In this study, the impact on the development of emphysema/COPD following inhalation of aerosol from two tobacco products, a reference cigarette (3R4F) and a prototypic modified risk tobacco product (pMRTP), was evaluated in C57BL/6 mice. The mice were exposed to an aerosol from 3R4F (750 µg/L TPM, 34.4 µg/L nicotine), pMRTP (nicotine concentration-matched) or filtered air (sham) for 4 hours per day, 5 days per week, up to 7 months. After 2 months of exposure to 3R4F, switching and cessation groups were exposed to pMRTP or filtered air, respectively. To analyze the progression of emphysema at molecular level, quantitative proteomics approach using 2d-page was performed on lung tissues at months 1, 3, 5 and 7. Six biological replicates were analyzed to assess repeatability and reproducibility across measurements. The gel images were aligned and analyzed using imaging software (samespots; totalab). The differentially expressed proteins/spots were excised, digested and analyzed using MALDI-TOF/TOF for protein identification by conducting the searches against the mouse Uniprot/Swissprot reference database. The protein profiles showed minimal changes associated with pMRTP exposure, and recovery near to sham-exposed levels following either switching or cessation. The generated proteomics datasets of the differentially expressed proteins will be presented (e.g. ctsd, fabp5; sftpa). Exposure of mice to mainstream CS-induced acute inflammatory changes in the lung and airways in a time-dependent manner across. The results complement the data from iTRAQ LC MS/MS approach on lung tissues, verification by reverse-phase microarray and the analysis of the other endpoints (transcriptomics) within the study. The generated output will further establish the foundation of PMI’s systems biology approach to assess the impact of pMRTP on biological systems.