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Lenz"],"technology_type":["Mass Spectrometry","diaPASEF","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Dental erosion","Salivary pellicle","Smoker","Proteome","Saliva"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD055361"],"tissue":["Saliva"],"sample_protocol":["Salivary pellicle formation On days 2 and 3, splints were inserted in the oral cavity after the collection of saliva samples. Splints were either loaded with eight resin specimens (day 2) or enamel and dentin specimens (day 3). Enamel and dentin specimens (each n=4) were randomly selected and alternatingly loaded into the splints. After 120 min, specimens were removed from the splints, rinsed with deionized water, and transferred into Eppendorf cups. Salivary pellicle sample preparation for proteome analysis The salivary pellicle formed on the resin specimens was dissolved in 375 µL radioimmunoprecipitation assay buffer (R0278, Sigma-Aldrich) mixed with tris(hydroxymethyl)aminomethane hydrochloride (ratio 1:1). Cups were placed on a vibrating plate at 4°C overnight followed by ultrasonication for 5 min in ice water. Afterwards, samples were pooled, transferred into Eppendorf cups, and stored at -20°C. Due to the overall low protein concentration in salivary pellicle samples, proteins were concentrated by acetone precipitation. Briefly, sample aliquots were added to a 4x volume of ice-cold acetone and kept at -20°C overnight. Precipitates were pelleted by centrifugation in a benchtop centrifuge (13,300 rpm, 30 min, 4°C), the supernatant removed, and the pellets washed with ice-cold ACN/water (80:20, v/v). Pellets were then resuspended in 25 µl 2 % sodium dodecyl sulfate (SDS) buffer in 100mM aqueous HEPES (pH 8.0) on ice. Following protein determination by a BCA assay (Pierce BCA Protein Assay Kit, Thermo Fisher Scientific), 15 µg aliquots of protein were processed as outlined for saliva above. Mass spectrometry-based proteome profiling by data-independent acquisition mass spectrometry (DIA MS) Proteome profiling was performed based on 250 saliva and 50 salivary pellicle samples. Two technical replicates per biological replicate were acquired. Samples were analyzed on a nanoflow chromatography system (nanoRSLC, Thermo Fisher Scientific) hyphenated to a hybrid timed ion mobility-quadrupole-time of flight mass spectrometer (timsTOF Pro 2, Bruker). In brief, 150 ng equivalents of peptides were enriched on a reversed-phase C18 trapping column (0.3 cm × 300 µm, Thermo Fisher Scientific) and separated on a reversed-phase C18 column with an integrated CaptiveSpray Emitter (PepSep MAX, 15 cm × 150 µm, Bruker) using a 13 min linear gradient of 5-35 % ACN / 0.1 % FA (v:v) at 850 nl min-1 and a column temperature of 50°C. Data-independent acquisition (DIA) analysis was performed in diaPASEF mode using an 8×2 variable size window acquisition method from m/z 400 to 1,200 to include the 2+/3+/4+ population in the m/z-ion mobility plane. The collision energy was ramped linearly as a function of the mobility from 59 eV at 1/K0=1.5 Vs cm-2 to 20 eV at 1/K0=0.7 Vs cm-2."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Protein identification was achieved using the Pulsar algorithm in Spectronaut Software (version 19.1, Biognosys) using default settings against 50 randomly selected DIA files. Data were searched against the UniProtKB Homo sapiens reference proteome (revision 08-2023) augmented with a set of 51 known common laboratory contaminants at default settings. The proteomes of 15 commonly observed bacterial species from the oral microbiome were included to account for bacterial contributions. For quantitation, up to the 6 most abundant fragment ion traces per peptide, and up to the 10 most abundant peptides per protein were integrated and summed up to provide protein area values. Mass and retention time calibration as well as the corresponding extraction tolerances were dynamically determined. Both identification and quantification results were trimmed to a false discovery rate (FDR) of 1 % using a forward-and-reverse decoy database strategy."],"omics_type":["Proteomics"],"labhead":["Christof Lenz"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Core Facility Proteomics, Department of Clinical Chemistry, Universitry Medical Center Göttingen, Germany"],"species":["Homo Sapiens (human)"],"publication":["10.1016/J.JDENT.2026.106517"],"submitter_mail":["christof.lenz@mpibpc.mpg.de"],"submitter_affiliation":["Max Planck Institute for Biophysical Chemistry"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"Saliva and salivary pellicle composition and proteomic profile in smokers vs. non-smokers and its effect on dental erosion (pellicle data)","description":"Aim: This study aimed to analyse the salivary composition and proteomic profile of saliva and the salivary pellicle in smokers compared to non-smokers, and to examine potential differences of the erosion-protective capacity of the salivary pellicle. Materials and Methods: Twenty-five smokers and 25 non-smokers were included. Unstimulated and stimulated saliva samples were analysed regarding