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PXD000420

PXD000420 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleHuman alveolar bone and dental cementum LC-MSMS
DescriptionFirst 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.
HostingRepositoryPRIDE
AnnounceDate2013-09-09
AnnouncementXMLSubmission_2013-09-09_06:50:37.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterCristiane R. Salmon
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListCarbamidomethyl; Oxidation: Methionine; phosphorylated residue
InstrumentLTQ FT
Dataset History
RevisionDatetimeStatusChangeLog Entry
02013-08-16 02:30:38ID requested
12013-09-09 06:20:31announced
12014-07-25 01:34:26announced
22013-09-09 06:50:37announcedAdd reference
Publication List
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]
Keyword List
submitter keyword: Human, alveolar bone, dental cementum, LC-MSMS
Contact List
Cristiane R. Salmon
contact affiliationDepartment of Prosthodontics and Periodontics
contact emailcris.r.salmon@gmail.com
Full Dataset Link List
Dataset FTP location