AUGUST 2013 | 685
