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Li et al. Microbiome Res Rep 2024;3:26 https://dx.doi.org/10.20517/mrr.2023.57 Page 11 of 16

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.