PXD007535

PXD007535 is an original dataset announced via ProteomeXchange.

Title	LFQ and SRM proteome analysis of Saliva reveals transition signatures from health to periodontal disease
Description	Phase 1: The whole saliva samples were obtained from 66 systemically healthy subjects consisting of patients with chronic periodontitis (CP), generalized aggressive periodontitis (G-AgP), gingivitis and individuals with periodontal health. The use of humans for study satisfied the requirements of the Ege University Institutional Review Board (Ethics number 16-12.1/16) and and was conducted in accordance with the guidelines of the World Medical Association Declaration of Helsinki. It is confirmed that this cross-sectional study conforms to STROBE guidelines for observational studies. Complete medical and dental histories were taken from all participants. Systemic exclusion criteria were the presence of cardiovascular and respiratory diseases, diabetes mellitus, HIV infection, systemic inflammatory conditions or non-plaque-induced oral inflammatory conditions, immunosuppressive chemotherapy, and current pregnancy or lactation. Smoking status was also recorded. None of the patients had taken medication such as antibiotics or anti-inflammatory drugs that could affect their periodontal status for at least 6 months before the study. Patients eligible for the study returned to the clinic for clinical measurement screening one-week after being pre-screened. Before being enrolled in the study, participants provided written and informed consent to use their saliva samples and individual data for scientific purposes. The clinical periodontal indices including probing depth (PPD), clinical attachment level (CAL), plaque index (PI) and bleeding on probing (BOP) were recorded by a manual periodontal probe by a trained and calibrated examiner (V.O.O). The extent and severity of alveolar bone support were evaluated radiographically in each patient. The participants were classified into four groups based on their periodontal conditions according to the criteria proposed by the 1999 International Workshop for a Classification of Periodontal Diseases and Conditions (REF). Generalized Aggressive Periodontitis (G-AgP): The G-AgP group included 17 patients with ≥16 teeth. The patients had a non- contributory medical history and demonstrated with an early age of clinical manifestations with a generalized pattern of rapid attachment loss and bone destruction. These individuals had minimum of CAL ≥ 5 mm and PD ≥ 6 mm on eight or more teeth; at least three of these were other than central incisors or first molars. Radiographic bone loss was above ≥ 30 % of root length affecting ≥3 permanent teeth other than first molars and incisors. Generalized Chronic Periodontitis (CP): The CP group included 17 patients with severe generalized chronic periodontitis. These individuals had a minimum four non-adjacent teeth with sites with CAL ≥ 5 mm and PPD ≥ 6 mm, and ≥50 % alveolar bone loss in at least two quadrants which was commensurate with the amount of plaque accumulation. Phase 2: We aimed to develop SRM-based workflow for detecting and quantitating the relative abundance of the candidate proteins in an independent saliva cohort . 82 subjects (48 females and 34 males; age range 24-59 years) were recruited for the study at the Department of Periodontology, School of Dentistry, Adnan Menderes University, Aydın, Turkey. Ethical clearance was obtained from the Ethics Committee of the School of Medicine, Ege University with the protocol number ((Ethics number 70198063-050.06.04). Each participant gave written and verbal informed consent after the purpose and procedures of the study were explained. A dental and medical history was compiled for all subjects as detailed in phase 1 and participants were clustered into four groups according to the criteria proposed by the 1999 International Workshop for a Classification of Periodontal Diseases and Conditions as detailed at Phase 1
HostingRepository	PRIDE
AnnounceDate	2018-04-10
AnnouncementXML	Submission_2018-04-10_01:30:22.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jonas Grossmann
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q TRAP; LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2017-08-23 00:14:06	ID requested
⏵ 1	2018-04-10 01:30:23	announced

Bostanci N, Selevsek N, Wolski W, Grossmann J, Bao K, Wahlander A, Trachsel C, Schlapbach R, Ö, zt, ü, rk V Ö, Afacan B, Emingil G, Belibasakis GN, Targeted Proteomics Guided by Label-free Quantitative Proteome Analysis in Saliva Reveal Transition Signatures from Health to Periodontal Disease. Mol Cell Proteomics, 17(7):1392-1409(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: SRM, LFQ, data integration, LC-MS/MS

Nagihan Bostanci
contact affiliation	Department of Dental Medicine, Karolinska Institute Alfred Nobels Alle 8, 14104, Huddinge, Sweden
contact email	nagihan.bostanci@ki.se
lab head
Jonas Grossmann
contact affiliation	Functional Genomics Center Zurich (UZH/ETHZ)
contact email	jg@fgcz.ethz.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD007535
     1. Label: PRIDE project
     2. Name: LFQ and SRM proteome analysis of Saliva reveals transition signatures from health to periodontal disease