PXD043901

PXD043901 is an original dataset announced via ProteomeXchange.

Title	Probing the Salivary Proteome for Prognostic Biomarkers in Response to Non-Surgical Management of Periodontitis
Description	This prospective study aimed to investigate salivary proteome changes in periodontitis patients in response to treatment. Ten systemically healthy, non-smokers with stage III, grade C periodontitis (32-43yrs, F:M:5:5) underwent non-surgical periodontal treatment. Saliva (n=30) was collected pre- (T0), and one (T1) and six (T6) month post-treatment. Whole-mouth plaque (PI) and gingival index (GI), probing depth (PD), bleeding on probing (BOP) and clinical attachment loss (CAL) were measured. The saliva proteome was investigated by label-free quantitative proteomics. Normalized protein intensities were measured and protein changes modeled over time (linear model) with significant protein regulation considered at false discovery rate (FDR)<0.05. Treatment significantly reduced PI, GI, BOP, percentages of sites with PD≥5mm and PD≥5mm+BOP (T1vsT0 and T6vsT0), PD and CAL (T6vsT0). Overall, 1713 proteins (5927 peptides) were identified. Following analysis, considering proteins quantified by ≥2 peptides, resulted in 878 distinct proteins. At T1, 80 (T1vsT0:60↑:20↓), and at T6, 118 human proteins (T6vsT0:67↑:51↓) were regulated. Top-regulated disease categories were shared between T1vsT0 and T6vsT0, with highest activity patterns for ‘cellular movement’. The post-treatment proteome (T6vsT1) remained stable. Periodontal treatment reduced clinical disease parameters and these changes were reflected in the salivary proteome.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:44:14.680.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Angelika Silbereisen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-19 04:04:42	ID requested
1	2024-06-10 04:02:32	announced
⏵ 2	2024-10-22 06:44:15	announced	2024-10-22: Updated project metadata.

10.1111/jcpe.13990;

Silbereisen A, Bao K, Wolski W, Nanni P, Kunz L, Afacan B, Emingil G, Bostanci N, Probing the salivary proteome for prognostic biomarkers in response to non-surgical periodontal therapy. J Clin Periodontol, 52(1):56-67(2025) [pubmed]

submitter keyword: label-free quantitative proteomics, periodontal treatment,biomarkers, saliva, periodontitis

Nagihan Bostanci
contact affiliation	Section of Oral Health and Periodontology, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
contact email	nagihan.bostanci@ki.se
lab head
Angelika Silbereisen
contact affiliation	Karolinska Institutet
contact email	angelika.silbereisen@ki.se
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD043901

PRIDE project URI

• PRIDE
  1. PXD043901
     1. Label: PRIDE project
     2. Name: Probing the Salivary Proteome for Prognostic Biomarkers in Response to Non-Surgical Management of Periodontitis