GPMDB00166OtherGraessel A, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Humankathrin.suttner@lrz.tu-muenchen.de25991687http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020141http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020140http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020123http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020101http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020145http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020144http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020100http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020122http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020143http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020121http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020142http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020120http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020105http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020127http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020104http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020126http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020103http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020125http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020124http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020146http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020102http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020109http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020108http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020107http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020106http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020128http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020130http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020134http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020112http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020111http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020133http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020099http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020132http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020110http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020131http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020116http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020138http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020137http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020115http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020114http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020136http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020113http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020135http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020119http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020118http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020139http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020117Technische Universitaet und Helmholtz Zentrum Muenchen, et al.Not availableGPMDBNaive CD4(+) T cells are the common precursors of multiple effector and memory T-cell subsets and possess a high plasticity in terms of differentiation potential. This stem-cell-like character is important for cell therapies aiming at regeneration of specific immunity. Cell surface proteins are crucial for recognition and response to signals mediated by other cells or environmental changes. Knowledge of cell surface proteins of human naive CD4(+) T cells and their changes during the early phase of T-cell activation is urgently needed for a guided differentiation of naive T cells and may support the selection of pluripotent cells for cell therapy. Periodate oxidation and aniline-catalyzed oxime ligation technology was applied with subsequent quantitative liquid chromatography-tandem MS to generate a data set describing the surface proteome of primary human naive CD4(+) T cells and to monitor dynamic changes during the early phase of activation. This led to the identification of 173 N-glycosylated surface proteins. To independently confirm the proteomic data set and to analyze the cell surface by an alternative technique a systematic phenotypic expression analysis of surface antigens via flow cytometry was performed. This screening expanded the previous data set, resulting in 229 surface proteins, which were expressed on naive unstimulated and activated CD4(+) T cells. Furthermore, we generated a surface expression atlas based on transcriptome data, experimental annotation, and predicted subcellular localization, and correlated the proteomics result with this transcriptional data set. This extensive surface atlas