Dataset Information

Human alveolar bone and dental cementum LC-MSMS

ABSTRACT: First report of proteomic composition of human matched-samples (n=7) of alveolar bone (AB) and dental cementum (DC). Bone samples were harvested from tooth extraction sites, whereas DC samples were obtained from the apical root portion of extracted third molars. Samples were denatured, followed by protein extraction reduction, alkylation and digestion for analysis by nanoAcquity HPLC system and LTQ-FT Ultra. Peak lists (msf) were generated from the raw data files using Proteome Discover version 1.3 (Thermo Fisher Scientific) with Sequest search engine and searched against Human International Protein Database, version 3.86 (91,522 sequences; 36,630,302 residues, release July 2011) with carbamidomethylation (+57.021 Da) as fixed modifications; oxidation of methionine (+ 15.995 Da); phosphorylation of serine, threonine, and tyrosine (+79.966 Da) as variable modifications; one trypsin missed cleavage and a tolerance of 10 ppm for precursor and 1 Da for fragment ions. For protein quantification, the data files were analyzed in Scaffold Q+ (version 3.3.1, Proteome Software, Inc., Portland, OR, USA) and the quantitative value (normalized spectral counts) was obtained with the protein thresholds established at a minimum 90.0% probability and at least 1 peptide with thresholds set up to minimum 60.0% probability and filtered using XCorr cutoffs (+1 > 1.8, +2 > 2.2, +3 > 2.5, and +4 > 3.5) to have less than 1% FDR. Only peptides with a minimum of five amino acid residues which showed significant threshold (p<0.05) in Sequest-based score were considered as a product of peptide cleavage. The peptide was considered unique when it differed in at least 1 amino acid residue; covalently modified peptides, including N- or C-terminal elongation (i.e. missed cleavages) were counted as unique, and different charge states of the same peptide and modifications were not counted as unique.

INSTRUMENT(S): LTQ FT

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Cristiane R. Salmon

LAB HEAD: Cristiane R. Salmon

PROVIDER: PXD000420 | Pride | 2013-09-09

REPOSITORIES: Pride

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Proteomic analysis of human dental cementum and alveolar bone.

Salmon Cristiane R CR Tomazela Daniela M DM Ruiz Karina Gonzales Silvério KG Foster Brian L BL Paes Leme Adriana Franco AF Sallum Enilson Antonio EA Somerman Martha J MJ Nociti Francisco H FH

Journal of proteomics 20130902

Dental cementum (DC) is a bone-like tissue covering the tooth root and responsible for attaching the tooth to the alveolar bone (AB) via the periodontal ligament (PDL). Studies have unsuccessfully tried to identify factors specific to DC versus AB, in an effort to better understand DC development and regeneration. The present study aimed to use matched human DC and AB samples (n=7) to generate their proteomes for comparative analysis. Bone samples were harvested from tooth extraction sites, wher ...[more]

PMID: 24007660

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			Action	DRS
	APCLD_bone_REP1.RAW	Raw
	APCLD_bone_REP1.msf	Msf
	APCLD_bone_REP2.RAW	Raw
	APCLD_bone_REP2.msf	Msf
	APCLD_bone_REP3.RAW	Raw