{"id":"https://openalex.org/W7204922727","doi":"https://doi.org/10.1021/acs.analchem.6c04898","title":"Structure\u2013Spectrum Fidelity in Tandem Mass Spectrometry: Quantifying the Limits of Similarity-Based Structural Inference","display_name":"Structure\u2013Spectrum Fidelity in Tandem Mass Spectrometry: Quantifying the Limits of Similarity-Based Structural Inference","publication_year":2026,"publication_date":"2026-08-26","ids":{"openalex":"https://openalex.org/W7204922727","doi":"https://doi.org/10.1021/acs.analchem.6c04898","pmid":"https://pubmed.ncbi.nlm.nih.gov/42708754"},"language":"en","primary_location":{"id":"doi:10.1021/acs.analchem.6c04898","doi":"https://doi.org/10.1021/acs.analchem.6c04898","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.analchem.6c04898","pdf_url":null,"source":{"id":"https://openalex.org/S191963794","display_name":"Analytical Chemistry","issn_l":"0003-2700","issn":["0003-2700","1520-6882"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"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":"Analytical Chemistry","raw_type":"journal-article"},"volume":null,"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/A5058294756","display_name":"Winnie Uritboonthai","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Winnie Uritboonthai","raw_affiliation_strings":["Scripps Research , , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Scripps Research , , , ,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5148844222","display_name":"Linh Hoang","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Linh Hoang","raw_affiliation_strings":["Scripps Research , , , ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Scripps Research , , , ,","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067311581","display_name":"Gary E. Siuzdak","orcid":"https://orcid.org/0000-0002-4749-0014","observed_orcids":["https://orcid.org/0000-0002-4749-0014"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Gary Siuzdak","raw_affiliation_strings":["Scripps Research , , , ,"],"raw_orcid":"https://orcid.org/0000-0002-4749-0014","affiliations":[{"raw_affiliation_string":"Scripps Research , , , ,","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5067311581"],"corresponding_institution_ids":[],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.50749803,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"98","issue":"35","first_page":"26104","last_page":"26116"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9063000082969666,"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":0.9063000082969666,"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":0.06400000303983688,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.011099999770522118,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/tandem-mass-spectrometry","display_name":"tandem mass spectrometry","score":0.8980000019073486},{"id":"https://openalex.org/keywords/spectral-similarity","display_name":"spectral similarity","score":0.9670000076293945},{"id":"https://openalex.org/keywords/structural-inference","display_name":"structural inference","score":0.8999999761581421},{"id":"https://openalex.org/keywords/collision-energy","display_name":"collision energy","score":0.5270000100135803},{"id":"https://openalex.org/keywords/cosine-similarity","display_name":"cosine similarity","score":0.5870000123977661},{"id":"https://openalex.org/keywords/ecfp4","display_name":"ECFP4","score":0.6499999761581421},{"id":"https://openalex.org/keywords/molecular-formula","display_name":"molecular formula","score":0.5600000023841858},{"id":"https://openalex.org/keywords/fragmentation","display_name":"fragmentation","score":0.42399999499320984},{"id":"https://openalex.org/keywords/structural-analogs","display_name":"structural analogues","score":0.5400000214576721}],"concepts":[{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.7523999810218811},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.6779000163078308},{"id":"https://openalex.org/C2780762811","wikidata":"https://www.wikidata.org/wiki/Q1784941","display_name":"Cosine similarity","level":3,"score":0.6226999759674072},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.5996000170707703},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5710999965667725},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5259000062942505},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5141000151634216},{"id":"https://openalex.org/C2776459999","wikidata":"https://www.wikidata.org/wiki/Q2119376","display_name":"Fidelity","level":2,"score":0.4442000091075897},{"id":"https://openalex.org/C12426560","wikidata":"https://www.wikidata.org/wiki/Q189569","display_name":"Basis (linear algebra)","level":2,"score":0.43779999017715454},{"id":"https://openalex.org/C2777814067","wikidata":"https://www.wikidata.org/wiki/Q1752317","display_name":"Tandem","level":2,"score":0.4196000099182129},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.38600000739097595},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37529999017715454},{"id":"https://openalex.org/C4839761","wikidata":"https://www.wikidata.org/wiki/Q212111","display_name":"Spectral line","level":2,"score":0.3700000047683716},{"id":"https://openalex.org/C191015642","wikidata":"https://www.wikidata.org/wiki/Q1132459","display_name":"Fragmentation (computing)","level":2,"score":0.3668999969959259},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3450999855995178},{"id":"https://openalex.org/C152822103","wikidata":"https://www.wikidata.org/wiki/Q7575207","display_name":"Spectral shape analysis","level":3,"score":0.3434000015258789},{"id":"https://openalex.org/C2221639","wikidata":"https://www.wikidata.org/wiki/Q2877","display_name":"Discrete cosine transform","level":3,"score":0.3070000112056732},{"id":"https://openalex.org/C178009071","wikidata":"https://www.wikidata.org/wiki/Q93344","display_name":"Trigonometric functions","level":2,"score":0.29899999499320984},{"id":"https://openalex.org/C176641082","wikidata":"https://www.wikidata.org/wiki/Q2446767","display_name":"Spectral