Respiratory failure is a syndrome of impaired gas exchange resulting in abnormal oxygenation and carbon dioxide elimination. Lung damage seen in Acute Respiratory Distress Syndrome (ARDS) and Idiopathic Pneumonia Syndrome (IPS) cause acute respiratory failure and result in a high mortality and morbidity. Our objective is to gain novel insights into the pathways and biological processes that occur in response to diffuse lung injury by using comprehensive protein expression profiling in combination with bioinformatics tools. We characterized the protein expression in the Bronchoalveolar lavage fluid (BALF) from subjects with ARDS and also in hematopoietic stem cell transplantation (HSCT) recipients. For our studies, ARDS cases were grouped into survivors and non-survivors. The HSCT recipients were assigned to either infectious lung injury or IPS, i.e. non-infectious lung injury. The BALF samples were processed by desalting, concentration and removal of high abundance proteins. Enriched medium and low abundant protein fractions were trypsin digested and labeled with the iTRAQ reagent for mass spectrometry (MS). The complex mixture of iTRAQ labeled peptides was analyzed by 2D capillary LC-MS/MS on an Orbitrap Velos system in HCD mode for data-dependent peptide tandem MS. Protein identification employed a target decoy strategy using ProteinPilot. To determine the biologic relevance of the differentially expressed proteins we used Database for Visualization and Annotation for Integrated Discovery (DAVID) and Ingenuity Pathway Analysis (IPA). In the studies done on pooled BALF described in Chapter 3, we identified 792 proteins at a global FDR of <= 1%. The proteins that were more abundant in early phase survivors represented the GO groups involved in coagulation, fibrinolysis and wound healing, cation homeostasis and activation of the immune response. In contrast, non-survivors had evidence of carbohydrate catabolism, collagen deposition and actin cytoskeleton reorganization. These proof of concept studies identified early differences in the BALF from ARDS survivors compared to non-survivors. As a follow-up, we characterized BALF from the individual subject with ARDS, 20 survivors and 16 non-survivors (Chapter 4). To accomplish this we performed six eight-plex iTRAQ LC-MS/MS experiments, and we identified 1122 unique proteins in the BALF. The proteins that had a differential expression between survivors and non-survivors represented three canonical pathways -- acute phase response signaling, complement system activation, LXR/RXR activation- and four IPA Diseases and Functions- cellular movement, immune cell trafficking, hematological system development and inflammatory response. Similar to our prior studies, GO biological processes annotated to these proteins included programmed cell death, collagen metabolic processes, and acute inflammatory response. The sparse logistic regression model identified twenty proteins that predicted survival in ARDS. For the studies conducted in HSCT recipients (Chapter 5), we performed five eight-plex iTRAQ LC-MS/MS experiments and identified 1125 unique proteins. The proteins that had a differential expression between IPS and infectious lung injury enrich GO biological terms of immune response, leucocyte adhesion, coagulation, wound healing, cell migration, glycolysis, and apoptosis. In summary, the BALF protein expression profile identifies key differences in the biological processes in different subgroups of patients with diffuse lung injury. These differences position us to develop diagnostic and prognostic biomarkers and identify new targets for pharmacological therapy.