flow rate, pH, buffer capacity, calcium, phosphate, fluoride, and protein content. Salivary pellicles were formed intraorally on resin specimens (n=8). Saliva and salivary pellicle samples were used for data-independent acquisition mass spectrometry. Proteins were identified using the UniProtKB Homo sapiens reference proteome. For the saliva samples, proteomes of 15 commonly observed bacterial species from the oral microbiome were also included. In an in situ experiment, the participants used intraoral splints loaded with bovine enamel and dentin specimens for 120 min (each n=4). Pellicle-covered specimens were extraorally eroded (1mL HCl, pH 2.3, 60 s). Calcium release into the acid was determined photometrically and compared to pellicle-free specimens (control, each n=30). Differentially abundant proteins between smokers and non-smokers were identified using t tests (≥1.5-fold differences and padj.≤0.05). In addition, a pathway enrichment analysis of the associated genes was performed (KEGG, Reactome). Statistical analysis of the salivary samples was performed by one-way ANOVAs followed by pairwise t tests, t tests, Pearson correlations, and multiple linear regression analysis (p<0.05).  Results: Except for phosphate in stimulated saliva (smokers: 5.5±2.1 mmol/L, non-smokers: 3.6±1.0 mmol/L; padj.=0.003), salivary parameters were not significantly different between smokers and non-smokers. For both saliva and the salivary pellicle, gene set enrichment analysis indicated common biological themes of genes enriched in either the smokers or the non-smokers. Despite the different proteomic profiles, the erosion-protective capacity of the salivary pellicle of smokers and non-smokers did not differ, and calcium release was not correlated with or predicted by the assessed salivary parameters. The salivary pellicle had a significant erosion-protective effect in enamel compared to the control (41.4±6.3 nmol/mm2), but no differences between smokers (33.2±10.6 nmol/mm2, padj.=0.001 ) and non-smokers (32.7±8.6 nmol/mm2, padj.=0.001) were found. Calcium release did not correlate with or was predicted by the assessed salivary parameters. Conclusion: The proteomic profiles of both unstimulated and stimulated saliva and the salivary pellicle differ between smokers and non-smokers. Evidence for different activity of different biological metabolic pathways such as carcinogesis exists. However, there was no detectable influence on the erosion-protective capacity of the pellicle.","dates":{"publication":"2026-06-30","submission":"2024-08-29"},"accession":"PXD055361","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:1131","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:1334565","NEWT:625351","NEWT:258594","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:6819","NEWT:475174","NEWT:111205","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:1590","NEWT:10034","NEWT:33114","NEWT:1596","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:3767","NEWT:1589","NEWT:135622","NEWT:672127","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:1582","NEWT:1584","NEWT:36630","NEWT:1585","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:49928","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:55350","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:410658","NEWT:5516","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:1310173","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:150808","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NCBITaxon:37162","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10891","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:926571","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2499525","NEWT:2853422","NEWT:487","NEWT:1538553","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:237610","NEWT:95486","EFO:0001352","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:987059","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:1509","NEWT:491","NEWT:460523","NEWT:45954","NEWT:235443","NEWT:1579","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:1640278","NEWT:472","NEWT:940825","NEWT:29459","NEWT:529507","NEWT:1071661","NEWT:28128","NEWT:470","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:11723","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:1290454","NEWT:906914","NEWT:28141","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:3728","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:548","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:2126348","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:207340","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:33941","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:771870","NEWT:51338","NEWT:9995","NEWT:575412","NEWT:28112","NEWT:49012","NEWT:6493","NEWT:10832","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:595495","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:1613","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:353153","NEWT:227377","NEWT:1774284","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:74426","NEWT:443906","NE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