provides an overall naive CD4(+) T cell surface resource and will enable future studies aiming at a deeper understanding of mechanisms of T-cell biology allowing the identification of novel immune targets usable for the development of therapeutic treatments.A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation.Graessel Anke A,Hauck Stefanie M SM,von Toerne Christine C,Kloppmann Edda E,Goldberg Tatyana T,Koppensteiner Herwig H,Schindler Michael M,Knapp Bettina B,Krause Linda L,Dietz Katharina K,Schmidt-Weber Carsten B CB,Suttner Kathrin K,Graessel Anke A, Hauck Stefanie M SM, von Toerne Christine C, Kloppmann Edda E, Goldberg Tatyana T, Koppensteiner Herwig H, Schindler Michael M, Knapp Bettina B, Krause Linda L, Dietz Katharina K, Schmidt-Weber Carsten B CB, Suttner Kathrin KTC-NER, first cervical vertebra, advanced, atlas, human being, T-cell surface antigen T4/Leu-3, external covering of organism, T-cell surface antigen T4|Leu-3, T-lymphocyte receptor complex, transcription-coupled repair, organism surface, Homo sapiense, Cell, Responder protein Smok-Tcr, surface, Homo spaiens, L3T4, 2.7.11.1, Homo sapien, TCR complex, responder protein Smok-Tcr, T-cell differentiation antigen L3T4, Homo sapian, Homo sapians, Ly-4, precocious, Homo sapeins, cervical atlas, Smoktcr, integumentum commune, T lymphocyte receptor complex, TCR, Tcr, Homo sapients, cervical vertebra 1, transcription-coupled NER, body surface, C1, T-cell surface glycoprotein CD4, Humo sapiens, CD4mut, man, Homo sapines, human, early, SmokTcr, Homo spiens, "human" EXACT genbank_common_name [], vertebra 1, Homo sapience, integumentary system, Homo sampiens, Dominant negative form of Smok, CD4, atlas (CI), T-cell receptor complex, dermal system, atlas vertebra, Home sapiens, dominant negative form of Smok, activation., C1 vertebra, atlas [C I]sodium salt, liquid chromatography tandem mass spectroscopy, advanced, human being, T-cell surface antigen T4/Leu-3, aniline perchlorate, number, aniline hydrobromide, aniline phosphate (1:1), 3-(13)C-labeled cpd, Homo sapiense, presence, LC-MS-MS, 4.3.2.5, surface, Homo spaiens, L3T4, Homo sapien, Peptidylamidoglycolate lyase, Homo sapians, LC-MSMS, Ly-4, aniline hydrofluoride, 4-(13)C-labeled cpd, PGL, aniline, aniline monosulfate, integumentum commune, aniline sulfate (2:1), HGAD, Homo sapients, LCMSMS, aniline hydrogen iodide, PHM, man, Ligations, 1.14.17.3, aniline aluminium salt, Homo sapience, Homo sampiens, aniline hydrochloride-(14)C-labeled cpd, aniline dihydrofluoride, Pal, PAL, Home sapiens, aniline nitrate, PAM, activation., LC-MS2, data, peptidylamidoglycolate peptidylamide-lyase activity, Data Set, external covering of organism, T-cell surface antigen T4|Leu-3, Arts, LC-MS/MS, 15N-labeled cpd, 3H-labeled cpd, organism surface, aniline diphosphate (4:1), Cell, aniline diphosphate (1:1), count in organism, LC/MS/MS, count, T-cell differentiation antigen L3T4, Homo sapian, benzenamine, aniline sulfate, peptidylamidoglycolate peptidylamide-lyase (glyoxylate-forming), precocious, Ligature, aniline phosphate (2:1), Homo sapeins, magnesium (1:1) salt, Ligatures, Industrial, Industrial Arts, body surface, aniline phosphonate (1:1), T-cell surface glycoprotein CD4, monolithium salt, Humo sapiens, aniline hydrochloride-(15)N-labeled cpd, CD4mut, ion(1+), FIGLER9, alpha-hydroxyglycine amidating dealkylase activity, (13)C-labeled cpd, Peptidylglycine alpha-hydroxylating monooxygenase, Homo sapines, Peptidyl-alpha-hydroxyglycine alpha-amidating lyase, human, early, 2-(13)C-labeled cpd, aniline diphosphate (3:1), conjugate acid, Homo spiens, "human" EXACT genbank_common_name [], integumentary system, liquid chromatography-tandem mass spectroscopy, LRRC21, aniline hydrochloride, liquid chromatography tandem mass spectrometry, CD4, peptidyl-alpha-hydroxyglycine alpha-amidating lyase activity, quantitative, (14)C-labeled cpd, aniline phosphate (1:2), Lrrc21, dermal system, Proteomes, presence or absence in organismfirst cervical vertebra, advanced, atlas, human being, T-cell surface antigen T4/Leu-3, external covering of organism, pancreatic T effector cell, T-cell surface antigen T4|Leu-3, organism surface, Homo sapiense, Th1, Cell, Th2, surface, Homo spaiens, L3T4, Homo sapien, T-cell differentiation antigen L3T4, Homo sapian, Homo sapians, Ly-4, precocious, Homo sapeins, cervical atlas, immature T cell, T lymphocyte, integumentum commune, T-cell, Homo sapients, cervical vertebra 1, body surface, C1, T-cell surface glycoprotein CD4, Humo sapiens, CD4mut, T-lymphocyte, man, Homo sapines, human, early, Homo spiens, "human" EXACT genbank_common_name [], T cell, vertebra 1, Homo sapience, integumentary system, Homo sampiens, mature T cell, CD4, T-lymphocytes, atlas (CI), dermal system, atlas vertebra, Home