Cigarette smoke is the primary risk factor in the development and progression of COPD. In smokers, smoking cessation, however, is still associated with a higher risk of pulmonary disease, compared to in never-smokers. In this study, we analyzed the progression of emphysema over a 7-month period of exposure to cigarette smoke (CS, 750 μg/l total particle matter from 3R4F cigarettes) or to CS for two months, followed by up to 5 months cessation (fresh air) in C57BL/6 mice. Exposure of C57BL/6 mice to mainstream CS induced acute inflammatory changes in the lung and airways in a time-dependent manner. A quantitative proteomics approach using isobaric tags for absolute and relative quantification (iTRAQ®) was performed on lung tissues of C57BL/6 mice to detect changes in protein expression levels between control, 3R4F and cessation group of samples. Six biological replicates were analyzed to assess repeatability and reproducibility across measurements. Mass-spectrometry data were searched against the mouse uniprot/swissprot database and a database generated from an animal-specific transcriptome prepared in-house. Proteomics datasets of differential proteins will be presented. The results will complement those obtained from other endpoints such as transcriptomics, lipidomics as well as lung histopathology, thereby providing a unique opportunity to identify disease biomarkers and to reveal underlying molecular mechanisms of cigarette smoke induced emphysema, cell infiltration, lung cytokines and oxysterol analyses captured within this study and will further establish the foundation of our systems biology approach to assess the impact of conventional and modified risk tobacco products (MRTPs) on biological systems.