{"id":"https://openalex.org/W7131430024","doi":"https://doi.org/10.1021/acs.jcim.5c02981","title":"Cycle-MS: A Closed-Loop End-to-End Framework for Mass Spectrometry Structure Elucidation","display_name":"Cycle-MS: A Closed-Loop End-to-End Framework for Mass Spectrometry Structure Elucidation","publication_year":2026,"publication_date":"2026-02-25","ids":{"openalex":"https://openalex.org/W7131430024","doi":"https://doi.org/10.1021/acs.jcim.5c02981","pmid":"https://pubmed.ncbi.nlm.nih.gov/41740157"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02981","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02981","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015595044","display_name":"Jinglong Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinglong Lin","raw_affiliation_strings":["Peking University","School of Materials Science and Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Peking University","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"School of Materials Science and Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065859286","display_name":"Hui Li","orcid":"https://orcid.org/0000-0001-9198-3951"},"institutions":[{"id":"https://openalex.org/I4210128628","display_name":"Peking University Shenzhen Hospital","ror":"https://ror.org/03kkjyb15","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128628"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Li","raw_affiliation_strings":["Peking University Shenzhen Graduate School","School of Electronic and Computer Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Peking University Shenzhen Graduate School","institution_ids":["https://openalex.org/I4210128628"]},{"raw_affiliation_string":"School of Electronic and Computer Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126812534","display_name":"Chengchun Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chengchun Liu","raw_affiliation_strings":["Peking University","School of Materials Science and Engineering"],"raw_orcid":"https://orcid.org/0009-0002-5550-4145","affiliations":[{"raw_affiliation_string":"Peking University","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"School of Materials Science and Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126803841","display_name":"Zhiyuan Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210128628","display_name":"Peking University Shenzhen Hospital","ror":"https://ror.org/03kkjyb15","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128628"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiyuan Yan","raw_affiliation_strings":["Peking University Shenzhen Graduate School","School of Electronic and Computer Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Peking University Shenzhen Graduate School","institution_ids":["https://openalex.org/I4210128628"]},{"raw_affiliation_string":"School of Electronic and Computer Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126831408","display_name":"Li Yuan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210128628","display_name":"Peking University Shenzhen Hospital","ror":"https://ror.org/03kkjyb15","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128628"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Yuan","raw_affiliation_strings":["Peking University Shenzhen Graduate School","School of Electronic and Computer Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Peking University Shenzhen Graduate School","institution_ids":["https://openalex.org/I4210128628"]},{"raw_affiliation_string":"School of Electronic and Computer Engineering","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124866657","display_name":"Fanyang Mo","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210128628","display_name":"Peking University Shenzhen Hospital","ror":"https://ror.org/03kkjyb15","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128628"]},{"id":"https://openalex.org/I4210166566","display_name":"Preferred Networks (Japan)","ror":"https://ror.org/05xeefy56","country_code":"JP","type":"company","lineage":["https://openalex.org/I4210166566"]}],"countries":["CN","JP"],"is_corresponding":true,"raw_author_name":"Fanyang Mo","raw_affiliation_strings":["AI for Science (AI4S)-Preferred Program","Peking University","Peking University Shenzhen Graduate School","School of Advanced Materials","School of Materials Science and Engineering"],"raw_orcid":"https://orcid.org/0000-0002-4140-3020","affiliations":[{"raw_affiliation_string":"AI for Science (AI4S)-Preferred Program","institution_ids":["https://openalex.org/I4210166566"]},{"raw_affiliation_string":"Peking University","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Peking University Shenzhen Graduate School","institution_ids":["https://openalex.org/I4210128628"]},{"raw_affiliation_string":"School of Advanced Materials","institution_ids":[]},{"raw_affiliation_string":"School of Materials Science and Engineering","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5124866657"],"corresponding_institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210128628","https://openalex.org/I4210166566"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.24425476,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"66","issue":"5","first_page":"2709","last_page":"2718"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9200999736785889,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9200999736785889,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.019600000232458115,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.012600000016391277,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.8138999938964844},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.5551000237464905},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4666999876499176},{"id":"https://openalex.org/keywords/refining","display_name":"Refining (metallurgy)","score":0.41659998893737793},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.3750999867916107},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.3702000081539154},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.361299991607666}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8138999938964844},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6366999745368958},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.5551000237464905},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4666999876499176},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4185999929904938},{"id":"https://openalex.org/C60044698","wikidata":"https://www.wikidata.org/wiki/Q1283324","display_name":"Refining (metallurgy)","level":2,"score":0.41659998893737793},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3815000057220459},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.3750999867916107},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.3702000081539154},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.361299991607666},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.3562000095844269},{"id":"https://openalex.org/C207467116","wikidata":"https://www.wikidata.org/wiki/Q4385666","display_name":"Inverse","level":2,"score":0.3456000089645386},{"id":"https://openalex.org/C178910836","wikidata":"https://www.wikidata.org/wiki/Q2196961","display_name":"Molecular model","level":2,"score":0.34279999136924744},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.33959999680519104},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3091000020503998},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3034000098705292},{"id":"https://openalex.org/C2989255885","wikidata":"https://www.wikidata.org/wiki/Q500256","display_name":"Molecular conformation","level":3,"score":0.2752000093460083},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.2728999853134155},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.2678999900817871},{"id":"https://openalex.org/C40325409","wikidata":"https://www.wikidata.org/wiki/Q2360668","display_name":"Mass spectrum","level":3,"score":0.2603999972343445}],"mesh":[{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c02981","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02981","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:41740157","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41740157","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320317136","display_name":"Shenzhen Government","ror":null},{"id":"https://openalex.org/F4320334944","display_name":"Shenzhen Graduate School, Peking University","ror":"https://ror.org/02v51f717"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1761787460","https://openalex.org/W2023096047","https://openalex.org/W2032555174","https://openalex.org/W2069364332","https://openalex.org/W2086337711","https://openalex.org/W2126020661","https://openalex.org/W2129265015","https://openalex.org/W2140985419","https://openalex.org/W2290847742","https://openalex.org/W2462785116","https://openalex.org/W2561730314","https://openalex.org/W2778051509","https://openalex.org/W2914836620","https://openalex.org/W2921388451","https://openalex.org/W2922522932","https://openalex.org/W2947763854","https://openalex.org/W2979579661","https://openalex.org/W3093062675","https://openalex.org/W3209814067","https://openalex.org/W3210740626","https://openalex.org/W4200271038","https://openalex.org/W4211236956","https://openalex.org/W4213077304","https://openalex.org/W4281688302","https://openalex.org/W4293192370","https://openalex.org/W4295022004","https://openalex.org/W4311480785","https://openalex.org/W4317938055","https://openalex.org/W4378716419","https://openalex.org/W4380870591","https://openalex.org/W4381804451","https://openalex.org/W4383905164","https://openalex.org/W4386863955","https://openalex.org/W4388623498","https://openalex.org/W4391993349","https://openalex.org/W4393981121","https://openalex.org/W4403380203","https://openalex.org/W4406586549","https://openalex.org/W4411470477","https://openalex.org/W4416386453","https://openalex.org/W4416575602"],"related_works":[],"abstract_inverted_index":{"Mass":[0],"spectrometry":[1],"(MS)":[2],"is":[3],"indispensable":[4],"for":[5],"molecular":[6,11,49,59],"analysis;":[7],"however,":[8],"elucidating":[9],"complex":[10],"structures":[12],"from":[13],"spectra":[14],"remains":[15],"a":[16,90,98],"major":[17],"challenge.":[18],"Here,":[19],"we":[20],"present":[21],"Cycle-MS,":[22],"an":[23],"end-to-end":[24],"framework":[25,95],"that":[26,68,96],"unifies":[27],"inverse":[28],"spectrum-to-molecule":[29],"prediction":[30],"with":[31,35],"forward":[32],"spectrum":[33],"reconstruction,":[34],"cycle-consistency":[36],"losses":[37],"refining":[38],"latent":[39],"representations.":[40],"Cycle-MS":[41,69,88],"demonstrates":[42],"enhanced":[43],"accuracy":[44],"in":[45],"predicting":[46],"atomic":[47],"compositions,":[48],"formulas,":[50],"scaffolds,":[51],"and":[52,61,81,93],"functional":[53],"groups,":[54],"offering":[55],"robust":[56],"recovery":[57],"of":[58],"scale":[60],"key":[62],"chemical":[63,79],"features.":[64],"Interpretability":[65],"analysis":[66],"shows":[67],"prioritizes":[70],"structurally":[71],"diagnostic":[72],"fragments":[73],"over":[74],"nonspecific":[75],"abundant":[76],"peaks,":[77],"ensuring":[78],"plausibility":[80],"structural":[82],"reliability.":[83],"Together,":[84],"these":[85],"advances":[86],"establish":[87],"as":[89],"robust,":[91],"accurate,":[92],"interpretable":[94],"offers":[97],"path":[99],"toward":[100],"fully":[101],"automated,":[102],"high-precision":[103],"MS-based":[104],"structure":[105],"elucidation.":[106]},"counts_by_year":[],"updated_date":"2026-06-14T07:44:22.658603","created_date":"2026-02-26T00:00:00"}