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

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Weiwei Qin ◽  
Xiao Zhang ◽  
Lingnan Chen ◽  
Qiujie Li ◽  
Benwang Zhang ◽  
...  
Keyword(s):  
Lung Injury ◽  
Quantitative Proteomics ◽  
Urinary Biomarkers ◽  
Reaction Monitoring ◽  
Label Free ◽  
Parallel Reaction ◽  
Ventilator Induced Lung Injury ◽  
Parallel Reaction Monitoring ◽  
Free Data ◽  
Differential Proteins

AbstractUrine 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.

scholarly journals The Differential Urine Proteome Analysis of a Ventilator-induced Lung Injury Rat Model by Label-free Quantitative and Parallel Reaction Monitoring Proteomics

2021 ◽  
Author(s):  
Weiwei Qin ◽  
Xiao Zhang ◽  
Lingnan Chen ◽  
Qiujie Li ◽  
Benwang Zhang ◽  
...  
Keyword(s):  
Lung Injury ◽  
Quantitative Proteomics ◽  
Urinary Biomarkers ◽  
Reaction Monitoring ◽  
Label Free ◽  
Parallel Reaction ◽  
Ventilator Induced Lung Injury ◽  
Parallel Reaction Monitoring ◽  
Free Data ◽  
Differential Proteins

Abstract Background: 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). Methods: 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.Results: In all, 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. Conclusions: 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.

scholarly journals Development of parallel reaction monitoring (PRM)-based quantitative proteomics applied to HER2-Positive breast cancer

Oncotarget ◽  
2018 ◽  
Vol 9 (73) ◽  
pp. 33762-33777 ◽  
Author(s):  
Mathilde Guerin ◽  
Anthony Gonçalves ◽  
Yves Toiron ◽  
Emilie Baudelet ◽  
Matthieu Pophillat ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Quantitative Proteomics ◽  
Reaction Monitoring ◽  
Parallel Reaction ◽  
Her2 Positive ◽  
Her2 Positive Breast Cancer ◽  
Parallel Reaction Monitoring ◽  
Positive Breast Cancer

scholarly journals Development of a novel nanoflow liquid chromatography-parallel reaction monitoring mass spectrometry-based method for quantification of angiotensin peptides in HUVEC cultures

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9941
Author(s):  
Chuan He ◽  
Simiao Hu ◽  
Wanxing Zhou
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Culture Supernatant ◽  
Reaction Monitoring ◽  
Ang Ii ◽  
Parallel Reaction ◽  
Parallel Reaction Monitoring ◽  
Relative Standard ◽  
Ang Iv ◽  
Nanoflow Liquid Chromatography

Background This study aimed to develop an analytical method using liquid chromatography tandem mass spectrometry (LC-MS/MS) for the determination of angiotensin (Ang) I, Ang (1-9), Ang II, Ang (1-7), Ang (1-5), Ang III, Ang IV in human umbilical vein endothelial cell (HUVEC) culture supernatant. Methods HUVEC culture supernatant was added with gradient concentrations (0.05–1,000 ng/ml) of standard solutions of the Ang peptides. These samples underwent C18 solid-phase extraction and separation using a preconcentration nano-liquid chromatography mass spectrometry system. The target peptides were detected by a Q Exactive quadrupole orbitrap high-resolution mass spectrometer in the parallel reaction monitoring mode. Ang converting enzyme (ACE) in HUVECs was silenced to examine Ang I metabolism. Results The limit of detection was 0.1 pg for Ang II and Ang III, and 0.5 pg for Ang (1-9), Ang (1-7), and Ang (1-5). The linear detection range was 0.1–2,000 pg (0.05–1,000 ng/ml) for Ang II and Ang III, and 0.5–2,000 pg (0.25–1,000 ng/ml) for Ang (1-9) and Ang (1-5). Intra-day and inter-day precisions (relative standard deviation) were <10%. Ang II, Ang III, Ang IV, and Ang (1-5) were positively correlated with ACE expression by HUVECs, while Ang I, Ang (1-7), and Ang (1-9) were negatively correlated. Conclusion The nanoflow liquid chromatography-parallel reaction monitoring mass spectrometry-based methodology established in this study can evaluate the Ang peptides simultaneously in HUVEC culture supernatant.

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