Cassava (Manihot esculenta Crantz) is a food security crop for approximately 800 million people, primarily in developing economies. Cassava root yield is determined by the allocation of photoassimilated carbon within the plant, yet there is limited molecular and biochemical information about source-sink relationships in this globally important crop. Here we conducted label free protein quantification using proteomics of Cassava roots before pruning (0 DAP) and 10 days after pruning (10 DAP). This dataset complements transcriptomics analyses and metabolomics analyses described in the associated publication by David et al.