Updated project metadata. Cyclin-dependent kinases (Cdks) are the catalytic subunits of a family of mammalian heterodimeric serine/threonine kinases that play critical roles in control of cell-cycle progression, transcription and neuronal functions. To systematically investigate the regulations and functions of CDKs, we conducted a proteomic analysis of human CDK family and identified their associated protein complexes in two different cell lines using a modified SAINT (Significance Analysis of INTeractome) method. We discovered 753 HCIPs (high-confidence candidate interaction proteins) in HEK293T cells and 352 HCIPs in MCF10A cells.