{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/P23-440.xlsx"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/Sample_name.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/checksum.txt"],"Mzml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/P23-440.mzML"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/4_D25_NS_minus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/7_D25_NS_plus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/12_D23_S_minus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/6_D23_NS_minus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/13_D25_S_plus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/14_D24_S_plus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/15_D23_S_plus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/8_D24_NS_plus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/10_D25_S_minus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/9_D23_NS_plus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/5_D24_NS_minus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/2_D24_E_plus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/3_D23_E_plus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/1_D25_E_plus.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/11_D24_S_minus.raw"],"Mzid":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063958/P23-440.mzid"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["kamal.Mustafa@uib.no"],"submitter":["Niyaz Alsharabi"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Isolation methods","Proteomic","Wharton’s jelly mesenchymal stem cells"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063958"],"tissue":["Umbilical Cord"],"sample_protocol":["Umbilical cord (UC) samples were aseptically collected from full-term pregnancies (n=3, GA 39-41 weeks) with informed consent, following Ethics Committee approval, Bergen, Norway. Blood vessels were removed, and Wharton’s jelly was segmented into 3-5 mm pieces for MSC isolation using three methods: non-scraped explant, scraped explant, and enzymatic. In the non-scraped method, UC segments were placed in culture dishes with growth medium (αMEM, 15% FBS, 1% penicillin/streptomycin) and 40 ng/ml bFGF2 in one dish, incubated at 37°C with 5% CO2. In the scraped method, the gelatinous mass was scraped off, segmented, and cultured with or without 40 ng/ml bFGF2. For the enzymatic method, UC slices were treated with collagenase IV, incubated, filtered, centrifuged, and cultured in MSC medium with or without 40 ng/ml bFGF2. For generating CM, WJ-MSCs at passages 3-4 were seeded at 5000 cells/cm² and cultured until 70-80% confluence. Cells were washed with PBS and cultured in serum-free αMEM for 48 hours. The medium was collected, centrifuged twice to remove cell remnants, filtered through a 0.2 μm filter, and identified as complete WJ-MSC-CM. The CM was aliquoted and stored at -80°C. WJ-MSC-CM from different donors (n=3) were concentrated 30 times using 3 kDa MWCO centrifugal filter units at 4°C. Protein concentration was measured with a BCA assay, and 25 µg of protein from each sample was used. Approximately 0.5 µg of tryptic peptides in 2% acetonitrile (ACN) and 0.5% formic acid (FA) was injected into an Ultimate 3000 RSLC system connected to a Q-Exactive HF mass spectrometer with an EASY-spray nano-electrospray ion source"],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["The LC-MS/MS raw files were processed using Proteome Discoverer (v2.5.0.400) and analyzed with Perseus (v2.3.0.1). Contaminants and proteins with fewer than two peptide ions were excluded. Proteins that were not present in at least two donors per group were filtered out. Functional enrichment of common proteins was assessed using Gene Set Enrichment Analysis (GSEA v4.3.2), with significant gene sets identified by FDR q-value < 0.25 and NES > 1. Differentially expressed proteins (DEPs) were identified using post hoc Tukey’s TSH for one-way ANOVA (FDR < 0.05). Gene ontology and interaction network analyses of upregulated proteins were conducted using the STRING database, with a minimum interaction score of 0.4. Relevant GO terms were retrieved from QuickGO and compared with common proteins and DEPs."],"omics_type":["Proteomics"],"labhead":["kamal Mustafa"],"instrument_platform":[""],"labhead_affiliation":["Head of TIssue Engineering Group at the Departmnet of Dentistry"],"submission_type":["COMPLETE"],"species":["Homo Sapiens (human)"],"submitter_mail":["n.al-sharabi@uib.no"],"publication":["41860834 Nguyen JL, Mohamed-Ahmed S, Saleem R, Mustafa K, Al-Sharabi N, Bentsen MHL. Isolation methods influence the biological properties of Wharton's Jelly-derived mesenchymal stem cells: A comparative study of yield, viability, proliferation, differentiation potential, and proteomic profiles. PLoS One. 2026 21(3):e0345081 10.1371/journal.pone.0345081"],"submitter_affiliation":["University of Bergen"],"submitter_country":["Norway"],"doi":["10.6019/PXD063958"],"additional_accession":[]},"is_claimable":false,"name":"Proteomic Analysis of Wharton’s Jelly Mesenchymal Stem Cells Isolated by Different Methods","description":"Wharton’s Jelly mesenchymal stem cells (WJ-MSC) are stem cells from the umbilical cord, known for their regenerative properties. They offer advantages like unlimited availability, non-invasive and low-cost isolation, and minimal ethical concerns. WJ-MSCs are promising for allogeneic cell therapy, with clinical trials showing their safety and efficacy across various diseases. They are also considered non-tumorigenic. A critical step for clinical use is selecting the optimal isolation method. This study compares three techniques: two explant methods (with and without scraping) and one enzymatic method. Additionally, the effect of adding fibroblast growth factor 2 (FGF2) to enhance cell expansion is examined. While several studies have addressed differences in isolation methods, the impact on the protein profile of WJ-MSCs is less explored. Therefore, we aim to explore the proteomic profiles of WJ-MSCs isolated by different methods to better understand their mechanisms and functionalities","dates":{"publication":"2026-03-30","submission":"2025-05-15"},"accession":"PXD063958","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:6703","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2102","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:1247","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:281395","NEWT:10360","NEWT:1211601","NEWT:876138","NEWT:47664","NEWT:3654","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:82688","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:28903","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:3347","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:211586","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NEWT:1390363","NEWT:288705","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:374990","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:391619","NEWT:360104","NEWT:287","NEWT:246197","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:5508","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:35500","NEWT:1140","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:1336795","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:105023","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:47946","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:106590","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:1436733","NEWT:460519","NEWT:1187947","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:1182263","NEWT:2711","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:1883446","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:225117","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:38293","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:7237","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:9644","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:27592","NEWT:98334","NEWT:426428","NEWT:588858","NEWT:9639","NEWT:242231","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:2172103","NEWT:7460","NEWT:6491","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:162425","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","NEWT:13164","NEWT:216129","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581"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