Figure 1.

Study design, proteomic workflow and data processing pipeline. (A) Acute Leukemia patients were sampled in weekly interval during the time of hospitalization. In total 212 fecal samples of 56 patients with MRE gut colonization were analyzed, providing additional information about age, gender, and treatment conditions. (B) For the protein extraction, fecal samples were divided in supernatant and pellet fractions. Bacterial cells in the pellet fraction were lysed with ultrasonication and for both samples’ proteins were digested in gel. Thereafter, samples were measured with LC-MS/MS. (C) Raw files were searched with four different databases in separate and combined MaxQuant searches and post-processed with Percolator and with quantitative functional and taxonomic annotation analyzed.