Structure and results of the randomized incomplete block design. A. The matrix illustrated below allowed for a comparison of the protein profiles of all colonies. Each colony was sampled in triplicate and each sample was labeled with either light, medium or heavy isotopes, and was assigned to a block. Each block, represented by a triangle, contained three samples from different colonies and labels and was analysed in one Mass Spectrometry run. B. Due to the semi-stochastic nature of data-dependent acquisition in LC-MS/MS and the wide range of protein abundances, not all proteins were detected in every sample. Shown is a representative plot of the frequency where 1312 proteins were detected across 38 blocks in BL-Y1 sample set. The 476 proteins that were detected in at least 10 (25%) of the blocks were considered in the analysis.