{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report.pg_matrix.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report.stats.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/combined_peptide.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/combined_ion.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/combined_site_M_15.9949.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/combined_modified_peptide.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report.pr_matrix.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/combined_protein.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report.protein_description.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/combined_site_C_57.0215.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report.gg_matrix.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report.unique_genes_matrix.tsv"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report.log.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/checksum.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report.manifest.txt"],"Pdf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report_trends.pdf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report_runs.pdf"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/fragger.params","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report.parquet","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/fragpipe.workflow","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/D11_Lysate_KO_G1_1_42373.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/D11_Lysate_WT_RD12_1_42204.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/D11_Lysate_WT_RD12_1_42372.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/D11_Lysate_KO_G1_1_42205.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report-lib.parquet","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/fragpipe-files.fp-manifest","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD075443/report.site_report.parquet"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["davies@sund.ku.dk"],"submitter":["Luke Gamon"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","diaPASEF","Bottom-up proteomics","Data-independent acquisition"],"software":[""],"submitter_keywords":["Human","Ipsc"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD075443"],"tissue":["Whole Body"],"sample_protocol":["Proteomic sample preparation and mass spectrometry analysis Five micrograms of cell lysate from WT and SULF1/2 DKO samples collected at D11 of differentiation were subjected to SP3 bead-based protein cleanup prior to reduction, alkylation, and overnight proteolytic digestion with trypsin/Lys-C. Cleanup was performed as described by Batth et al., 2019 (REF Batth et al., 2019), with minor modifications. Briefly, samples (50 µL) were precipitated onto magnetic beads (Sera-Mag, GE Healthcare) by addition of acetonitrile (120 µL), washed (800 µL; 1 × 70% ethanol, 2 × 100% acetonitrile), and resuspended in 50 mM triethylammonium bicarbonate (TEAB; 50 µL). Proteins were reduced and alkylated for 10 min at 70 °C using tris(2-carboxyethyl)phosphine (TCEP; 10 mM) and chloroacetamide (CAA; 40 mM), followed by incubation with Lys-C (0.05 µg) for 1 h at 37 °C and overnight digestion with trypsin (0.1 µg) at 37 °C. Digested peptides were acidified with 10% trifluoroacetic acid (TFA) and subjected to StageTip solid-phase extraction using C18 discs (Affinisep). Peptides were analyzed on a timsTOF Pro mass spectrometer (Bruker) coupled online to a Dionex UltiMate 3000 nanoLC system (Thermo Fisher Scientific)."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Peptide separation was performed on a 15 cm × 75 µm C18 nanoflow column (Aurora, IonOpticks) at a flow rate of 400 nL min⁻¹ using a 22 min gradient of 0.1% formic acid in water (solvent A) and 99.9% acetonitrile/0.1% formic acid (solvent B). The mass spectrometer was operated in parallel accumulation-serial fragmentation mode using either data-dependent (DDA-PASEF) or data-independent (DIA-PASEF) acquisition, with a cycle time of 0.63 s and a TIMS ramp time of 100 ms. The MS scan range was set to 100-1700 m/z. For DIA-PASEF, isolation windows and collision energies were set to default values, with a base of 0.85 1/K₀ (V s cm⁻²) at 20 eV and 1.30 1/K₀ (V s cm⁻²) at 59 eV. Fragmentation spectra were searched against a FASTA database containing the human proteome and common contaminants using MSFragger (v4.3) implemented in FragPipe (v23.1) for DDA data, or DIA-NN (v2.2.0 Academia) for DIA data. Default settings were used with minor modifications (peptide length 7-50 for DDA and 7-35 for DIA; two missed cleavages for DDA and one missed cleavage for DIA). Fixed modifications included cysteine alkylation (+57), and variable modifications included N-terminal acetylation (+42) and methionine oxidation (+16). MS/MS spectral annotation was performed using FragPipe-PDV."],"omics_type":["Proteomics"],"labhead":["Michael Davies"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Department of Biomedical Sciences, University of Copenhagen, Denmark"],"species":["Homo Sapiens (human)"],"submitter_mail":["lgamon@sund.ku.dk"],"publication":["Not available"],"submitter_affiliation":["The University of Copenhagen"],"submitter_country":["Denmark"],"additional_accession":[]},"is_claimable":false,"name":"Heparan sulfate Sulfatases are essential for the patterning of human stem cell-derived midbrain dopaminergic neurons","description":"Midbrain dopaminergic neurons (mDA) are selectively lost in