Browse
Submit Data
Databases
API
Help

Dataset Information

307 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Salivary proteomics of sP and sNP rats

ABSTRACT: Sardinian alcohol-preferring (sP) and Sardinina alcohol-non preferring (sNP) rats have been selectively bred for opposite alcohol preference and consumption. The project proposed to identify salivary markers distinguishing the two rat lines possibly correlated to alcohol preference, by a proteomic approach.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Saliva

DISEASE(S): Disease Free

SUBMITTER: Tiziana Cabras

LAB HEAD: Tiziana Cabras

PROVIDER: PXD006997 | Pride | 2017-11-03

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ANNOTATED-SPECTRA_Bottom-up_proteome_discoverer.7z	Other
	ANNOTATED_SPECTRA_Top-down_proteome_discoverer.7z	Other
	GRP-B_EndoproteinaseV8_peptides_bottom-up_manual.xlsx	Xlsx
	GRP-B_Trypsin_peptides_bottom-up_manual.xlsx	Xlsx
	GRP-B_bottom-up_GluC_Fr_02_220915.raw	Raw

Items per page:

1 - 5 of 48

Publications

Marked Differences in the Submandibular Salivary Proteome between Sardinian Alcohol-Preferring and Sardinian Alcohol-Non Preferring Rats Revealed by an Integrated Top-Down-Bottom-Up Proteomic Platform.

Cabras Tiziana T D'Alessandro Alfredo A Serrao Simone S Isola Raffaella R Iavarone Federica F Vincenzoni Federica F Colombo Giancarlo G Ekström Jörgen J Messana Irene I Castagnola Massimo M

Journal of proteome research 20171116 1

Sardinian alcohol-preferring (sP) and Sardinian alcohol-non preferring (sNP) rats have been selectively bred for opposite alcohol preference and consumption. Aiming to verify possible differences at the proteomics level between sP and sNP rats, we investigated the salivary proteome by a a liquid chromatography-mass spectrometry top-down-bottom-up integrated approach. For this purpose, submandibular saliva was collected from alcohol-naive sP and sNP rats under isoprenaline stimulation. A total of ...[more]

PMID: 29083190

Similar Datasets

Human Salivary Neutrophil Defensins (Alpha-Defensins)

Project description:In the HPLC high-resolution ESI-MS profiles of both Predominantly Antibody Deficiency syndromes subjects and healthy controls saliva samples, four proteins, with exp. monoisotopic ion [M+H]+ at 3440.54 ± 0.06 m/z, 3369.50± 0.06 m/z, 3484.51 ± 0.06 m/z and 3707.77 ± 0.06, eluting between 24.5-26.6 minutes, were detected. The monoisotopic mass values and the manual inspection of the high-resolution MS/MS spectra of the ions at [M+5H]+5 at 689.31, 675.10, 698.11 and 742.76 m/z, and of the ions at [M+4H]+4 at 843.63, 872.39 m/z allowed to establish that the four proteins were alpha defensins 1, 2, 3 and 4.

2020-01-09 | PXD012688 | Pride

Human Salivary Prolactine Inducible Protein (PIP)

Project description:In the HPLC high-resolution ESI-MS profiles of both multiple sclerosis subjects and healthy controls saliva samples three proteins, with exp. monoisotopic ion [M+H]+ at 13493.9 ± 0.2 m/z, 13696.9 ± 0.2 m/z (+203 Da, with respect to 13493.9), and 13843.1 ± 0.2 m/z (+147 Da, with respect to 13696.9) eluting between 37.8-38.2 minutes, were detected. The mass difference of 203 Da suggested that the protein with exp. monoisotopic [M+H]+ at 13696.9 ± 0.2 m/z could correspond to the N-acetylhexosamine (theor. monoisotopic ion at 203.1 m/z) derivative of the 13493.9 ± 0.2 m/z protein. On the other hand, the mass difference of 146 Da between the proteins with exp. monoisotopic [M+H]+ at 13843.1 ± 0.2 m/z and 13696.9 ± 0.2 m/z was in agreement with an additional deoxyhesose moiety (theor. monoisotopic ion at 146.1 m/z). Manual inspection of the high-resolution MS/MS spectra of the [M+10H]+10 ions at 1351.00, 1371.32 and 1386.11 m/z allowed to establish that the three proteins were different proteoforms of PIP with the N-terminal glutamine residue converted to pyro-glutamic acid and with two disulfide bonds, but not to assign the glycosylation site. The presence in the MS/MS spectra of low-molecular weight saccharide oxoniun ions at 204.087 and 138.106 m/z confirmed the presence of an N-acetylhexosamine moiety in the protein with [M+H]+ at 13696.9 ± 0.2 m/z.

