The mass spectrometry dataset of cerebral organoid exosomes

The culture supernatant from mature cerebral organoids, which exhibit stable neuronal phenotypes between days 60 and 140, was collected for the preparation of exosomes. Briefly, the supernatant was subjected to sequential centrifugation (300g x 10min→2000g x 10min→10,000g x 30min) to remove residual cells, cell debris and apoptotic bodies. The resulting supernatant was then filtered through a 50kD ultrafiltration tube at 5,000g for 1h to collect exosomes, followed by ultracentrifugation at 120,000g for 90min using a Beckman Optima LX-80 ultracentrifuge. The pellets were resuspended in PBS, aliquoted and stored at -80℃.The EASY-nLC™+HFX system was utilized to chromatographically separate each OExo sample, with the raw files directly imported into Proteome Discoverer 2.5 software for database querying. The database employed was Homo sapiens uniprot 2023_10_18 SwissProt.fasta. Subsequently, Proteome Discoverer 2.5 software was employed to refine the search outcomes: peptide spectrum matches (PSMs) with a confidence level exceeding 99% were identified as reliable PSMs, and proteins harboring at least one unique peptide segment (specific peptide) were recognized as reliable proteins.