Updated project metadata. Ventilator associated pneumonia (VAP) is the 2nd most common hospital acquired infection associated with high morbidity, mortality and increased hospitalization. Current practice of diagnosis is based on clinical symptoms and bronchoalvolar lavage (BAL) culture. The procedures of BAL collections are invasive whereas, endotracheal aspirate (ETA), a matrix of upper airway collection is minimally invasive and underexplored in VAP diagnosis. The study describes first in detail characterization of proteome of longitudinal ETA collections from 16 intubated patients including 11 VAP patients and explores potential utility of ETA in VAP diagnosis.