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Sejberg Øhlenschlæger"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics","Data-independent acquisition"],"software":[""],"submitter_keywords":["Guided dorsal forebrain organoid","Phosphorylation","Gap43","Dynamin.","Subcellular enrichment","Stimulation","Growth cone","Air-liquid interface cerebral organoid","Synapse","Brain organoid","Proteomics","Nerve terminals","Neural organoid","Synaptosomes","Differential centrifugation"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD072589"],"sample_protocol":["Sample lysis and digestion of proteins The sucrose/EDTA buffer from the enrichment protocols was removed from the homogenate samples and cytosolic fractions with 10 kDa spin filters. All fraction and homogenate samples were dissolved in lysis buffer (1% sodium deoxycholate (SDC) in either 50 mM TEAB or 100 mM HEPES, pH 8). Samples were probe sonicated, and protein concentrations were measured using a Nanophotometer. 10-20 µg of protein was used for label-free DIA analysis and 50-70 µg for TMT-labeling and phosphopeptide enrichment. Proteins were reduced and alkylated with 10 mM DTT and subsequently 20 mM IAA. Samples were digested first with 0.04 U/mg Lys-C for 1h at RT followed by 5% trypsin at 37°C, pH 8. The following day, samples were incubated 1h at 37°C with 1% additional trypsin.  Data independent acquisition (DIA) workflow SDC was precipitated using 2% FA. Then samples were lyophilized and resuspended in 0.1% FA. Peptide concentrations were measured using Pierce Quantitative Fluorometric Peptide Assay and samples were diluted accordingly in 0.1% FA to 0.1 µg/µL. Most samples were analyzed the following way: a total of 2 µL (200ng of peptides) was loaded onto a 15 cm x 75 µm, C18 1.6 m Aurora Elite column (ESI Source Solutions) coupled directly to a timsTOF Pro (Bruker) instrument using buffers A (0.1% FA) and B (95% acetonitrile (ACN), 0.1% FA). Peptides were eluted during a 30 min gradient on a Dionex Ultimate 3000 HPLC)-system. Samples were run scanning from 100-1700 m/z using a standard DIA-PASEF method (mass range: 395.6 Da to 1020.6 Da, cycle time estimate: 1.06 sec). The ALI-CO differential centrifugation fractions were analyzed in the same way with minor modifications in the gradient and DIA-PASEF method (mass range: 400 Da to 1201 Da, cycle time estimate: 1.80 sec). The mouse (P2 and W8) samples were analyzed on an Orbitrap Exploris 480 mass spectrometer using DIA. 200 ng of peptides were loaded onto a Vanquish™ Neo UHPLC system using a 2-column setup. Peptides were eluted with increasing amount of buffer B at a flow rate of 0.3 µL/min during a 35 min gradient. Peptides were analyzed using a standard DIA method (precursor mass range (m/z): 400-1000, cycle time of 3 sec, orbitrap resolution: 30,000 FWHM).  TMT-labeling of samples for phosphopeptide enrichment After Lys-C/tryptic digestion, samples for phosphopeptide enrichment (high KCl stimulated fractions and controls) were labeled with TMTpro™ 16-plex/18-plex according to manufacturer instructions. After mixing, the SDC was precipitated using 2% FA and the sample was lyophilized to 100 µL. The enrichment of phosphopeptides was performed using TiO2. After binding of the phosphopeptides to the TiO2 resin in 5% TFA, 80% ACN and 1M glycolic acid for 10 min, the solution was centrifuged, and the supernatant was re-incubated with half the amount of TiO2 for another 10 min. The supernatant from the second incubation was collected, labeled as “non-modified” peptides and dried for further use. After washing the TiO2 beads, they were lyophilized for 5 min and subsequently the phosphopeptides were eluted with 5% ammonia water, pH 11. After incubation, the supernatant was collected and lyophilized.  High pH reversed-phase fractionation Peptide samples were fractionated into 15-20 concatenated fractions using High pH reversed-phase fractionation as described elsewhere (PMID: 36173113). Fractions were lyophilized and resuspended in 0.1% FA for HPLC- Tandem MS (MS/MS) analysis.  TMT LC-MSMS analysis All samples were dissolved in 0.1% FA and analyzed by nLC-MS/MS using an EASY-nLC (Thermo Fisher Scientific) with buffer A (0.1% FA) and buffer B (95% ACN, 0.1% FA) connected online to an Orbitrap Eclipse Tribrid Mass Spectrometer. The peptides were eluted with increasing amount of the buffer B (95% ACN, 0.1% FA) from 2 to 40% in 90 and 140 min for phosphopeptide fractions and “non-modified” peptides, respectively. The full MS was performed in the mass range of 450–1500, in the Orbitrap with a resolution of 120,000 FWHM, a maximum injection time of 50 ms and an Automatic Gain Control (AGC) target value of 1x106. Hereafter, peptides were selected for MS/MS using HCD with NCE setting as 35, resolution of 50,000 FWHM, AGC target value of 1x105 ions and maximum injection time of 150 ms.  