Differential urine proteome analysis of a ventilator-induced lung injury rat model by label-free quantitative and parallel reaction monitoring proteomics

Abstract

Urine is a promising resource for biomarker research. Therefore, the purpose of this study was to investigate potential urinary biomarkers to monitor the disease activity of ventilator-induced lung injury (VILI). In the discovery phase, a label-free data-dependent acquisition (DDA) quantitative proteomics method was used to profile the urinary proteomes of VILI rats. For further validation, the differential proteins were verified by parallel reaction monitoring (PRM)-targeted quantitative proteomics. In total, 727 high-confidence proteins were identified with at least 1 unique peptide (FDR ≤ 1%). Compared to the control group, 110 proteins (65 upregulated, 45 downregulated) were significantly changed in the VILI group (1.5-fold change, P < 0.05). The canonical pathways and protein–protein interaction analyses revealed that the differentially expressed proteins were enriched in multiple functions, including oxidative stress and inflammatory responses. Finally, thirteen proteins were identified as candidate biomarkers for VILI by PRM validation. Among these PRM-validated proteins, AMPN, MEP1B, LYSC1, DPP4 and CYC were previously reported as lung-associated disease biomarkers. SLC31, MEP1A, S15A2, NHRF1, XPP2, GGT1, HEXA, and ATPB were newly discovered in this study. Our results suggest that the urinary proteome might reflect the pathophysiological changes associated with VILI. These differential proteins are potential urinary biomarkers for the activity of VILI.

Urine Proteomic Signatures of Mild Hypothermia Treatment in Cerebral Ischemia–Reperfusion Injury in Rats

“…The peptide samples were analyzed using the Orbitrap Fusion Lumos Tribrid mass spectrometer coupled with EASY-nLC 1000 HPLC system (Thermo Scientific, Germany) as described previously (Qin et al 2021 ; Sun et al 2022 ). Briefly, the digested peptides were loaded onto a C18 trap column (3 µm, 75 µm × 2 cm, 100 A°) and then transferred to a C18 reversed-phase analytical column (2 µm, 50 µm × 250 mm, 100 A°).…”

Proteome profiling of hippocampus reveals the neuroprotective effect of mild hypothermia on global cerebral ischemia–reperfusion injury in rats

“…An Orbitrap Fusion Lumos Tribrid mass spectrometer coupled with an EASY-nLC 1000 HPLC system (Thermo Scientific, Germany) was used to analyze the peptide sample, as previously described 15 , 16 . In detail, the digested peptides were loaded onto a trap column (75 µm × 2 cm, 3 µm, C18, 100 A°), and then transferred to a reversed-phase analytical column (50 µm × 250 mm, 2 µm, C18, 100 A°).…”

“…The raw data files were processed using Progenesis QIP and Mascot software, as previously described 16 . Briefly, the search parameters were set as follows: SwissProt Rattus database (containing 8086 sequences), trypsin digestion, parent ion mass tolerance of 10 ppm, fragment ion mass tolerance of 0.02 Da, fixed modification of carbamidomethylated cysteine (+ 58.00 Da); variable modifications of deamidated glutamine asparagine (+ 0.984 Da) and oxidized methionine (+ 15.995 Da).…”

Prognostic Biomarkers Based on Proteomic Technology in COPD: A Recent Review

“…In addition to the urinary system, biomarkers in urine can be a sensitive indicator of respiratory diseases. Urine proteomic studies have identified biomarkers for several respiratory diseases, such as lung cancer 87 , pulmonary fibrosis, 88 ventilator-induced lung injury, 89 and acute respiratory distress syndrome (ARDS). 90 Therefore, urine is a promising resource for studying biomarkers of lung diseases.…”