signature","level":2,"score":0.2973000109195709},{"id":"https://openalex.org/C143271835","wikidata":"https://www.wikidata.org/wiki/Q254515","display_name":"Similitude","level":2,"score":0.290800005197525},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.29019999504089355},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.2822999954223633},{"id":"https://openalex.org/C121704057","wikidata":"https://www.wikidata.org/wiki/Q352070","display_name":"Collision","level":2,"score":0.2777000069618225},{"id":"https://openalex.org/C31827203","wikidata":"https://www.wikidata.org/wiki/Q874296","display_name":"Tandem mass spectrometry","level":3,"score":0.2703000009059906},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2547999918460846}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.analchem.6c04898","doi":"https://doi.org/10.1021/acs.analchem.6c04898","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.analchem.6c04898","pdf_url":null,"source":{"id":"https://openalex.org/S191963794","display_name":"Analytical Chemistry","issn_l":"0003-2700","issn":["0003-2700","1520-6882"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"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":"Analytical Chemistry","raw_type":"journal-article"},{"id":"pmid:42708754","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42708754","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,"listed_in":[],"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":"Analytical chemistry","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G5726262566","display_name":"Mummichog 3, aligning mass spectrometry data to biological networks","funder_award_id":"U01CA235493","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G9000868481","display_name":"Metabolomics Technologies to Advance Biomedical Research","funder_award_id":"R35GM130385","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G9000911046","display_name":"Links between rRNA and tRNA modifications, codon use, translation, and metabolism in cancer cells","funder_award_id":"1u01ca305256-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1995543670","https://openalex.org/W2028421938","https://openalex.org/W2039609876","https://openalex.org/W2055043387","https://openalex.org/W2084375915","https://openalex.org/W2096057003","https://openalex.org/W2144803530","https://openalex.org/W2504691963","https://openalex.org/W2756902045","https://openalex.org/W3216027541","https://openalex.org/W4290831374","https://openalex.org/W4410053882","https://openalex.org/W4412488394","https://openalex.org/W7155033017","https://openalex.org/W7164399956","https://openalex.org/W7167264737"],"related_works":["https://openalex.org/W1978312864","https://openalex.org/W3209680996","https://openalex.org/W1979763885","https://openalex.org/W3156075822","https://openalex.org/W1991789125","https://openalex.org/W2006849336","https://openalex.org/W2264332774","https://openalex.org/W3129424480","https://openalex.org/W2756902045","https://openalex.org/W1987556094"],"abstract_inverted_index":{"Tandem":[0],"mass":[1],"spectral":[2,36,57],"similarity":[3,37,51,58,65,75,193,198],"is":[4,199],"widely":[5],"used":[6],"to":[7,96,150,171,177],"infer":[8],"molecular":[9,117],"structural":[10,39,50,64,77,160,224,234],"relatedness,":[11],"yet":[12],"the":[13,63,88,102,169],"fidelity":[14],"of":[15,112,145,155],"this":[16,174],"relationship":[17],"has":[18],"not":[19,92,210,220],"been":[20],"systematically":[21],"quantified":[22],"using":[23],"authenticated":[24,43],"reference":[25],"spectra.":[26],"Here,":[27],"we":[28,48],"introduce":[29],"Structure-Spectrum":[30],"Fidelity":[31],"(SSF),":[32],"describing":[33],"how":[34],"faithfully":[35],"preserves":[38],"relatedness.":[40,225],"Using":[41],"12,432":[42],"compounds":[44],"from":[45],"METLIN":[46],"Core,":[47],"compared":[49],"across":[52],"77.3":[53],"million":[54],"pairs":[55,61,113,157],"with":[56],"in":[59,71,98,108],"4000":[60],"spanning":[62],"distribution":[66],"at":[67,105,181,187],"four":[68],"collision":[69,183],"energies":[70],"both":[72,99],"polarities.":[73],"Spectral":[74,197],"preserved":[76],"information,":[78],"but":[79,203],"SSF":[80,226],"was":[81,147],"moderate":[82],"(Spearman":[83],"rs":[84],"=":[85,127],"0.37-0.75)":[86],"and":[87,119,185,215],"underlying":[89],"distributions":[90],"were":[91,158],"unimodal,":[93],"causing":[94],"inference":[95],"fail":[97],"directions.":[100],"Across":[101],"full":[103],"database":[104],"20":[106],"eV":[107],"positive":[109],"mode,":[110],"42.5%":[111],"sharing":[114],"an":[115],"exact":[116],"formula":[118],"near-identical":[120],"structure":[121],"(ECFP4":[122],"Tanimoto":[123],"\u2265":[124],"0.9;":[125],"n":[126],"15,157)":[128],"produced":[129],"modified":[130,142],"cosine":[131,143],"scores":[132],"below":[133,137],"0.7,":[134],"including":[135],"24.1%":[136],"0.2.":[138],"Conversely,":[139],"when":[140],"a":[141,163,228],"threshold":[144,170],"0.7":[146],"applied":[148],"alone":[149],"exact-formula":[151],"candidates,":[152],"only":[153,176],"27.1%":[154],"accepted":[156],"close":[159,223],"analogs,":[161],"despite":[162],"27-fold":[164],"enrichment":[165],"over":[166],"background.":[167],"Increasing":[168],"0.9":[172],"raised":[173],"proportion":[175],"31.5%.":[178],"Discrimination":[179],"peaked":[180],"intermediate":[182],"energy":[184,189],"declined":[186],"higher":[188],"as":[190],"fragmentation":[191],"increased":[192],"among":[194],"unrelated":[195],"compounds.":[196],"therefore":[200],"structurally":[201],"informative":[202],"inherently":[204],"probabilistic:":[205],"closely":[206],"related":[207],"molecules":[208],"do":[209,219],"invariably":[211],"produce":[212],"similar":[213,217],"spectra,":[214],"highly":[216],"spectra":[218],"uniquely":[221],"indicate":[222],"provides":[227],"quantitative":[229],"basis":[230],"for":[231],"evaluating":[232],"similarity-based":[233],"inference.":[235]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-09-02T00:00:00"}
