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Preparation of the spike-in metaproteome samples
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Similar with the 12-species simulated communities, we constructed another three samples by mixing 6 species at different cell numbers (Supplementary Table 4). After that, bacterial proteins were extracted from the 6-species mixtures. For each mixture, 1 μg of bacterial proteins were taken and then spiked into 99 μg of microbial proteins extracted from the fecal sample to form the spiked samples.
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