The objective of this study is to analyze bronchoalveolar lavage fluid from patients with lung infiltrates in order to discover new biomarkers and protein expression patterns that are associated with specific types of pulmonary disease. Bronchoalveolar lavage (BAL) is a standard method to obtain lower airway samples to evaluate pulmonary infiltrates in order to diagnose infection, malignancy or non-infectious inflammation. After collecting the lavage, the clinical microbiology laboratory concentrates the formed elements (i.e. pathogens and cells) for stains and culture and discards the BAL supernatant. The supernatant however is a rich source of proteins and other molecules. We hypothesize that BAL fluid supernatant will be an important source of biomarkers that reflect host-pathogen interactions. The analysis of protein mass profiles and biomarker identification in BAL fluid supernatant may help develop new diagnostic methods and extend our understanding of mechanisms of lung inflammation due to infectious causes.