PXD000420-2

PXD000420 is an original dataset announced via ProteomeXchange.

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.
HostingRepository	PRIDE
AnnounceDate	2013-09-09
AnnouncementXML	Submission_2013-09-09_06:50:37.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cristiane R. Salmon
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Carbamidomethyl; Oxidation: Methionine; phosphorylated residue
Instrument	LTQ FT

Revision	Datetime	Status	ChangeLog Entry
0	2013-08-16 02:30:38	ID requested
1	2013-09-09 06:20:31	announced
1	2014-07-25 01:34:26	announced
⏵ 2	2013-09-09 06:50:37	announced	Add reference
3	2024-10-22 04:18:59	announced	2024-10-22: Updated project metadata.

Salmon CR, Tomazela DM, Ruiz KG, Foster BL, Paes Leme AF, Sallum EA, Somerman MJ, Nociti FH, Proteomic analysis of human dental cementum and alveolar bone. J Proteomics, 91():544-55(2013) [pubmed]

submitter keyword: Human, alveolar bone, dental cementum, LC-MSMS

Cristiane R. Salmon
contact affiliation	Department of Prosthodontics and Periodontics
contact email	cris.r.salmon@gmail.com

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