{"doi":"10.1021/acs.analchem.2c04742","title":"Super-Resolution Mass Spectrometry Enables Rapid, Accurate, and Highly Multiplexed Proteomics at the MS2 Level","abstract":"In tandem mass spectrometry (MS2)-based multiplexed quantitative proteomics, the complement reporter ion approaches (TMTc and TMTproC) were developed to eliminate the ratio-compression problem of conventional MS2-level approaches. Resolving all high m / z complement reporter ions (∼6.32 mDa-spaced) requires mass resolution and scan speeds above the performance levels of Orbitrap TM instruments. Therefore, complement reporter ion quantification with TMT/TMTpro reagents is currently limited to 5 out of 11 (TMT) or 9 out of 18 (TMTpro) channels (∼1 Da spaced). We first demonstrate that a Fusion TM Lumos TM Orbitrap can resolve 6.32 mDa-spaced complement reporter ions with standard acquisition modes extended with 3 s transients. We then implemented a super-resolution mass spectrometry approach using the least-squares fitting (LSF) method for processing Orbitrap transients to achieve shotgun proteomics-compatible scan rates. The LSF performance resolves the 6.32 mDa doublets for all TMTproC channels in the standard mass range with transients as short as ∼108 ms (Orbitrap resolution setting of 50,000 at m / z 200). However, we observe a slight decrease in measurement precision compared to 1 Da spacing with the 108 ms transients. With 256 ms transients (resolution of 120,000 at m / z 200), coefficients of variation are essentially indistinguishable from 1 Da samples. We thus demonstrate the feasibility of highly multiplexed, accurate, and precise shotgun proteomics at the MS2 level.","journal":"Analytical Chemistry","year":2023,"id":339286,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":16,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9564,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":360696,"name":"Alex Johnson","orcid":"0000-0003-1825-2962","position":1,"is_corresponding":false},{"id":267548,"name":"Konstantin O. Nagornov","orcid":"0000-0002-8993-5739","position":2,"is_corresponding":false},{"id":563322,"name":"Michael Stadlmeier","orcid":"0000-0001-7806-3077","position":3,"is_corresponding":false},{"id":481730,"name":"Warham Lance Martin","orcid":null,"position":4,"is_corresponding":false},{"id":1005646,"name":"Loı̈c Dayon","orcid":"0000-0002-8499-270X","position":5,"is_corresponding":false},{"id":1005647,"name":"John Corthésy","orcid":"0000-0003-2104-7425","position":6,"is_corresponding":false},{"id":308774,"name":"Martin Wühr","orcid":"0000-0002-0244-8947","position":7,"is_corresponding":false},{"id":267527,"name":"Yury O. Tsybin","orcid":"0000-0001-7533-0774","position":8,"is_corresponding":false},{"id":267544,"name":"Anton N. Kozhinov","orcid":"0000-0003-1961-075X","position":0,"is_corresponding":true}],"reference_count":45,"raw_metadata":null,"created_at":"2026-07-19T01:10:45.048445Z","pmid":"36749928","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":[]}