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Cell Laboratory, School of Molecular Science, La Trobe University, Bundoora, Victoria"],"cell_type":["Not available"],"repository":["GPMDB"],"pubmed_abstract":["Differentiation of CD8(+) T lymphocytes into effector and memory cells is key for an adequate immune response and relies on complex interplay of pathways that convey signals from the cell surface to the nucleus. In this study, we investigated the proteome of four cytotoxic T-cell subtypes; naïve, recently activated effector, effector, and memory cells. Cells were fractionated into membrane, cytosol, soluble nuclear, chromatin-bound, and cytoskeletal compartments. Following LC-MS/MS analysis, identified peptides were analyzed via MaxQuant. Compartment fractionation and gel-LC-MS separation resulted in 2399 proteins identified in total. Comparison between the different subsets resulted in 146 significantly regulated proteins for naïve and effector cells, followed by 116 for activated, and 55 for memory cells. Besides Granzyme B signaling (for activated and/ or effector cells vs. naïve cells), the most prominent changes occurred in the TCA cycle and aspartate degradation. These changes suggest that correct balancing of metabolism is key for differentiation processes. All MS data have been deposited in the ProteomeXchange with identifier PXD001065 (http://proteomecentral.proteomexchange.org/dataset/PXD001065)."],"pubmed_title":["Compartment resolved reference proteome map from highly purified naïve, activated, effector, and memory CD8⁺ murine immune cells."],"pubmed_authors":["Zanker Damien D,Otto Wolfgang W,Chen Weisan W,von Bergen Martin M,Tomm Janina M JM,","Zanker Damien D, Otto Wolfgang W, Chen Weisan W, von Bergen Martin M, Tomm Janina M JM"],"name_synonyms":["RUTBC3, rabGAPLP, MUTYH-Associated Polyposis, RUSC3, p32, Leu2, Cell., RabGAP-5, CD8, MYH-Associated Polyposis, MAL, Proteomes, MAP, RABGAP5"],"description_synonyms":["LC-MS2, liquid chromatography tandem mass spectroscopy, Gene., study, membrane, data, membrane of organ, LCMSMS, killer T-lymphocyte, alpha-beta cytotoxic T-lymphocyte, determination, killer T cell, cytotoxic T cell, Proteins, LC-MS/MS, killer T-cell, proteins, killer T lymphocyte, membranous organ component, cytotoxic T-cell, cytotoxic T-lymphocyte, Cell, LC-MS-MS, Protein Gene Products, Gene Proteins, polypeptide, Polypeptides, LC/MS/MS, Experiment, CD8-positive, soluble, liquid chromatography-tandem mass spectroscopy, chromosome scaffold, LC-MSMS, chemical analysis, Protein, Gene Products, Cytosols, liquid chromatography tandem mass spectrometry, alpha-beta cytotoxic T-cell, cytotoxic T lymphocyte, assay, Proteomes, alpha-beta cytotoxic T lymphocyte, Chromatins"],"pubmed_title_synonyms":["RUTBC3, rabGAPLP, MUTYH-Associated Polyposis, RUSC3, p32, Leu2, Cell., RabGAP-5, CD8, MYH-Associated Polyposis, MAL, Proteomes, MAP, RABGAP5"],"pubmed_abstract_synonyms":["liquid chromatography tandem mass spectroscopy, biochemical pathways, projections, biological signaling, Metabolic Process, determination, AI461847, Processes, lamellae, cytotoxic T cell, Metabolic Concepts, Gene, 116, killer T lymphocyte, Metabolic Processes, process of organ, cell associated, LC-MS-MS, protrusion, lamella, lymphocytes, Polypeptides, Metabolism, horsetail nucleus, LC-MSMS, Gene Products, Concepts, citric acid cycle, alpha-beta cytotoxic T-cell, Pgi, Metabolism Concept, Gpi-1, MAL, Phenomenon, Metabolism Phenomena, Chromatins, study, neuronal nucleus, LCMSMS, killer T-lymphocyte, catabolism, Gpi-1r, Nlk, Gpi-1s, nucleus of CNS, Phi, Gpi-1t, killer T-cell, Metabolic Concept, proteins, metabolic process resulting in cell growth, ridges, aspartate breakdown, cytotoxic T-cell, nucleus, signaling process, papilla, chromosome scaffold, biotransformation, Lymphoid, laminae, Catabolism, alpha-beta cytotoxic T lymphocyte, Lymphocyte, cytolytic T-lymphocyte, single