Workflow of systematic analysis on RYGB-treated subjects. (a) 10 Non-diabetic Obese (NO) and 9 Diabetic Obese (DO) were subjected to RYGB. The plasma samples of each subject on four stages (pre-RYGB, 1w, 3 m, and 1y after RYGB) were collected at three time points, including the fasting, postprandial 30 min and 45 min. (b) BMI and fasting glucose before and after RYGB showed the significant loss of weight in both group and decrease of fasting glucose in DO group. (c) Quantitative proteomic and metabolic data were detected at all four stages of each subject. (d) Sketch shows the computational methods to calculate molecular states either by nodes or by edges.