2018-08-10 | PXD009440 | Pride

Top Down Proteomic analysis of Gingival Crevicular Fluid in deciduous, exfoliating and permanent teeth in children

Project description:Gingival Crevicular Fluid, a plasma-derived exudate present in the gingival crevice was collected from deciduous, exfoliating and permanent teeth from 20 children (60 samples) with the aim to characterize and quantify by a mass spectrometry based top-down proteomic approach, the peptide/proteins in the fluid and verify possible variations occurring during the exfoliating process. The results obtained confirmed the presence in Gingival Crevicular Fluid of α-Defensins 1-4, Thymosin β4 and Thymosin β10, as described in previous works and revealed the presence of other interesting peptides never described before in Gingival Crevicular Fluid, such as specific fragments of α-1-antitrypsin, α-1-antichymotrypsin, Thymosin β4 and Thymosin β10 fragments, Fibrinopeptide A, Fibrinopeptide B, S100A, LVV Hemorphin-7 (hemoglobin chain β fragment), as well as some other peptides deriving from α and β subunits of hemoglobin. Statistical analysis evidenced different levels in 5 proteins/peptides in the three groups in particular with higher level in exfoliating teeth. Our study demonstrate that an in-depth analysis of a biological fluid like Gingival Crevicular Fluid, present in small amount, can provide useful information for the understanding of different biological processes like teeth eruption.

2020-07-09 | PXD016010 | Pride

Neutrophil Defensins (Alpha-Defensins)

Project description:In the HPLC high-resolution ESI-MS profiles of Gingival Crevicular Fluid, four proteins, with exp. monoisotopic ion [M+H]+ at 3440.54 ± 0.06 m/z, 3369.50± 0.06 m/z, 3484.51 ± 0.06 m/z and 3707.77 ± 0.06, eluting between 24.5-26.6 minutes, were detected. The monoisotopic mass values and the manual inspection of the high-resolution MS/MS spectra of the ions at [M+5H]+5 at 689.31, 675.10, 698.11 and 742.76 m/z, and of the ions at [M+4H]+4 at 843.63, 872.39 m/z allowed to establish that the four proteins were alpha defensins 1, 2, 3 and 4.

2020-07-09 | PXD016049 | Pride

Human Salivary Cystatins - SALIVARY CYSTATINS: EXPLORING NEW POST-TRANSLATIONAL MODIFICATIONS AND POLYMORPHISMS BY TOP-DOWN HIGH RESOLUTION MASS SPECTROMETRY

Project description:In the present study various proteoforms of cystatin A, cystatin B, cystatin D, cystatin S, cystatin SN and cystatin SA were detected and characterized by a top-down HPLC-ESI-MS platform integrated by bottom-up strategies in the acidic soluble fraction of human saliva. The several proteoforms derive from polymorphisms of the coding sequence and post-translational modifications, typically phosphorylation, N-terminal processing, and oxidation. The protein species detected in saliva collected from healthy subjects were: (i) cystatin AT96→M and its acetylated derivative; (ii) cystatin B N-terminally acetylated and carboxymethylated at C3; (iii) N-terminally truncated cystatin D with the N-terminal Q converted to pyro-E and lacking the first 5 amino acid residues (pGlu-cystatin D Des1-5); (iv) N-terminally truncated forms of cystatin SN and SNP11→L lacking the first 4 amino acids (cystatin SN Des1-4 and cystatin SNP11→L Des1-4) and the first 7 amino acids (cystatin SN Des1-7 and cystatin SNP11→L Des1-7); (v) N-terminally truncated cystatin SA lacking the first 7 amino acids (cystatin SA Des1-7); (vi) oxidized derivatives of cystatins SN and S1 at W23 and W107.

