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Shotgun LC-MS/MS of plasma in severe burns

ABSTRACT: Background: Recent advances in proteome analysis technology and mass spectrometry have made it possible to identify and quantify many proteins at once. The aim of this study was to identify proteins associated with severe burn pathology using mass spectrometry and to elucidate a novel molecular pathology classification that will be clinically useful. Methods: In this single-centre, retrospective, observational study, blood samples were collected from patients with severe burns at two time points, on the day of injury and 1 week after injury. Proteins were measured using mass spectrometry, and then prognosis-related proteins were extracted via comparison of 28-day survivor and non-survivor groups. Enrichment and ROC (receiver operating characteristics) analyses were performed to evaluate the extracted proteins. Subsequently, these proteins were used to perform latent class analysis. Findings: Measurements were performed on 83 burn patients. In the non-survivor group, ten proteins were significantly altered on the day of injury, and these were associated with multiple metabolic and response processes to toxins. Of these ten proteins that underwent ROC curve analysis with 28-day death as the objective variable, HBA1, TTR, and SERPINF2 on the day of injury had an area under the curve >0.8. Latent class analysis of these three proteins classified them into three molecular pathotypes. Interpretation: Comprehensive mass spectrometry of plasma revealed that ten proteins were associated with prognosis in severe burns. Molecular pathotypes based on HBA1, TTR, and SERPINF2 were significantly associated with patient outcomes.

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood

SUBMITTER: Fuminori Sugihara

LAB HEAD: Hisatake Matsumoto

PROVIDER: PXD043065 | Pride | 2023-07-10

REPOSITORIES: Pride

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Project description:Protein phosphorylation regulated by plant hormone is involved in the coordination of fundamental plant development. Brassinosteroids (BRs), a group of phytohormones, regulated phosphorylation dynamics remains to be delineated in plants. In this study, we performed a mass spectrometry (MS)-based phosphoproteomics to conduct a global and dynamic phosphoproteome profiling across five time points of BR treatment in the period between 5 minutes and 12 hours. MS coupling with phosphopeptide enrichment techniques has become the powerful tool for profiling protein phosphorylation. However, MS-based methods tend to have data consistency and coverage issues. To address these issues, bioinformatics approaches were used to complement the non-detected proteins and recover the dynamics of phosphorylation events. A total of 1,104 unique phosphorylated peptides from 739 unique phosphoproteins were identified. The time-dependent gene ontology (GO) analysis shows the transition of biological processes from signaling transduction to morphogenesis and stress response. The protein-protein interaction analysis found most of identified phosphoproteins have strongly connections with known BR signaling components. The analysis by using Motif-X was performed to identify 15 enriched motifs, 11 of which correspond to 6 known kinase families. To uncover the dynamic activities of kinases, the enriched motifs were combined with phosphorylation profiles and revealed that the substrates of casein kinase 2 and mitogen-activated protein kinase were significantly phosphorylated and dephosphorylated at initial time of BR treatment, respectively. The time-dependent kinase-substrate interaction networks were constructed and showed many substrates are the downstream of other signalings, such as auxin and ABA signalings. Comparing BR responsive phosphoproteome and gene expression data, we found most of phosphorylation changes were not led by gene expression changes. Our results suggested BR signaling not only induces gene expression, but also change protein activation by phosphorylation via various kinases. Through a large-scale dynamic profile of phosphoproteome coupling bioinformatics, a complicated kinase-centered network related to BR-regulated growth was deciphered. The phosphoproteins and phosphosites identified from our study provide a useful dataset for revealing signaling networks of BR regulation, and also expanded our knowledge of protein phosphorylation modification in plants as well as further deal to solve the plant growth problems.

			Action	DRS
	Dr.Onishi-Patient-Day-MS-MascotID-CorrespondingTable.csv	Csv
	F075901.dat	Other
	F075903.dat	Other
	F075905.dat	Other
	F075907.dat	Other

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Shotgun LC-MS/MS of plasma in severe burns

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