{"doi":"10.1021/pr400210m","title":"Deconvolution of Mixture Spectra and Increased Throughput of Peptide Identification by Utilization of Intensified Complementary Ions Formed in Tandem Mass Spectrometry","abstract":null,"journal":"Journal of Proteome Research","year":2013,"id":614212,"datarank":0.49983067652628066,"base_score":3.332204510175204,"endowment":3.332204510175204,"self_citation_contribution":0.49983067652628066,"citation_network_contribution":0.0,"self_endowment_contribution":0.49983067652628066,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":27,"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":1582692,"name":"Thiago Verano-Braga","orcid":null,"position":1,"is_corresponding":false},{"id":1091334,"name":"Thomas A. Hansen","orcid":"0000-0002-7950-8039","position":2,"is_corresponding":false},{"id":1582693,"name":"Richard R. Sprenger","orcid":null,"position":3,"is_corresponding":false},{"id":1371889,"name":"Frank Kjeldsen","orcid":"0000-0003-0785-2903","position":4,"is_corresponding":false},{"id":1146244,"name":"Fedor Kryuchkov","orcid":"0000-0002-8611-9330","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Deconvolution of Mixture Spectra and Increased Throughput of Peptide Identification by Utilization of Intensified Complementary Ions Formed in Tandem Mass Spectrometry","abstract":"A cornerstone of mass spectrometry based proteomics is to relate with high statistical significance experimentally obtained tandem mass spectrometry (MS/MS) data to peptide sequences from a protein database. Most sequence specific fragment ions in MS/MS spectra are represented by a subset of complementary ion pairs. Here, we investigated the reliabilities of complementary ion pairs formed in CAD and CAD/ETD MS/MS and developed a reliability-based approach of intensification of ion signals of complementary pairs prior to database searching. In a large-scale proteomics experiment using high-resolution orbitrap mass spectrometry, an increase in the number of peptide identifications was obtained relative to the original CAD MS/MS spectra when intensified golden complementary (+18.6%) and CAD complementary pairs (+17.2%) were submitted to the Mascot search engine. This also exceeded the results obtained by deisotoping/deconvolution of CAD MS/MS spectra. A novel approach for extracting sequence-specific fragment ions of co-isolated peptides was developed based on the complementarity rules. This technique demonstrated an impressive gain of 42.4% more peptide identifications as compared with the use of the initial data set.","is_dataset_classified":null,"base_score":3.332204510175204,"endowment":3.332204510175204,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"23725413","pmcid":null,"openalex_id":"https://openalex.org/W2323274923","authors":[],"funders":[],"total_grants":0,"fwci":2.0064,"citation_percentile":0.85313362,"influential_citations":0,"citation_trend":[{"year":2014,"count":4},{"year":2015,"count":4},{"year":2016,"count":4},{"year":2017,"count":2},{"year":2018,"count":2},{"year":2019,"count":2},{"year":2020,"count":1},{"year":2021,"count":2},{"year":2023,"count":2},{"year":2024,"count":1},{"year":2025,"count":3}],"oa_status":"closed","license":null,"oa_locations":[{"url":"https://pubs.acs.org/doi/pdf/10.1021/pr400210m","host_type":"publisher"},{"url":"https://doi.org/10.1021/pr400210m","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/23725413","host_type":"repository"},{"url":"https://portal.findresearcher.sdu.dk/da/publications/c45f3ebf-2ae0-45da-800c-c5ff2d7a2f60","host_type":"repository"}],"fields_of_study":["Advanced Proteomics Techniques and Applications","Mass Spectrometry Techniques and Applications","Metabolomics and Mass Spectrometry Studies","Algorithms","Databases, Protein","Humans","Ions","Mass Spectrometry","Peptides","Proteomics","Software","Tandem Mass Spectrometry"],"mesh_terms":["Algorithms","Humans","Ions","Peptides","Software","Mass Spectrometry","Databases, Protein","Proteomics","Tandem Mass Spectrometry"],"keywords":["Tandem mass spectrometry","Mass spectrometry","Chemistry","Orbitrap","Database search engine","Peptide","Deconvolution","Ion","Tandem mass tag","Mass spectrum","Chromatography","Analytical Chemistry (journal)","Proteomics","Quantitative proteomics","Search engine","Computer science","Algorithm","Biochemistry"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-02T11:34:01.890616Z","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":[]}