Fig. 4.

Label Free Quantification Strategy. Cartoon depicting our strategy for Label Free Quantification (LFQ) to select SUMO-2 target proteins and to identify significantly up- or down- regulated SUMO-2 target proteins in response to 2 h or 24 h HU treatment. Step 1: Protein lists generated by MaxQuant were further analyzed by Perseus and LFQ intensities were log₂ transformed. Step 2: Different experiments were divided into four groups based on experimental conditions: A parental control group for U2OS control samples and three experimental groups for SUMO-2 samples purified from U2OS cells expressing His10-SUMO-2 treated with HU for 2 h or 24 h or mock treated. Inclusion criteria are depicted. Step 3: Imputation of the missing values by normally distributed values with 1.8 downshift (log₂) and 0.3 randomized width (log₂). Step 4: Proteins were considered as SUMO-2 target proteins using the indicated criteria. Step 5: Significantly up- or down-regulated SUMO-2 target proteins in response to 2 h or 24 h HU treatment were identified as indicated.