Pseudomonas aeruginosa is the most widely distributed infecting organism within the Cystic Fibrosis (CF) community. It accounts for a significant degree of morbidity and mortality, and is associated with vastly shortened lifespan. In the dehydrated mucus of CF lungs, CF-associated P. aeruginosa form antibiotic resistant biofilms leading to chronic infection. Little in form of effective treatments exist, and vaccine candidates to date provide little to no protection. Sequentially isolated isogens of clinical P. aeruginosa representing an acute infecting phenotype (AES-1R), and 10 years of within-host adaptation (chronic infecting phenotype: AES-1M) were grown in a medium mimicking CF sputum to characterise process of adaptation and subsequently identify proteins associated with initial colonization of CF lungs. Proteins harvested from lysates at 18h (early infection) and compared to 48h (early biofilm), 72h (mature biofilm) and 96h (dispersing biofilm) were trypsin digested and iTRAQ labelled to quantify differences during AES-1R and AES-1M adaptation to CF lung. Additional experiments compared between-phenotype differences (AES-1R versus 1M) at 18h and 72h. Approximately 70% of total proteome was identified, with differences in abundance over time including pathways associated with early establishment of infection (e.g. type III/VI secretion pathway and motility). Adaptation trends over time were comparable with 2151 proteins commonly expressed between AES-1R and AES-1M over all four time points; whilst 575 proteins were differentially abundant between two phenotypes at 18h and 1059 proteins at 72h (FDR <0.01). AES-1R/1M differences included pyocyanin and pyoverdine biosynthesis. AES-1R displays a more virulent phenotype, with characteristics associated with increased capacity for biofilm formation, whilst many pathways associated with persistence are upregulated in AES-1M. Results obtained are a detailed analysis of adaptation of P. aeruginosa to CF sputum, and resulted in identification of 6 commonly expressed proteins important in persistence for use in further in vivo immunogenicity trials as possible vaccine candidates.