Dataset Information

Using SWATH-MS to Identify New Molecular Biomarkers in Gingival Crevicular Fluid for Detecting Periodontitis and its Response to Treatment

ABSTRACT: Over the last years, proteomic techniques have been demonstrated to be valuable tools for analysing the periodontal proteome in gingival crevicular fluid (GCF) samples contributing to identifying extensive and comprehensive protein profiles associated with periodontitis. However, the periodontal proteome has not yet been studied using sequential window acquisition of all theoretical mass spectra (SWATH-MS). Consequently, the objective of the present longitudinal research was to investigate the periodontal proteome in GCF in three clinical conditions (periodontal health, untreated periodontitis, and treated periodontitis), applying SWATH-MS to 1) analyse the periodontal proteome structure in the three clinical groups, 2) compare the differential protein expression between the three clinical groups, and 3) evaluate the diagnostic accuracy of the proteins quantified to identify new biomarkers with a high capacity to discriminate the three clinical conditions. A total of 84 subjects, 44 periodontally healthy and 40 with generalised untreated periodontitis in stages III-IV, were included, and GCF samples were collected. The diagnosis of periodontal status was conducted by two experienced dentists using clinical and radiographic criteria. The definition of periodontal status was established following the Classification of Periodontal Diseases and Conditions published in 2018. In the untreated periodontitis group, 38 underwent conventional non-surgical treatment and were evaluated clinically after two months (treated periodontitis group). In the revaluation, 25 individuals showed significant clinical improvement in probing pocket depth (PPD) at the selected sites, and GCF samples were collected from them.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Gingival Fluid

DISEASE(S): Periodontitis

SUBMITTER: Susana Bravo

LAB HEAD: Susana Belen Bravo Lopez

PROVIDER: PXD043474 | Pride | 2024-10-17

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 219

Publications

Impact of smoking habit on the subgingival proteome in patients with periodontitis.

Blanco-Pintos Triana T Regueira-Iglesias Alba A Kuz Iryna I Sánchez-Barco Alba A Seijas-Otero Noelia N Chantada-Vázquez María Del Pilar MDP Balsa-Castro Carlos C Tomás Inmaculada I

Journal of periodontology 20240916

<h4>Background</h4>Few investigations evaluated smoking's impact on the periodontal proteome. Therefore, this study aimed to analyse the influence of tobacco on the overall periodontal proteome and the differential expression of gingival crevicular fluid (GCF) proteins using sequential window acquisition of all theoretical mass spectra (SWATH-MS).<h4>Methods</h4>GCF samples were collected from 40 periodontitis subjects (stages III-IV). These were separated based on smoking status into smokers (1 ...[more]

PMID: 39282712

Similar Datasets

Project description:Chronic lymphocytic leukaemia (CLL) is renowned for its variable clinical course and response to therapy, suggesting a role for precision medicine. However, the molecular basis of CLL variability remains incompletely understood. Recent developments in data independent acquisition (DIA) -MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical fragments), provide an opportunity to study the pathophysiology of CLL at the proteome level. This report describes the sample replication and data handling requirements for SWATH-MS analysis of clinical samples. A CLL-specific spectral library compromising over 1,500,000 spectra with digital information for over 150,000 peptides has been generated to enable the quantification of up to 7736 proteins. To assess the reproducibility of the assay, SWATH-MS analysis was performed on 6 cryopreserved CLL patient samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins (<1% FDR) across 54 SWATH-MS acquisitions. These analyses showed that SWATH-MS is a highly reproducible technique. However, replicate sample preparations on different days was identified as the main source of variation. To overcome the effect of variation between sample preparation batches, different computational approaches for batch correction were tested. All approaches successfully removed technical variability whilst retaining proteomic differences between clinical subgroups. Functional enrichment analysis of proteins associated to IGHV mutational status highlighted the importance of metabolic remodelling in the biology of CLL and overlapped significantly with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was developed. This approach could be used to drive the design of future CLL SWATH-MS studies. These fundamental requirements for DIA approaches should be widely applicable to other clinical proteomics studies.

			Action	DRS
	GCF_H01.wiff	Wiff
	GCF_H01.wiff.scan	Wiff
	GCF_H02.wiff	Wiff
	GCF_H02.wiff.scan	Wiff
	GCF_H03.wiff	Wiff