sapiens, activation., C1 vertebra, atlas [C I]sodium salt, first cervical vertebra, T-cell surface antigen T4/Leu-3, single-organism developmental process, aniline perchlorate, determination, T-lymphocyte activation, selection process, Gene Expression Profile, Profiles, Homo sapiense, Cell Biologies, Th1, cell associated, Th2, L3T4, Readability, Homo sapien, responsivity, Homo sapians, T-cell activation, Ly-4, Antigen, Flow Microfluorimetry, establishment and maintenance of substrate location, primary stem, Cell Sortings, immature T cell, integumentum commune, treatment, Homo sapients, Identification, Fluorescence Activated Cell Sorting, Biology, C1, proteins, Signatures, vertebra 1, Homo sapience, Expression Signature, aniline hydrochloride-(14)C-labeled cpd, disease management, Transcriptomes, Therapies, memory T-lymphocyte, Home sapiens, Flow Cytofluorometry, Therapy, Cell Sorting, establishment and maintenance of substance location, Fluorescence-Activated Cell Sorting, Data Set, external covering of organism, T-cell surface antigen T4|Leu-3, Arts, Expression Profiles, Biologies, Liquid Chromatography, 15N-labeled cpd, 3H-labeled cpd, organism surface, aniline diphosphate (4:1), predicted, Microfluorimetry, Gene Expression, single organism localization, count, Homo sapian, Expression Signatures, precocious, aniline sulfate, Cellular, Ligature, Expression Profile, activation, Transcriptome Profiles, Epistemology, T-cell, Industrial, Cytofluorometries, Industrial Arts, T lymphocyte activation, T-cell surface glycoprotein CD4, aniline phosphonate (1:1), expanded, Identifications (Psychology), CD4mut, T-lymphocyte, Homo sapines, Fluorescence-Activated Cell, human, early, experimental procedures, aniline diphosphate (3:1), T cell, primary axis, enlarged, integumentary system, atlas (CI), cell bound, dermal system, Proteomes, establishment and maintenance of cellular component location, big, advanced, atlas, human being, experimental, Transcriptome Profile, number, aniline hydrobromide, Gene, stalk, aniline phosphate (1:1), 3-(13)C-labeled cpd, presence, Fluorescence-Activated, Homo spaiens, surface, large, Fluorescence-Activated Cell Sortings, Microfluorometry, Gene Products, establishment and maintenance of position, aniline hydrofluoride, 4-(13)C-labeled cpd, cervical atlas, aniline, aniline monosulfate, Cytofluorometry, reactivity, aniline sulfate (2:1), methods, Flow Cytofluorometries, cell, experimental section, Microfluorometries, Profile, aniline hydrogen iodide, Treatments., Cellular Biologies, man, culm, Ligations, aniline aluminium salt, Homo sampiens, great, mature T cell, aniline dihydrofluoride, Flow, Flow Microfluorometries, Cytometry, atlas vertebra, aniline nitrate, Cytometries, Sortings, atlas [C I], data, Characters, Transcriptome, pancreatic T effector cell, axis, Cellular Biology, Proteins, Flow Cytometries, Cell, whole transcriptome, memory T cell, polypeptide, aniline diphosphate (1:1), development, count in organism, T-cell differentiation antigen L3T4, benzenamine, Protein, chemical analysis, Gene Expression Signatures, establishment and maintenance of localization, Gene Expression Signature, Homo sapeins, aniline phosphate (2:1), Flow Microfluorometry, magnesium (1:1) salt, T lymphocyte, memory T lymphocyte, Regenerations, Ligatures, Cytology, cervical vertebra 1, body surface, monolithium salt, Humo sapiens, aniline hydrochloride-(15)N-labeled cpd, ion(1+), single-organism localization, Understanding, (13)C-labeled cpd, Protein Gene Products, 2-(13)C-labeled cpd, conjugate acid, Gene Proteins, Homo spiens, "human" EXACT genbank_common_name [], localisation, Therapeutic, Gene Expression Profiles, Sorting, aniline hydrochloride, CD4, T-lymphocytes, Treatment, assay, response, quantitative, (14)C-labeled cpd, aniline phosphate (1:2), Signature, memory T-cell, C1 vertebra, presence or absence in organism1606http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310020145dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0embl-pathogen~0pride~1human_diseases~0geo_datasets~0embl~0treefam~0project~1uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.0049352251696483650.01.0falseA combined omics approach to generate the surface atlas of human naive CD4+ T cells during early TCR activation.Data from ProteomeXchange, PXD ID: PXD001432. File: SUK5557A8MA2__008-Spender2_3hP SUK5557A8MA2-40-215297.mzml. Published as part of . From the Abstract: {{i}} ... Periodate oxidation and aniline-catalyzed oxime ligation (PAL) technology was applied with subsequent quantitative LC-MS/MS (PAL-qLC-MS/MS) to generate a dataset describing the surface proteome of primary human naive CD4+ T cells and to monitor dynamic changes during the early phase of activation ... {{/i}}2015-05-28GPM3231002014525991687PXD001432PXD001432