LUX Score is a metric for comparing lipidomes that is based on sequence alignment methods, which are widely used in genetics. LUX Score compares lipid structures that were identified by mass spectrometric analysis and computes the homology between lipidomes. Smoking is the major risk factor for developing Lung Cancer and for Chronic Obstructive Pulmonary Disorders (COPD). Previous studies have shown lipid perturbations in sputum of COPD patients. Lipid perturbations in tissue biopsies of lung cancer patients provide insights into pathological processes that are causal for disease progression. I describe a data analysis workflow to compare lipid structural differences between tumor and alveolar tissues using LUX Score.