{"doi":"10.1021/acs.jproteome.9b00347","title":"Mass Spectrometry-Compatible Subcellular Fractionation for Proteomics","abstract":null,"journal":"Journal of Proteome Research","year":2020,"id":601213,"datarank":0.5101796072493234,"base_score":3.4011973816621555,"endowment":3.4011973816621555,"self_citation_contribution":0.5101796072493234,"citation_network_contribution":0.0,"self_endowment_contribution":0.5101796072493234,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":29,"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":1541492,"name":"Naoyuki Sugiyama","orcid":null,"position":1,"is_corresponding":false},{"id":29264,"name":"Masaru Tomita","orcid":"0000-0003-3423-377X","position":2,"is_corresponding":false},{"id":670847,"name":"Sumio Ohtsuki","orcid":"0000-0003-4634-7133","position":3,"is_corresponding":false},{"id":838947,"name":"Yasushi Ishihama","orcid":"0000-0001-7714-203X","position":4,"is_corresponding":false},{"id":670841,"name":"Takeshi Masuda","orcid":"0000-0003-0121-4783","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Mass Spectrometry-Compatible Subcellular Fractionation for Proteomics","abstract":"We found that nuclear envelopes stabilize against surfactants in the presence of ethylene glycol (EG). We, therefore, developed a novel subcellular fractionation approach for proteomics using RIPA buffer containing EG and phase transfer surfactants. This method involves separating the cells into the cytoplasm, organelles, and nucleus, including intermediate filaments without ultracentrifugation. These fractions are directly applicable to sample preparation for shotgun proteomics as they have no mass spectrometry (MS)-incompatible chemicals, whereas those separated by traditional fractionation protocols require desalting. This protocol is successfully applied to subcellular fractionation with only 3.5 × 105 cells. Here, it was combined with phosphoproteomics and proteomics to identify phosphorylation sites regulating protein subcellular localization. In total, 59 phosphorylation sites on 42 phosphopeptides and 32 proteins showing different enrichment patterns between phosphoproteomics and the corresponding proteomics were identified, which are potential candidate sites to regulate the protein subcellular localization, including serine 706 on CD44 and serine 22 on lamin A/C.","is_dataset_classified":null,"base_score":3.4011973816621555,"endowment":3.4011973816621555,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"31599158","pmcid":null,"openalex_id":"https://openalex.org/W2980121198","authors":[],"funders":[{"funder_name":"Japan Society for the Promotion of Science","grant_id":"17K15042","title":null},{"funder_name":"Japan Society for the Promotion of Science","grant_id":"19K05544","title":null},{"funder_name":"Japan Society for the Promotion of Science","grant_id":"23710218","title":null}],"total_grants":3,"fwci":1.9855,"citation_percentile":0.85807545,"influential_citations":0,"citation_trend":[{"year":2020,"count":1},{"year":2021,"count":10},{"year":2022,"count":6},{"year":2023,"count":3},{"year":2024,"count":4},{"year":2025,"count":4},{"year":2026,"count":1}],"oa_status":"closed","license":"https://doi.org/10.15223/policy-029","oa_locations":[{"url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.9b00347","host_type":"publisher"},{"url":"https://doi.org/10.1021/acs.jproteome.9b00347","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/31599158","host_type":"repository"}],"fields_of_study":["Advanced Proteomics Techniques and Applications","Mass Spectrometry Techniques and Applications","Glycosylation and Glycoproteins Research","Medicine","Chemistry","Biology","Materials Science"],"mesh_terms":["Chemical Fractionation","Phosphopeptides","Proteins","Mass Spectrometry","Subcellular Fractions","Proteomics"],"keywords":["Phosphoproteomics","Proteomics","Shotgun proteomics","Cell fractionation","Chemistry","Quantitative proteomics","Proteome","Protein subcellular localization prediction","Subcellular localization","Phosphorylation","Organelle","Fractionation","Phosphopeptide","Mass spectrometry","Biochemistry","Protein phosphorylation","Chromatography","Cytoplasm","Protein kinase A","Membrane"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Clean water and sanitation"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-29T15:32:12.239880Z","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":[]}