Project PXD000420

Summary

Title

Human alveolar bone and dental cementum LC-MSMS

Description

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.

Sample Processing Protocol

See details in reference PMID : 24007660

Data Processing Protocol

See details in reference PMID : 24007660

Contact

Cristiane R. Salmon, Department of Prosthodontics and Periodontics

Submission Date

16/08/2013

Publication Date

09/09/2013

Tissue

Not available

Instrument

LTQ FT

Software

Not available

Quantification

Not available

Experiment Type

Bottom-up proteomics

Publication

    Salmon CR, Tomazela DM, Ruiz KG, Foster BL, Leme AF, Sallum EA, Somerman MJ, Nociti FH Jr; Proteomic analysis of human dental cementum and alveolar bone., J Proteomics, 2013 Sep 2, PubMed(s) : 24007660