Parkinson’s disease (PD), driving sustained efforts to generate bona fide mDA neurons from human-induced pluripotent stem cells (iPSCs) for replacement therapy. While morphogen gradients and transcription factors have been extensively studied, extracellular regulators remain largely overlooked. Here, we identify the heparan sulfate-modifying enzymes SULF1 and SULF2 as essential for establishing mDA neuron identity in vitro. Using CRISPR/Cas9-engineered iPSCs, we show that loss of SULF1/2 increases 6-O-sulfation of heparan sulfate chains and disrupts anterior-posterior and dorsoventral patterning in cells exposed to a midbrain differentiation protocol. Double-knockout cells fail to acquire midbrain fate and instead adopt caudal and neural crest-like identities, as revealed by single-nucleus RNA sequencing. Mechanistically, we find enhanced FGF signaling and demonstrate that FGF inhibition redirects cells toward midbrain progenitors, without fully restoring ventral identity. These findings establish a critical role for SULF1/2 in human mDA neuron development and uncover a previously unrecognized layer of extracellular control over neuronal patterning, opening for novel strategies to refine differentiation protocols for PD and beyond.","dates":{"publication":"2026-07-16","submission":"2026-03-10"},"accession":"PXD075443","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:241368","NEWT:2","NEWT:157546","NEWT:190802","NEWT:35554","NEWT:9778","NEWT:150475","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:5180","NEWT:256737","NEWT:2042546","NEWT:115104","NEWT:1081927","NEWT:67825","NEWT:185579","NEWT:43179","NEWT:13076","NEWT:1249668","NEWT:376741","NEWT:317","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:1211601","NEWT:415540","NEWT:876138","NEWT:4081","NEWT:554","NEWT:98334","NEWT:426428","NEWT:237561","NEWT:6928","NEWT:10036","NEWT:7574","NEWT:1351","NEWT:7215","NEWT:29204","NEWT:272563","NEWT:507601","NCBITaxon:79857","NCBITaxon:6157","NEWT:95648","NEWT:3885","NEWT:746360","NEWT:6239","NEWT:3888","NEWT:1589","NEWT:470150","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:4054","NEWT:3880","NEWT:272559","NEWT:226186","NEWT:3641","NEWT:383379","NEWT:8782","NEWT:1263854","NEWT:1000589","NEWT:435590","NEWT:1902","NEWT:85962","NEWT:160488","NEWT:28104","NEWT:317447","NEWT:7955","NCBITaxon:2","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:216595","NEWT:243230","NEWT:8355","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:9685","NEWT:7029","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:334747","NEWT:61235","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:436486","NEWT:6287","NEWT:2242","NEWT:300641","NEWT:4784","NEWT:727","NEWT:9796","NEWT:725","NEWT:360106","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NCBITaxon:6191","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:83334","NEWT:185431","NEWT:83332","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:44685","NEWT:2697049","NEWT:1148","NEWT:11676","NEWT:55571","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:1123869","NEWT:7370","NEWT:75058","NEWT:83906","NEWT:607699","NEWT:6282","NEWT:1094343","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:296543","NEWT:1773","NEWT:38783","NEWT:8727","NEWT:1895","NEWT:4006","NEWT:1182590","NEWT:8726","NEWT:6669","NEWT:10090","NEWT:935293","NEWT:64152","NEWT:749200","NEWT:4120","NEWT:51515","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:230741","NEWT:284812","NCBITaxon:10359","NCBITaxon:1313","NEWT:43330","NEWT:242619","NEWT:44544","NEWT:632957","NEWT:373995","NEWT:5689","NEWT:645463","NEWT:544404","NEWT:3702","NEWT:129249","NEWT:9925","NEWT:8839","NEWT:4232","NEWT:990119","NEWT:2758385","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:421932","NEWT:196627","NEWT:408172","NEWT:5691","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:627025","NEWT:400772","NEWT:1097677","NEWT:3708","NEWT:128161","NEWT:106592","NEWT:536231","NEWT:61674","NEWT:1117957","NEWT:9913","NEWT:1432138","NEWT:10312","NEWT:1424507","NEWT:4100","NEWT:1076","NEWT:6763","NEWT:803","NEWT:8030","NEWT:29722","NEWT:380394","NEWT:1692259","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:180066","NEWT:67767","NEWT:46835","NEWT:135588","NEWT:1843183","NEWT:95486","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:1416333","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:10306","NCBITaxon:2759","NEWT:1911079","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:1480154","NEWT:1274414","NEWT:27606","NEWT:59202","NEWT:9975","NEWT:3197","NEWT:9615","NEWT:10299","NEWT:860688","NEWT:411483","NEWT:884019","NEWT:411490","NEWT:169963","NEWT:36329","NEWT:1147787","NCBITaxon:3044782","NEWT:72407","NEWT:476272","NEWT:349741","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:641501","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:915099","NEWT:74940","NEWT:9721","NEWT:1450511","NEWT:360094","NEWT:470","NEWT:411901","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:9838","NCBITaxon:9615","NCBITaxon:5811","NEWT:58334","NEWT:411464","NEWT:1193501","NEWT:3055","NEWT:6326","NEWT:6689","NEWT:411460","NEWT:2762","NEWT:5476","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NEWT:1274432","NEWT:1274426","NEWT:1423","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:1274423","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:3847","NEWT:39946","NEWT:9823","NEWT:178876","NEWT:9940","NEWT:327160","NEWT:573","NEWT:521001","NEWT:9031","NEWT:1274420","NEWT:7091","NEWT:578458"],"ORCID":["0000-0001-7894-8035"]}}