{"doi":"10.1007/978-1-0716-1311-5_23","title":"Quantifying Proteome and Protein Modifications in Activated T Cells by Multiplexed Isobaric Labeling Mass Spectrometry","abstract":null,"journal":"Methods in Molecular Biology","year":2021,"id":599655,"datarank":0.24141568686511508,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.0,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":287645,"name":"Daniel Bastardo Blanco","orcid":"0000-0001-8232-7522","position":1,"is_corresponding":false},{"id":498251,"name":"Boer Xie","orcid":null,"position":2,"is_corresponding":false},{"id":1487947,"name":"Yuxin Li","orcid":"0000-0001-6593-1453","position":3,"is_corresponding":false},{"id":110360,"name":"Zhiping Wu","orcid":"0000-0002-5554-3681","position":4,"is_corresponding":false},{"id":110364,"name":"Hongbo Chi","orcid":"0000-0002-9997-2496","position":5,"is_corresponding":false},{"id":97162,"name":"Junmin Peng","orcid":"0000-0003-0472-7648","position":6,"is_corresponding":false},{"id":110351,"name":"Haiyan Tan","orcid":"0000-0001-6687-2563","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Quantifying Proteome and Protein Modifications in Activated T Cells by Multiplexed Isobaric Labeling Mass Spectrometry","abstract":"The dynamic regulation of protein function by altered protein expression and post-translational modifications (PTMs) is essential for T cell function, but it has remained difficult to systemically quantify such events. Mass spectrometry (MS)-based proteomics has become a mainstream tool for comprehensive profiling of proteome and PTMs, especially with the development of multiplexed isobaric labeling methods, such as tandem mass tag (TMT), coupled with high-resolution two-dimensional liquid chromatography and tandem mass spectrometry (LC/LC-MS/MS). Here, we introduce a deep proteomics profiling protocol with an optimized 11-plex TMT-LC/LC-MS/MS platform to quantitate whole proteome, phosphoproteome, acetylome, and methylome in activated T cells. The major steps include preparation of activated T cells, protein extraction and digestion, TMT labeling, basic pH reverse phase LC, modified peptide enrichment, acidic pH reverse phase LC-MS/MS, and computational data processing. Approximately 10,000 proteins, 30,000 phosphosites, 2,000 lysine acetylated sites, and 1,000 lysine methylated sites can be identified and quantified from 1 mg of proteins per sample. Quality control steps are implemented in this protocol, and future development, such as nanoscale 16-plex TMT analysis, is discussed. This multiplexed and robust method provides a powerful tool for dissecting proteomic and PTM signatures in T cells at the systems level, and it is equally suitable for other biological samples, including effector T cell subsets.","is_dataset_classified":null,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"33928561","pmcid":null,"openalex_id":"https://openalex.org/W3157795800","authors":[],"funders":[],"total_grants":0,"fwci":1.1385,"citation_percentile":0.77335984,"influential_citations":0,"citation_trend":[{"year":2021,"count":2},{"year":2025,"count":2}],"oa_status":"closed","license":"https://www.springer.com/tdm","oa_locations":[{"url":"https://link.springer.com/content/pdf/10.1007/978-1-0716-1311-5_23","host_type":"publisher"},{"url":"https://doi.org/10.1007/978-1-0716-1311-5_23","host_type":"book series"},{"url":"https://pubmed.ncbi.nlm.nih.gov/33928561","host_type":"repository"}],"fields_of_study":["Advanced Proteomics Techniques and Applications","Mass Spectrometry Techniques and Applications","Peptidase Inhibition and Analysis","Acetylation","Animals","Chromatography, High Pressure Liquid","Chromatography, Reverse-Phase","Humans","Immunomagnetic Separation","Lymphocyte Activation","Methylation","Phosphorylation","Protein Processing, Post-Translational","Proteins","Proteome","Proteomics","Research Design","T-Lymphocytes","Tandem Mass Spectrometry","Workflow"],"mesh_terms":["Acetylation","Animals","Chromatography, High Pressure Liquid","Humans","Lymphocyte Activation","Methylation","Phosphorylation","Protein Processing, Post-Translational","Proteins","Research Design","T-Lymphocytes","Immunomagnetic Separation","Proteome","Proteomics","Tandem Mass Spectrometry","Chromatography, Reverse-Phase","Workflow"],"keywords":["Isobaric labeling","Tandem mass tag","Proteome","Proteomics","Chemistry","Tandem mass spectrometry","Mass spectrometry","Quantitative proteomics","Stable isotope labeling by amino acids in cell culture","Label-free quantification","Computational biology","Protein mass spectrometry","Chromatography","Biochemistry","Biology","Post-translational modifications","T cell","methylome","Phosphoproteome","Acetylome"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-29T10:57:31.668793Z","pmid":null,"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":[]}