{"doi":"10.1126/sciadv.abd0957","title":"Spatially resolved 3D metabolomic profiling in tissues","abstract":"Spatially resolved RNA and protein molecular analyses have revealed unexpected heterogeneity of cells. Metabolic analysis of individual cells complements these single-cell studies. Here, we present a three-dimensional spatially resolved metabolomic profiling framework (3D-SMF) to map out the spatial organization of metabolic fragments and protein signatures in immune cells of human tonsils. In this method, 3D metabolic profiles were acquired by time-of-flight secondary ion mass spectrometry to profile up to 189 compounds. Ion beams were used to measure sub-5-nanometer layers of tissue across 150 sections of a tonsil. To incorporate cell specificity, tonsil tissues were labeled by an isotope-tagged antibody library. To explore relations of metabolic and cellular features, we carried out data reduction, 3D spatial correlations and classifications, unsupervised K-means clustering, and network analyses. Immune cells exhibited spatially distinct lipidomic fragment distributions in lymphatic tissue. The 3D-SMF pipeline affects studying the immune cells in health and disease.","journal":"Science Advances","year":2021,"id":157113,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":51,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8547,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":663332,"name":"Thomas Hu","orcid":"0000-0001-7801-7070","position":1,"is_corresponding":false},{"id":663333,"name":"Eric Woods","orcid":"0000-0002-1169-893X","position":2,"is_corresponding":false},{"id":423616,"name":"Mayar Allam","orcid":"0000-0002-1550-2316","position":3,"is_corresponding":false},{"id":74206,"name":"Shuangyi Cai","orcid":"0000-0002-2653-6335","position":4,"is_corresponding":false},{"id":663334,"name":"Walter Henderson","orcid":"0000-0002-7999-3388","position":5,"is_corresponding":false},{"id":423617,"name":"Ahmet F. Coskun","orcid":"0000-0002-5797-1524","position":6,"is_corresponding":false},{"id":531769,"name":"Shambavi Ganesh","orcid":"0000-0003-0577-2600","position":0,"is_corresponding":true}],"reference_count":57,"raw_metadata":null,"created_at":"2026-07-18T23:44:17.471040Z","pmid":"33571119","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}