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Comparison of DeepPhospho with other models We compared our method with several published models, including pDeep2, DeepMS2, and MS2PIP on three datasets: RPE1 DDA, RPE1 DIA, and U2OS DIA

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It is likely that the larger number of statistically significant changes to the microbiome observed in the groups switched from WD to LD reflects their more numerous exposures to different diets, longitudinal changes in dietary exposure, the stress associated with diet switch, the negative energy state achieved by treatment and/or diet-driven weight loss, or a combination of these factors, but it may also be related to differences in terminal body weight and fat mass since both adiposity and diet composition have been shown to modulate the mouse gut microbiome profile