2017-10-13 | PXD007170 | Pride

The Cystatin D Interactome Associated to Systemic Mastocytosis

Project description:he aim of the project is to characterize qualitatively and quantitatively the interaction of cystatin D in other protein partner and the formation of a complex in whole saliva of patients affected by different forms of systemic mastocytosis (SM), with and without skin involvement. The different composition of the complex could be useful to distinguish patients from healthy subject and the different forms of systemic mastocytosis. Pools of whole saliva from SM (SM-C and SM+C) patients, and from sex/age matched healthy controls were submitted to immunoprecipitation assay using cystatin D antibody followed by SDS-PAGE in reducing conditions, tryptic digestion, and nano-HPLC-high-resolution-MS/MS analysis.

2023-10-24 | PXD042567 | Pride

Genotyping of 75 individuals from the Afrikaner population of South Africa

Project description:The Afrikaner population of South Africa are the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the “Coloured" populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5%-7.2%. NB two individuals withdrew consent so this data contains only 75 individuals as compared to the 77 cited in the article.

2020-01-28 | E-MTAB-8757 | biostudies-arrayexpress

Affymetrix SNP6.0 on Ollier disease-related tumors

Project description:Mutations in the PTH1R gene were reported but these mutations are limited to a small subgroup of patients. The etiology of Ollier disease is unknown. We therefore undertook genome-wide copy number and loss of heterozygosity (LOH) analysis using Affymetrix SNP 6.0 arrays on 37 tumors of 28 Ollier patients in combination with expression array using Illumina Beadarray v3.0 for 7 tumors of 6 patients. We used Affymetrix SNP 6.0 to find out LOH and copy number alterations in Ollier tumors. To understand the genetic mechanism behind the development of enchondroma, we mainly focus on enchondromas and found alterations were validated. We used 14 enchondromas and 23 chondrosarcomas of 28 Ollier patients. We also used 30 controls (blood, saliva or frozen tissue). As controls, normal DNA derived from fresh frozen muscle tissue (n=3), peripheral blood lymphocytes (n=4) or saliva (n=4) was available for 11 Ollier patients and 3 patients with unrelated bone diseases. We used blood lymphocyte DNA from 12 healthy controls and 1 HapMap sample. We also isolated DNA from saliva for 3 of these controls to validate the use of saliva DNA in this study.

2011-08-26 | E-GEOD-22984 | biostudies-arrayexpress

Epigenome analysis of saliva samples from alcohol users

Project description:Genome wide DNA methylation profiling of saliva DNA from 197 alcohol dependent subjects. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in saliva samples. Bisulphite converted DNA were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2011-12-01 | E-GEOD-34035 | biostudies-arrayexpress

Genotyping of 327 individuals from 14 populations across the Sahel/Savannah belt that were genotyped on the Illumina H3Africa Consortium Array.

Project description:The Sahel/Savannah belt harbours diverse populations with different demographic histories and different subsistence patterns. However, populations from this large African region are notably under-represented in genomic research. To investigate the population structure and adaptation history of populations from the Sahel/Savannah space, we generated dense genome-wide genotype data of 327 individuals—comprising 14 ethnolinguistic groups, including ten previously unsampled populations. DNA samples were genotyped on the Illumina H3Africa Consortium Array (BeadChip type: H3Africa_2017_20021485_A2; designed for SNP-genotyping of 2,267,346 SNPs) at the SNP&SEQ Technology Platform, NGI/SciLifeLab Genomics (Sweden). Reference: Demographic and Selection Histories of Populations Across the Sahel/Savannah Belt. Fortes-Lima C, Tříska P, Čížková M, Podgorná E, Diallo MY, Schlebusch CM, Černý V. Molecular Biology and Evolution 2022 39(10):msac209. doi: 10.1093/molbev/msac209. PMID: 36173804 .

2022-10-31 | E-MTAB-12243 | biostudies-arrayexpress