The synthesis of starch-like glucans can be reconstituted in S. cerevisiae using the genes from Arabidopsis thaliana: heterologous expression of SS1 to SS4, BE2, BE3, ISA1, and ISA2, together with a bacterial ADPglucose pyrophosphorylase gene for substrate provision in yeast strain 29, yielded insoluble granules with a semi-crystalline structure similar to that of plant amylopectin (Pfister et al., 2016). Here we conducted a label-free proteomics experiment to compare yeast strains with and without glucan production. This experiment was performed on strains 29, 48A, 362.1, 363.1 and WT (n = 4 replicates each, arising from independent replicate cultures). Strains including genotypes are described in the associated publication. Reference: Pfister, B., Sánchez-Ferrer, A., Diaz, A., Lu, K., Otto, C., Holler, M., Shaik, F.R., Meier, F., Mezzenga, R., and Zeeman, S.C. (2016). Recreating the synthesis of starch granules in yeast. Elife 5: 1–29.