Additionally, the “non-modified” samples were run on the Eclipse Orbitrap in TMT Synchronous Precursor Selection Multi-Stage Mass Spectrometry (SPS-MS3) mode with real-time search enabled against a Uniprot human/mouse protein database (static modifications: carbamidomethyl (C), TMTpro™ 16- or 18-plex (Kn), maximum missed cleavages: 1) with a maximum search time of 35 ms. The MS/MS isolation window was set to 2 m/z and identified peptides were selected for MS3 fragmentation using HCD with NCE setting at 55, Orbitrap resolution of 30,000 FWHM, AGC target value of 500% with a scan range of 100-500 m/z."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Peptide identification and label-free quantification The raw data from DIA-MS analyses was searched with DIA-NN (v1.8.1) against computationally generated spectral libraries of human and mouse proteomes performed with the following search parameters: mass accuracy was set to 10 ppm whereas for MS1 mass accuracy to 15 ppm , peptide length range of 7-30 amino acids, precursor m/z range of 100-1700, fragment ion m/z range of 100-1700, neural network classifier in Single-pass mode, Robust LC (high precision) mode was used with retention time (RT)-dependent normalization enabled, maximum of 2 missed cleavages, N-terminal methionine (M) excision and methionine oxidation as variable modification was enabled, C carbamidomethylation was used as fixed modification.  Peptide identification and quantification of “non-modified” peptide and phosphopeptide samples All raw files were searched against the Uniprot database of Homo sapiens or Mus Musculus in Proteome Discoverer (PD) 2.5.0.305 (Thermo Fisher Scientific, USA) using an in-house Mascot server (v2.6) and SEQUEST HT. For HCD fragmentation, search parameters were as follows: cleavage specificity Trypsin/P; precursor mass tolerance of 10 ppm and fragment mass tolerance of 0.05 Da. The phosphopeptides search included the parameters: Maximum missed cleavages, 2; Static modifications, TMTpro (K), TMTpro (N-term) and Carbamidomethyl (C); Dynamic modifications, Phosphorylation (S, T, Y). For SPS-MS3 of “non-modified” peptides, the data were searched in PD 2.5.0.305 using SEQUEST with the same Uniprot Human/Mouse database as the real time search on the Eclipse. Search parameters were as following: cleavage specificity Trypsin/P; precursor mass tolerance of 10 ppm and fragment mass tolerance of 0.8 Da. The search included the parameters: Maximum missed cleavages, 2; Static modifications, TMTpro (K), TMTpro (N-term) and Carbamidomethyl (C). For the phosphopeptides the search was performed first in Mascot and then in SEQUEST using the same Uniprot databases and same search parameters, except for 0.05 mass tolerance in MS2 data and variable phosphorylation on S/T/Y. The percolator software in PD 2.5 was used for filtering for false discovery rate (FDR) of <1% for proteins and peptides. All datasets from PD 2.5 were exported to Excel (Microsoft) for further processing. For the Mascot searches peptides were accepted if the Mascot score was ≥15."],"omics_type":["Proteomics"],"labhead":["Martin Røssel Larsen"],"instrument_platform":[""],"labhead_affiliation":["Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)","Mus Musculus (mouse)"],"publication":["42108706 Øhlenschlæger MS, Criscuolo L, Jensen P, Lloyd-Davies Sánchez DJ, Sutcliffe M, Bhosale S, Bogetofte H, Tahir M, Jakobsen LA, Pihl M, Brewer J, Schwämmle V, Poulsen FR, Freude K, Lancaster MA, Robinson PJ, Larsen MR. Modeling Synaptic Maturation From Growth Cone to Synapse in Human Organoids. J Neurochem. 2026 170(5):e70458 10.1111/jnc.70458"],"submitter_mail":["masoe@bmb.sdu.dk"],"submitter_affiliation":["SDU"],"submitter_country":["Denmark"],"pubmed_abstract":["Human neural organoids (NOs) provide a powerful platform for investigating synaptic development and dysfunction during early neurodevelopment. However, methodologies for isolating functional synaptic structures from these models remain limited. Here, we present a differential centrifugation protocol enabling the enrichment of growth cone particles (GCPs) and immature synaptosomes from air-liquid interface cerebral organoids (ALI-COs) at distinct developmental stages (Day 90 and 150). Notably, the method avoids density gradients, requires minimal starting material while maintaining reproducibility across human and murine tissues. Quantitative proteomic profiling revealed significant enrichment of growth cone markers (e.g., GAP43) and classical synaptosomal proteins (e.g., PCLO, BSN, SYN1). Transmission electron microscopy (TEM) confirmed the presence of membrane-enclosed GCPs with fibrous content and mitochondria in Day 90 isolates, and immature synaptosomes containing synaptic vesicles on day 150. Functional viability of both types of synaptic structures was demonstrated through KCl-induced depolarization, which triggered phosphorylation changes in growth cone proteins (GAP43, MARCKS, MARCKSL1), cytoskeletal regulators (DCLK1, SHTN1, MARK4, MAP1B) and protein kinases (CAMK2G, PRKCE) in Day 90 GCPs, as well as classical synaptic vesicle cycle proteins (SYN1, DNM1, RPH3A) at Day 150. Overall, this study establishes a centrifugation-based protocol for isolating growth cones and immature synapses from human organoids, capturing key stages of synaptic development and enabling scalable, patient-compatible