Lung transplant is an effective therapy, however, long-term survival is currently limited due to the high rate of bronchiolitis obliterans syndrome (BOS). The longitudinal biological changes that occur as a patient progresses to BOS are not well understood. The objective of this study was to evaluate the bronchoalveolar lavage fluid (BALF) proteome, seeking to identify proteins and their representative biological functions that have coherent changes in the development of BOS. Methods: Isobaric

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... ag for relative and absolute quantification(iTRAQ ® ) with LC MS/MS were performed on BALF enriched for medium and low abundance proteins from three time points (range 699 days pre-BOS to 83 days post-BOS) taken from four patients that developed BOS. Controls consisted of pooled samples from nine patients who did not develop BOS within five years of sample acquisition. We investigated how the protein profiles changed longitudinally as the patient progressed towards BOS using Short Time-series Expression Miner, (STEM), analysis and identified gene ontology terms associated with these protein clusters. Results: We identified 871 unique proteins at a 5% FDR. STEM analysis revealed three models that met statistical significance.Gene ontology revealed three biological processes that associated with these models and included: sequestering of actin monomers, cytoskeletal organization and an inflammatory or defense response. Conclusion: Longitudinal and gene cluster models reveal coherent changes in BALF proteins as patients approach BOS.