1, 2). Monocytes in the blood circulation migrate to the site of infection/inflammation and 48 differentiate into macrophages for effective host defense, tissue remodeling, and repair (3). 49Furthermore, macrophages exhibit a high level of plasticity, depending on their local 50 microenvironment, specialized functions and varied phenotype acquired (1, 4). 51Several models are employed to study the mechanisms of immune-modulation in monocytes 52 and macrophages during inflammatory diseases. The most frequently used include primary 53 peripheral blood mononuclear cells (PBMCs) and monocyte cell lines. However, due to donor-54 to-donor variations and technical disparities involved in handling of PBMCs in vitro, the 55 human leukemia monocytic cell line, THP-1, is widely accepted and used as a 56 monocyte/macrophage model (5, 6). Several studies have indicated that THP-1 cells can be 57 differentiated into macrophage-like cells using phorbol-12-myristate-13-acetate (PMA), 58 which markedly resembles PBMC monocyte-derived macrophages (MDMs) in cytokine 59 production, metabolic and morphological properties, including differential expression of 60 macrophage surface markers such as CD14, CD11b (ITGAM) and scavenger receptors-CD163, 61 MSR1, and SCARB2 (5, 7-10). Nonetheless, depending on the parameters of the differentiation 62 protocol employed, such as the concentration (ranging from 5 to 400 ng/mL), and duration of 63 incubation (1 to 5 days) with PMA; the degree of differentiation and the functional changes 64 may vary significantly (5,(11)(12)(13)(14)(15). 65At the molecular level, multiple proteins including growth factors, antigenic markers, 66 chemokine-receptors, cytokines, and cell adhesion molecules, are known to govern and reflect 67 underlying monocyte-macrophage differentiation processes (16)(17)(18)(19)(20). However, the effect of 68 various differentiation protocols on the cellular proteome and intracellular signaling networks 69 4 during monocyte-to-macrophage differentiation remains poorly understood. Hence, it is crucial 70 to determine the most suitable differentiation conditions when using these cells as model 71 system, as this can significantly impact their response to various innate immune stimuli. 72Quantitative high-resolution mass spectrometry-based proteomic approaches have been widely 73 employed to investigate the proteomes of monocytes and macrophages as well as altered 74 cellular proteomes and complex cellular/biological mechanisms in several biological 75 conditions (21-23). However, to date, no studies have directly compared the proteome changes 76 of the PMA-mediated differentiation process. 77In the present study, we evaluate the effect of three PMA-based differentiation protocols on 78 the changes in the proteome profiles upon THP-1 differentiation using stable isotope dimethyl 79 labeling quantitative proteomics. We demonstrate that various differentiation conditions such 80 as concentration and incubation time, prior to any stimuli, are critical consideration factors for 81 hetero...