models to study synaptic function and dysfunction in neurodevelopmental and neurodegenerative disorders."],"pubmed_title":["Modeling Synaptic Maturation From Growth Cone to Synapse in Human Organoids."],"pubmed_authors":["Øhlenschlæger Marie S MS, Criscuolo Lucrezia L, Jensen Pia P, Lloyd-Davies Sánchez Daniel J DJ, Sutcliffe Magdalena M, Bhosale Santosh S, Bogetofte Helle H, Tahir Muhammad M, Jakobsen Lene A LA, Pihl Maria M, Brewer Jonathan J, Schwämmle Veit V, Poulsen Frantz R FR, Freude Kristine K, Lancaster Madeline A MA, Robinson Phillip J PJ, Larsen Martin R MR"],"additional_accession":[]},"is_claimable":false,"name":"Modelling Synaptic Maturation from Growth Cone to Synapse in Human Organoids","description":"Human neural organoids (NOs) provide a powerful platform for investigating synaptic development and dysfunction during early neurodevelopment. However, methodologies for isolating functional synaptic structures from these models remain limited. Here, we present a differential centrifugation protocol enabling the enrichment of growth cone particles (GCPs) and immature synaptosomes from air-liquid interface cerebral organoids (ALI-COs) at distinct developmental stages (day 90 and 150). Notably, the method avoids density gradients, requires minimal starting material while maintaining reproducibility across human and murine tissues. Quantitative proteomic profiling revealed significant enrichment of growth cone markers (e.g. GAP43) and classical synaptosomal proteins (e.g. PCLO, BSN, SYN1). Transmission electron microscopy (TEM) confirmed the presence of membrane-enclosed GCPs with fibrous content and mitochondria in day 90 isolates, and immature synaptosomes containing synaptic vesicles on day 150. Functional viability of both types of synaptic structures was demonstrated through KCl-induced depolarization, which triggered phosphorylation changes in growth cone proteins (GAP43, MARCKS, MARCKSL1), cytoskeletal regulators (DCLK1, SHTN1, MARK4, MAP1B) and protein kinases (CAMK2G, PRKCE) in day 90 GCPs, as well as classical synaptic vesicle cycle proteins (SYN1, DNM1, RPH3A) at day 150. Overall, this study establishes a centrifugation-based protocol for isolating growth cones and immature synapses from human organoids, capturing key stages of synaptic development and enabling scalable, patient-compatible models to study synaptic function and dysfunction in neurodevelopmental and neurodegenerative disorders.","dates":{"publication":"2026-05-25","submission":"2026-01-03"},"accession":"PXD072589","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:1131","NEWT:35795","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:1334565","NEWT:625351","NEWT:258594","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:1073882","NEWT:6819","NEWT:475174","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:1590","NEWT:10034","NEWT:33114","NEWT:1596","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:3767","NEWT:1589","NEWT:135622","NEWT:4615","NEWT:672127","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:1582","NEWT:3760","NEWT:1584","NEWT:36630","NEWT:1585","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:7719","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:49928","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:410658","NEWT:5516","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:1310173","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:150808","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NCBITaxon:37162","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10891","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:926571","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2499525","NEWT:2853422","NEWT:487","NEWT:1538553","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:237610","NEWT:95486","EFO:0001352","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:987059","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:1509","NEWT:491","NEWT:460523","NEWT:45954","NEWT:235443","NEWT:1579","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:191701","NEWT:373153","NEWT:1640278","NEWT:472","NEWT:940825","NEWT:29459","NEWT:529507","NEWT:1071661","NEWT:28128","NEWT:470","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:11723","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:1290454","NEWT:906914","NEWT:81231006","NEWT:28141","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:3728","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:548","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:2126348","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:207340","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:33941","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:771870","NEWT:51338","NEWT:9995","NEWT:575412","NEWT:28112","NEWT:49012","NEWT:6493","NEWT:10832","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:1613","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:353153","NEWT:227377","NEWT:1774284","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:74426","NEWT:443906","NEWT:13037","NEWT: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