Funding and salary support

This work was supported by a Venture Sinai award to A.-C.G.; a Canadian Institute of Health Research to A.-C.G. (MOP-84314); the US National Institutes of Health to A.-C.G. (5R01GM94231); the Ontario Research Fund via a Global Leadership Award Round 2 to T.P. and A.-C.G.; the European Research Council (#ERC-2008-AdG 233226) to R.A.; SystemsX.ch, the Swiss Initiative for Systems Biology to R.A.; the US National Human Genome Research Institute (R01HG001715 and P50HG004233) and the US National Cancer Institute (R33CA132073) to M.V; a Canada Research Chair in Functional Proteomics and the Lea Reichmann Chair in Cancer Proteomics to A.-C.G.; and postdoctoral awards from the Canadian Institutes of Health Research and the Canadian National Sciences and Engineering Research Council postdoctoral award to J.-P.L.

Other acknowledgments

We thank Lorne Taylor for input and initial SWATH data analysis, Elizabeth Polvi for help with subcloning, Karen Colwill for the construction of pDEST-5'Triple-FLAG-pcDNA5-FRT-TO and Brian Raught for critical reading of the manuscript. The website for the supplementary material was designed by Guomin Liu and Jian Ping Zhang.