organism signaling, LC-MS2, Data Set., incorporation, Gpi, membrane, data, adequate, aspartate catabolism, anatomical protrusion, alpha-beta cytotoxic T-lymphocyte, degradation, Process, killer T cell, Krebs cycle, anatomical process, metabolism resulting in cell growth, Proteins, LC-MS/MS, lamina, Leu2, flanges, membranous organ component, MF, Amf, Cell, Concept, Metabolic Phenomena, polypeptide, Metabolism Concepts, LC/MS/MS, mOC-X, soluble, nervous system nucleus, chemical analysis, Protein, Phenomena, shelf, cell nucleus, Lymphoid Cell, cytotoxic T lymphocyte, NK|GPI, metabolism, flange, Lymphoid Cells, organ process, NK, Metabolic Phenomenon, mobilization, multicellular organism metabolic process, Org, ORG, membrane of organ, biodegradation, Metabolic, p32, shelves, Gpi1-r, Gpi1-s, nucleus of neuraxis, Gpi1-t, projection, neuraxis nucleus, cytotoxic T-lymphocyte, ridge, turnover, signalling, cytolytic T-cell, Protein Gene Products, Gene Proteins, process, processes, single-organism metabolic process, TCA cycle, CD8-positive, signalling process, spine, liquid chromatography-tandem mass spectroscopy, Cells, Cytosols, liquid chromatography tandem mass spectrometry, processus, assay, CD8, cell bound, CTL, Proteomes, Bglap-rs1, Gpi1s, aspartate degradation, Anabolism"],"view_count":["63"],"citation_count":["0"],"search_count":["5"],"full_dataset_link":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310006565"],"search_domains":["dbgap_ncbi~0","patentfamilies~0","rfam~0","merops~0","complex-portal~0","uniprot~0","wormbaseparasite~0","embl-covid19~0","reactome~0","emdb~0","wgs_masters~0","ebiweb_resources~0","opentargets_genetics~0","biomodels_all~0","ipd-mhc~0","ebiweb_teams~0","taxonomy~0","genome_assembly~0","sc-experiments~0","ebiweb_people~0","enzymeportal_enzymes~0","ipd-nhkir~0","cellosaurus~0","pdbe~0","chebi~0","patentproteins~0","interpro7~0","uniref~0","chembl~0","pdbekb~0","gpcrdb~0","hgnc~0","sc-genes~0","intact~0","rhea~0","ebiweb_training~0","alphafold~0","imgt-hla~0","patentnucleotides~0","ensemblroot~0","eva_studies~0","non-coding~0","europepmc~0","pubmed~1","identifiers_registry~0","pdbechem~0","hpa-covid19~0","eva-variants-covid19~0","biosamples~0","gwas_catalog~0","biotools~0","tls_masters~0","mesh~0","coding~0","sra~0","opentargets~0","efo~0","embl-pathogen~0","project~0","pride~1","human_diseases~0","geo_datasets~0","embl~0","treefam~0","uniparc~0","ols~0","dgva~0","intenz~0","go~0","tsa_masters~0","biosamples-covid19~0","ebiweb_corporate~0","omim~0","lrg~0","earlycause-molecular-sequences~0","ipd-kir~0","empiar~0","rnacentral~0","orcid_data_claims~0","gpmdb~2","lineage-covid19~0","metagenomics~0","pfam~0","pride archive~1","varsite~0"],"reanalysis_count":["0"],"submitter_keywords":["Resource Reanalysis"],"citation_count_scaled":["0.0"],"reanalysis_count_scaled":["0.0"],"view_count_scaled":["0.019432449105490437"],"download_count_scaled":["0.0"],"normalized_connections":["1.0"],"additional_accession":[]},"is_claimable":false,"name":"Compartment resolved reference proteome map from highly purified na-ve, activated, effector, and memory CD8+ murine immune cells.","description":"Data from ProteomeXchange, PXD ID: PXD001065. Experiment: Aus7, file: Aus7_35.mzml. Published as part of Proteomics. 2015 Jan 23  . From the Abstract: {{i}} In this study, we investigated the proteome of four cytotoxic T cell subtypes; na-ve, recently activated effector, effector and memory cells. Cells were fractionated into membrane, cytosol, soluble nuclear, chromatin-bound and cytoskeletal compartments. Following LC-MS/MS analysis, identified peptides were analyzed via MaxQuant. Compartment fractionation and gel-LC-MS separation resulted in 2399 proteins identified in total. {{/i}}","dates":{"submission":"2015-02-06"},"accession":"GPM32310006565","cross_references":{"pubmed":["25643623"],"Pride":["PXD001065"],"pride":[],"Pride Archive":["PXD001065"]}}