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Wang"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":["Not available"],"submitter_keywords":["Lc ms/ms","Archaic human","Bone"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD073112"],"tissue":["Bone","Tooth"],"sample_protocol":["The conventional acid insoluble approach was conducted on 100-200mg of bone powders of three hominin bones. And the protein was digested with trypsin. Additional extraction was conducted on BFD767 and three fractions were collected, including “acid soluble fraction 3KD”, “acid insoluble fraction trypsin” and “acid insoluble fraction elastase” fractions. The first two fractions were digested with trypsin and the last fraction was digested with elastase. For two teeth, an acid etch approach was conducted on the enamel, resulting in a “acid etch fraction”. No digestion was performed on this fraction. Around 30 mg of dentine powder was drilled from each tooth for protein extraction, and three dentine fractions were collected, including “acid soluble fraction 3KD”, “acid insoluble fraction trypsin 1” and “acid insoluble fraction trypsin 2”. The dentine fractions were digested by trypsin.All the (digested) peptide mixture was desalted with Pierce C18 Pipette Tips. The eluted peptides was dried up for the LC MS/MS analysis. An EASY-nanoLC was used for liquid chromatography, with an Exploris 480 or an Orbitrap Fusion Lumos for shotgun proteomics mass spectrometry, in HCD mode."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["All the raw datafiles from the hominin samples as well as the negative control samples were searched using PEAKS Online (v. 12) . Raw files from bone or dentine were searched against a custom “Hominidae bone database”, which is composed of the entire human proteome (downloaded from Uniprot, one protein sequence per gene, 20,575 entries) with the addition of the common bone and dentine protein sequences translated from four ancient human individuals (Denisova 3, Altai Neanderthal, Vindija19, Ust’-Ishim). The published specific sequences for several archaic individuals were also included in the database. Peptide de novo, PEAKS DB, PTM and SPIDER, were performed with the following parameters: parent ion tolerance of 10 ppm, fragment ion mass tolerance of 0.05 Da, enzyme specificity setting to SemiTryptic, maximal missed cleavages of two, maximal modification number of six for each peptide, and the variable modifications including Deamidation (NQ), Oxidation (M), Hydroxylation (P), Pyro-glu from E and Pyro-glu from Q. Peptide length range was set to 8-45. The false discovery rate (FDR) was set at 1% (Peptide level), and protein scores were filtered with -10lgP ≥ 20 and ALC (%) ≥ 50 (de novo only).  Raw files from enamel fractions were searched against the custom-built “Homonidae enamel database” for each tooth. The parameters were set as follows: precursor ion mass tolerance of 10 ppm, fragment ion mass tolerance of 0.05 Da, enzyme specificity of “unspecific”, variable modifications including Deamidation (NQ), Oxidation (M), Hydroxylation (P), Phosphorylation (STY), Pyro-Glu from E, and Pyro-Glu from Q, maximum modifications per peptide of three, and peptide length range of 6-45. False discovery rate (FDR) was set to 1% at the spectral level and protein scores were filtered with -10lgP ≥ 20 and ALC (%) ≥ 50 (de novo only)."],"omics_type":["Proteomics"],"labhead":["Qiaomei Fu"],"instrument_platform":[""],"labhead_affiliation":["Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences"],"submission_type":["COMPLETE"],"species":["Homo Sapiens (human)"],"submitter_mail":["wangxiao@ivpp.ac.cn"],"publication":["Not available"],"submitter_affiliation":["CAS"],"submitter_country":["China"],"doi":["10.6019/PXD073112"],"additional_accession":[]},"is_claimable":false,"name":"Ancient proteins identify Denisovan radius and teeth from Southwest China","description":"Two parietal and one radius fragmentary hominin bones were identified from a systematical morphological prescreening of ~60,000 mammalian bone fragments and subsequent ZooMS analysis at Bianfu Cave in Yunan, Southwest China. Combined with two hominin teeth discovered during the excavation, all the five hominin specimens were attributed to Denisovans though shotgun palaeoproteomic analyses, SAP assignment and phylogenetic analyses.","dates":{"publication":"2026-07-24","submission":"2026-01-15"},"accession":"PXD073112","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:35554","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:1129","NEWT:55153","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:96731","NEWT:383379","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:3112","NEWT:4442","NEWT:192875","NEWT:1214915","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:108061","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:931281","NEWT:658457","NEWT:77133","NEWT:295358","NEWT:145481","NCBITaxon:79824","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:44447","NEWT:5759","NEWT:1736231","NEWT:1392","NEWT:498217","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:633149","NEWT:10239","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:935293","NEWT:375146","NEWT:118698","NEWT:263","NEWT:118696","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:3702","NEWT:243277","NEWT:7067","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:33548","NEWT:274","NEWT:408172","NEWT:408170","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:1436733","NEWT:460519","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:9483","NEWT:1513458","NCBITaxon:40559","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NCBITaxon:4932","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:983964","NEWT:118499","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:2014887","NEWT:33952","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:272634","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:141262","NEWT:108931","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:303","NEWT:267872","NEWT:7111","NEWT:347515","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:4090","NEWT:4092","NEWT:9541","NEWT:4093","NEWT:4096","NEWT:185579","NEWT:941442","NEWT:13076","NEWT:7108","NEWT:40479","NEWT:4076","NEWT:317","NEWT:1006581","NEWT:885318","NEWT:39488","NEWT:550","NEWT:4081","NEWT:273068","NEWT:554","NEWT:98334","NEWT:451516","NEWT:36185","NEWT:1225786","NEWT:7574","NEWT:1715256","NEWT:30640","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:28112","NEWT:114155","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:1268063","NEWT:1263854","NEWT:118503","NEWT:2059687","NEWT:160488","NEWT:28104","NEWT:407821","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7159","NEWT:28532","NEWT:353152","NEWT:8496","NEWT:27448","NEWT:1194669","NEWT:51329","NEWT:243230","NEWT:1080772","NEWT:519","NEWT:8479","NEWT:8485","NEWT:6063","NEWT:49240","NEWT:104395","NEWT:6289","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:469008","NEWT:256318","NEWT:9321","NEWT:206411","NCBITaxon:6191","NEWT:596153","NEWT:229533","NEWT:1836","NEWT:80863","NEWT:105231","NEWT:52638","NEWT:57075","NEWT:4097","NEWT:884204","NEWT:9785","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NCBITaxon:780","NCBITaxon:1502","NEWT:6282","NEWT:1134506","NEWT:38783","NEWT:4006","NEWT:6426","NCBITaxon:5476","NEWT:6669","NEWT:9935","NEWT:89453","NEWT:287889","NEWT:51515","NEWT:588596","NEWT:51511","NEWT:8845","NEWT:92867","NEWT:92866","NEWT:5334","NEWT:51750","NEWT:202950","NEWT:382352","NEWT:413071","NEWT:632957","NEWT:9925","NEWT:89462","NEWT:8839","NEWT:90690","NEWT:4232","NEWT:2758385","NEWT:11298","NEWT:171101","NEWT:714","NEWT:421932","NEWT:312017","NEWT:196627","NEWT:200308","NEWT:200302","NEWT:870435","NEWT:284593","NEWT:100392","NEWT:5315","NEWT:9913","NEWT:265872","NEWT:105841","NEWT:337330","NEWT:2666255","NEWT:2285",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