Schematic overview of the experimental workflow. The workflow used in the proteomics analysis of human endobronchial biopsies. Proteins were extracted and digested, before the peptides were labelled with iTRAQ® Reagents in a four-plex set. Each four-plex, containing one reference pool and three samples, were fractionated using ion exchange chromatography. Each fraction was then subjected to nano LC-MS/MS. The resulting spectra were searched for identification and quantification. The identified and quantified proteins were then analysed using Ingenuity Pathways Analysis.