Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/umedacementry.sdrf.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/README_umedacementry.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/mqpar_2_final.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/mqpar_1_OSSD.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/4_E_uc06_08_B308_R501_8_20240528.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/11_Blank_S.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/7_P_uc06_07_B313_R506_1_20240528.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/18_uc02_03_P.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/13_uc02_01_S.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/1_P_Blank_20240528.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/8_E_uc06_07_B313_R506_1_20240528.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/19_uc02_04_S.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/15_uc02_02_S.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/12_Blank_P.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/2_E_Blank_20240528.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/10_E_uc06_06_B318_R518_1_20240528.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/16_uc02_02_P.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/5_P_uc06_09_B312_R505_1_20240528.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/9_P_uc06_06_B318_R518_1_20240528.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/20_uc02_04_P.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/3_P_uc06_08_B308_R501_8_20240528.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/6_E_uc06_09_B312_R505_1_20240528.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/14_uc02_01_P.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/17_uc02_03_S.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/merged_umeda_dedupli0909re.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/OSSD-database-V1.0-20191117.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/1_OSSD_results.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075594/2_final_results.zipprimaryOK200tsuta16@gmail.comYoko Uchida-FukuharaData-dependent acquisitionMass Spectrometrydental calculusPalaeoproteomics; dental calculus; premodern japanPalaeoproteomicspremodern japanhttps://www.ebi.ac.uk/pride/archive/projects/PXD075594Supragingival dental calculus was collected from teeth using a sterilized dental explorer. Dental calculus from each individual was collected separately into a 1.5 mL Protein LoBind tube. All laboratory procedures were conducted in a clean laboratory dedicated to ancient biomolecular analyses at the Graduate University for Advanced Studies (SOKENDAI). Protein extraction followed the EDTA-based Tryps-IN protocol for ancient protein analysis (Jensen et al., 2023). The mass of dental calculus used for protein extraction was less than 10 mg for all samples. Dental calculus samples were decalcified using EDTA. The supernatant obtained after decalcification was collected as the EDTA fraction, while the remaining material constituted the pellet fraction. The pellet fractions were washed three times with 100 μL of 50 mM Tris buffer. Protein concentrations of both pellet and EDTA fractions were measured using the Bradford assay. Based on the measured concentrations, approximately 20 μg of protein was used from each fraction for downstream analysis. Protein digestion was performed using two proteases, trypsin and Lys-C. Peptides were purified using in-house StageTips containing two stacked layers of C18 membranes. Purified peptides were analyzed by liquid chromatography–tandem mass spectrometry (LC–MS/MS) using an Orbitrap Q Exactive Plus mass spectrometer.PrideNot availableLC–MS/MS data were first screened using the Oral Signature Screening Database (OSSD) v1.0. Raw LC–MS/MS data were then analyzed using a two-step database search strategy. First, open searches were performed using pFind3 against the databases.Proteins identified with at least two peptides were compiled to generate a customized integrated database.Second, raw files were searched against this customized database using MaxQuant (version 2.6.3.0). Protein groups were considered present only if they were identified with ≥2 unique and razor peptides at a 1.0% false discovery rate. The MaxQuant parameters for post-translational modifications were carbamidomethylation for fixed modification and oxidation (M), deamidation (N, Q), hydroxyproline, and pyroglutamic acid for variable modifications (up to five per peptide). Digestion efficiency was selected as “Specific” with a maximum of 2 missed cleavages for protease-digested samples.ProteomicsTakumi TsutayaPARTIALKyushu University; Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies (SOKENDAI)Homo Sapiens (human)10.1537/ASE.260519yok.uchifukuhara423@gmail.comIntegrative Evolutionary Science, Graduate Institute for Advanced Studies, The Graduate University for Advanced Studies (SOKENDAI)JapanfalseProteomic analysis of dental calculus from Edo-period individuals excavated from the Umeda cemetery, Osaka, JapanFood systems is an analytical framework developed in agricultural economics that encompasses the entire process from food production, processing, distribution, preparation, to consumption. In archaeology, the distinction between food supply, which indicates the presence of food resources within a region, and accessibility, which reflects the extent to which individuals could actually obtain these resources, potentially enables a more nuanced reconstruction of past human diets. In this study, we utilised this food system framework to investigate the accessibility of food items for commoners in premodern Osaka, a logistical hub with a diverse food supply. Carbon and nitrogen stable isotope analysis of bone collagen and palaeoproteomic analysis of dental calculus were performed for eight skeletal individuals from the Osaka Ofukacho site. The stable isotope ratios were within the previously reported ranges for premodern commoners in Japan. A total of 38 dietary proteins across 17 taxa were identified in the calculus. The identified food items included Pagrus major, which was an economically high-grade fish, Salmonidae, which was traded over long distances, the meat of terrestrial mammals, which were publicly avoided during this period, and cottonseed, which was possibly used as an edible oil. These findings reflect high accessibility to diverse food items even among commoners, which was maintained by the well-developed transport network of premodern Osaka. These results emphasize the pivotal role of commoners in the development of Japan’s culinary culture.2026-07-312026-03-13PXD075594NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:150475NEWT:9417NEWT:347515NEWT:1216979NEWT:307972NEWT:32046NEWT:544496NEWT:5180NEWT:256737NEWT:115104NEWT:1081927NEWT:67825NEWT:13076NEWT:1249668NEWT:376741NEWT:317NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:876138NEWT:4081NEWT:554NEWT:98334NEWT:237561NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:746360NEWT:6239NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:8782NEWT:1000589NEWT:1902NEWT:85962NEWT:160488NEWT:28104NEWT:317447NEWT:7955NCBITaxon:2NEWT:985076NEWT:7959NEWT:2261NEWT:4565NEWT:1264690NEWT:6192NEWT:28532NCBITaxon:38727NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:216595NEWT:243230NEWT:8355NEWT:931281NEWT:7029NEWT:1283300NEWT:334747NEWT:61235NCBITaxon:79824NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NCBITaxon:6191NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:83332NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:44685NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:1123869NEWT:7370NEWT:83906NEWT:6282NEWT:1134506NEWT:575584NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:1182590NEWT:8726NEWT:10090NEWT:935293NEWT:749200NEWT:4120NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:632957NEWT:373995NEWT:5689NEWT:544404NEWT:3702NEWT:129249NEWT:8839NEWT:4232NEWT:990119NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:106592NEWT:1117957NEWT:9913NEWT:1432138NEWT:10312NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:180066NEWT:67767NEWT:46835NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:5664NEWT:2157NEWT:146479NEWT:10306NEWT:1911079NEWT:8022NEWT:145943NEWT:3635NEWT:5811NEWT:235443NEWT:1480154NEWT:1274414NEWT:59202NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:1147787NEWT:9606NEWT:367830NEWT:157295NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:1450511NEWT:470NEWT:84023NEWT:9838NCBITaxon:9615NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:33952NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:9940NEWT:573NEWT:9031NEWT:1274420NEWT:70910000-0002-3697-1162