fig2

Figure 2. Evaluating the effects of stool sample processing methods. (A) Experimental design. Gauze filtration (Gauze), 100 µm vacuum filtration (Vaccum), 100 µm spin tube filtration (Spin) and 100 g spinning (100 g) workflows were compared; (B) Number of MS/MS identified in each multiplexed sample set; (C) Number of peptides identified in each multiplexed sample set; (D) Number of protein groups quantified in each multiplexed sample set; (E) Principal component analysis of the sample processing study. Different colors indicate fecal samples from three different individuals. Sizes of data points represent different conditions (small - 0 h baseline, medium - blank, large - kestose). Four different shapes indicate different processing methods. Ellipses indicate the 95% confidence interval for each individual-condition subgroup; (F) Hierarchical clustering of individual samples processed using different sample processing protocols and treated with or without kestose.