{"doi":"10.1021/pr500630a","title":"Comparing SILAC- and Stable Isotope Dimethyl-Labeling Approaches for Quantitative Proteomics","abstract":null,"journal":"Journal of Proteome Research","year":2014,"id":602407,"datarank":0.7023196840686331,"base_score":4.68213122712422,"endowment":4.68213122712422,"self_citation_contribution":0.7023196840686331,"citation_network_contribution":0.0,"self_endowment_contribution":0.7023196840686331,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":107,"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":1544957,"name":"Hyong Won Suh","orcid":null,"position":1,"is_corresponding":false},{"id":418805,"name":"Martin Golkowski","orcid":"0000-0002-0996-1655","position":2,"is_corresponding":false},{"id":31797,"name":"Shao-En Ong","orcid":null,"position":3,"is_corresponding":false},{"id":58016,"name":"Ho-Tak Lau","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Comparing SILAC- and Stable Isotope Dimethyl-Labeling Approaches for Quantitative Proteomics","abstract":"Stable isotope labeling is widely used to encode and quantify proteins in mass-spectrometry-based proteomics. We compared metabolic labeling with stable isotope labeling by amino acids in cell culture (SILAC) and chemical labeling by stable isotope dimethyl labeling and find that they have comparable accuracy and quantitative dynamic range in unfractionated proteome analyses and affinity pull-down experiments. Analyzing SILAC- and dimethyl-labeled samples together in single liquid chromatography-mass spectrometric analyses minimizes differences under analytical conditions, allowing comparisons of quantitative errors introduced during sample processing. We find that SILAC is more reproducible than dimethyl labeling. Because proteins from metabolically labeled populations can be combined before proteolytic digestion, SILAC is particularly suited to studies with extensive sample processing, such as fractionation and enrichment of peptides with post-translational modifications. We compared both methods in pull-down experiments using a kinase inhibitor, dasatinib, and tagged GRB2-SH2 protein as affinity baits. We describe a StageTip dimethyl-labeling protocol that we applied to in-solution and in-gel protein digests. Comparing the impact of post-digest isotopic labeling on quantitative accuracy, we demonstrate how specific experimental designs can benefit most from metabolic labeling approaches like SILAC and situations where chemical labeling by stable isotope-dimethyl labeling can be a practical alternative.","is_dataset_classified":null,"base_score":4.68213122712422,"endowment":4.68213122712422,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"25077673","pmcid":"PMC4156256","openalex_id":"https://openalex.org/W2318773378","authors":[],"funders":[{"funder_name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","grant_id":"R01AR065459","title":null},{"funder_name":"National Cancer Institute","grant_id":"R21CA177402","title":null},{"funder_name":"National Institutes of Health","grant_id":"5R21CA177402-03","title":"Kinase Profiling with Quantititative Chemoproteomics"},{"funder_name":"National Institutes of Health","grant_id":"4R01AR065459-04","title":"Characterizing Muscle Regulatory Elements with Mass Spectrometry-Based Proteomics"},{"funder_name":"Fundação para a Ciência e a Tecnologia, I.P.","grant_id":"PTDC/CCI-INF/6762/2020","title":"MS3: New foundations for micro-services and serverless systems"}],"total_grants":5,"fwci":5.1716,"citation_percentile":0.96802326,"influential_citations":0,"citation_trend":[{"year":2014,"count":1},{"year":2015,"count":12},{"year":2016,"count":12},{"year":2017,"count":8},{"year":2018,"count":15},{"year":2019,"count":11},{"year":2020,"count":15},{"year":2021,"count":7},{"year":2022,"count":8},{"year":2023,"count":8},{"year":2024,"count":5},{"year":2025,"count":4},{"year":2026,"count":1}],"oa_status":"closed","license":"publisher-specific-oa","oa_locations":[{"url":"https://pubs.acs.org/doi/pdf/10.1021/pr500630a","host_type":"publisher"},{"url":"https://doi.org/10.1021/pr500630a","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/25077673","host_type":"repository"},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.793.5509","host_type":""},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4156256","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC4156256","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC4156256?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1021/pr500630a","host_type":""},{"url":"https://dx.doi.org/10.1021/pr500630a","host_type":""}],"fields_of_study":["Advanced Proteomics Techniques and Applications","Mass Spectrometry Techniques and Applications","Metabolomics and Mass Spectrometry Studies","0301 basic medicine","0303 health sciences","03 medical and health sciences","Amino Acids","HeLa Cells","Humans","Isotope Labeling","Models, Chemical","Proteins","Proteome","Proteomics"],"mesh_terms":["Amino Acids","HeLa Cells","Humans","Isotope Labeling","Models, Chemical","Proteins","Proteome","Proteomics","Hela Cells"],"keywords":["Stable isotope labeling by amino acids in cell culture","Quantitative proteomics","Proteomics","Chemistry","Stable isotope ratio","Isotope","Computational biology","Chromatography","Biology","Biochemistry","Models, Chemical","Proteome","Isotope Labeling","Humans","Proteins","Amino Acids","HeLa Cells"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-29T19:17:40.431184Z","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":[]}