{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077920/PR857_AS1_AllSamples_Human_GO_NoScaling_20250624.xlsx"],"Msf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077920/PR857_AS1_HOB_C.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077920/PR857_AS1_HOB_T_RR.msf"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077920/checksum.txt"],"Mzml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077920/PR857_AS1_AllSamples_Human_GO_NoScaling_20250624.mzML"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077920/PR857_AS1_HOB_C.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077920/PR857_AS1_HOB_T_RR.raw"],"Mzid":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077920/PR857_AS1_AllSamples_Human_GO_NoScaling_20250624.mzid"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077920/uniprotkb_homo_isoform_2025_05_13_concatenated.fasta"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077920/PR857_AS1_AllSamples_Human_GO_20250613.sf3"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["lucy.di_silvio@kcl.ac.uk"],"submitter":["Agata Szubska"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":[""],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD077920"],"tissue":["Osteoblast","Cell Culture"],"sample_protocol":["For decellularisation, samples were rinsed with PBS at room temperature before treatment with 0.5–1% Triton X-100 for 30 min at 37°C to disrupt cell membranes. This was followed by 2 mM ammonium hydroxide for 5 min at room temperature with gentle agitation to aid nuclear material removal. Samples were then washed 3–4 times with PBS to remove residual detergent and cellular debris, and the resulting dECM was stored in PBS at −80°C before lyophilisation.  50 µg aliquots of lyophilised human osteoblast control and decellularised extracellular matrix samples were prepared by in-solution reduction, alkylation and enzymatic digestion. Cysteine residues were reduced with dithiothreitol, alkylated with iodoacetamide to form carbamidomethyl derivatives, acetone precipitated, washed with methanol, reconstituted in TEAB and digested overnight with trypsin at 37°C. Dried peptide samples were resuspended in MS sample buffer containing 2% acetonitrile and 0.05% formic acid before LC-MS/MS analysis.  Peptides were separated by reversed-phase chromatography using a Vanquish Neo NanoLC system and a 75 µm C18 PepMap column over a 52-minute gradient of 80% acetonitrile in 0.1% formic acid at 300 nL/min. MS analysis was performed using electrospray ionisation on an Orbitrap Ascend Tribrid operating in Xcalibur v4.7. Full MS scans were acquired in the Orbitrap at 120,000 resolution over m/z 375–1500, with MS/MS fragmentation by collision-induced dissociation in the ion trap."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Raw mass spectrometry data were processed into peak list files using Proteome Discoverer v2.5 and searched using the Sequest algorithm against the UniProt Human Taxonomy database containing 51,624 entries. Database searching was performed at 1% FDR with decoy searching. Carbamidomethylation of cysteine was included as a static modification, while methionine oxidation and peptide N-terminal acetylation were included as variable modifications.  Search outputs were imported into Scaffold v5.1.2 for visualisation and manual verification. Label-free quantification was performed using peptide precursor ion intensities, with peptides grouped to generate total protein signal values for each sample. Raw protein intensity values were log₂-transformed and used to calculate fold-change values between samples. More than 1,000 proteins were identified across the sample set at high stringency."],"omics_type":["Proteomics"],"labhead":["Lucy Di Silvio"],"instrument_platform":[""],"labhead_affiliation":["Centre for Oral, Clinical and Translational Science, King's College London, London, United Kingdom"],"submission_type":["COMPLETE"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["agata.szubska@kcl.ac.uk"],"submitter_affiliation":["King's College London"],"submitter_country":["United Kingdom"],"doi":["10.6019/PXD077920"],"additional_accession":[]},"is_claimable":false,"name":"Proteomic Characterisation of Human Osteoblast-Derived Decellularised Extracellular Matrix for Osteogenic Repair","description":"This project investigated cell-derived extracellular matrix (ECM) preparation for matrix-guided bone tissue engineering. A detergent-based decellularisation protocol using NH4OH and Triton X-100 was optimised using fibroblast-derived ECM to improve DNA removal while preserving ECM-associated protein content.  To provide a more bone-relevant molecular reference, the same decellularisation approach was also applied to HOB-derived ECM. Proteomic analysis of HOB-derived dECM identified ECM-associated proteins linked to osteogenic activity, including collagens, laminins, annexins, and calcium-binding proteins. This dataset is presented as a descriptive reference for osteoblast-derived ECM composition, rather than as a direct comparison with the fibroblast-derived ECM used in functional assays.","dates":{"publication":"2026-05-26","submission":"2026-05-01"},"accession":"PXD077920","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:1211601","NEWT:876138","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:10029","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1094343","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:408169","NEWT:44544","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:460519","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:2711","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:29159","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:499175","NEWT:476272","NEWT:3747","NEWT:367830","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:28038","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:7091","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:5180","NEWT:256737","NEWT:115104","NEWT:1121114","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:415540","NEWT:675060","NEWT:4081","NEWT:554","NEWT:98334","NEWT:426428","NEWT:7574","NEWT:7215","NEWT:575412","NEWT:29204","NEWT:2172103","NEWT:507601","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NEWT:1908","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581","NEWT:216599","NEWT:216595","NEWT:243230","NEWT:8355","NEWT:9685","NEWT:7029","NEWT:1080772","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:334747","NEWT:61235","NEWT:6289","NEWT:436486","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:170187","NEWT:260707","NCBITaxon:6191","NEWT:1836","NEWT:185431","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:2697049","NEWT:105231","NEWT:1216981","NCBITaxon:6073","NEWT:884204","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NEWT:607699","NEWT:6282","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:38783","NEWT:8727","NEWT:4006","NEWT:8726","NEWT:6426","NEWT:6669","NEWT:10090","NEWT:4120","NEWT:51515","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:5334","NEWT:37334","NEWT:382352","NCBITaxon:10359","NEWT:242619","NEWT:632957","NEWT:373995","NEWT:5689","NEWT:544404","NEWT:9925","NEWT:8839","NEWT:4232","NEWT:2758385","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:714","NEWT:421932","NEWT:196627","NEWT:5691","NEWT:48479","NEWT:627025","NEWT:1097677","NEWT:61674","NEWT:1117957","N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