{"id":"https://openalex.org/W1488520384","doi":"https://doi.org/10.1186/s13321-016-0116-8","title":"Fragmentation trees reloaded","display_name":"Fragmentation trees reloaded","publication_year":2016,"publication_date":"2016-02-01","ids":{"openalex":"https://openalex.org/W1488520384","doi":"https://doi.org/10.1186/s13321-016-0116-8","mag":"1488520384","pmid":"https://pubmed.ncbi.nlm.nih.gov/26839597"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-016-0116-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0116-8","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0116-8","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0116-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033025664","display_name":"Sebastian B\u00f6cker","orcid":"https://orcid.org/0000-0002-9304-8091"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Sebastian B\u00f6cker","raw_affiliation_strings":["Friedrich-Schiller-University, Ernst-Abbe-Platz 2, 07743 Jena, Germany","Friedrich-Schiller-University Jena, , Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Friedrich-Schiller-University, Ernst-Abbe-Platz 2, 07743 Jena, Germany","institution_ids":["https://openalex.org/I76198965"]},{"raw_affiliation_string":"Friedrich-Schiller-University Jena, , Germany","institution_ids":["https://openalex.org/I76198965"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074854279","display_name":"Kai D\u00fchrkop","orcid":"https://orcid.org/0000-0002-9056-0540"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Kai D\u00fchrkop","raw_affiliation_strings":["Friedrich-Schiller-University, Ernst-Abbe-Platz 2, 07743 Jena, Germany","Friedrich-Schiller-University Jena, , Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Friedrich-Schiller-University, Ernst-Abbe-Platz 2, 07743 Jena, Germany","institution_ids":["https://openalex.org/I76198965"]},{"raw_affiliation_string":"Friedrich-Schiller-University Jena, , Germany","institution_ids":["https://openalex.org/I76198965"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5033025664"],"corresponding_institution_ids":["https://openalex.org/I76198965"],"apc_list":{"value":2190,"currency":"USD","value_usd":2190},"apc_paid":{"value":2190,"currency":"USD","value_usd":2190},"fwci":6.7346,"has_fulltext":true,"cited_by_count":218,"citation_normalized_percentile":{"value":0.97319243,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"8","issue":"1","first_page":"5","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9846000075340271,"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"}},"topics":[{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9846000075340271,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.005900000222027302,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.00279999990016222,"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/fragmentation","display_name":"Fragmentation (computing)","score":0.8268970251083374},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5525689125061035},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3978666663169861},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.0718601644039154}],"concepts":[{"id":"https://openalex.org/C191015642","wikidata":"https://www.wikidata.org/wiki/Q1132459","display_name":"Fragmentation (computing)","level":2,"score":0.8268970251083374},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5525689125061035},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3978666663169861},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0718601644039154}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13321-016-0116-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0116-8","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0116-8","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:26839597","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26839597","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 cheminformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4736045","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4736045","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-016-0116-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0116-8","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0116-8","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G400350187","display_name":null,"funder_award_id":"BO 1910/16","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1488520384.pdf","grobid_xml":"https://content.openalex.org/works/W1488520384.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W102279446","https://openalex.org/W1598925596","https://openalex.org/W1969727638","https://openalex.org/W1972960408","https://openalex.org/W1973985148","https://openalex.org/W1978312864","https://openalex.org/W1978880986","https://openalex.org/W1979597489","https://openalex.org/W1979763885","https://openalex.org/W1980557641","https://openalex.org/W1982793517","https://openalex.org/W1987007197","https://openalex.org/W1997062226","https://openalex.org/W1997848191","https://openalex.org/W1999426587","https://openalex.org/W2001881195","https://openalex.org/W2002473101","https://openalex.org/W2011403239","https://openalex.org/W2013178512","https://openalex.org/W2015503332","https://openalex.org/W2018764772","https://openalex.org/W2022275929","https://openalex.org/W2026834364","https://openalex.org/W2036381632","https://openalex.org/W2040285328","https://openalex.org/W2046965677","https://openalex.org/W2052575038","https://openalex.org/W2053385401","https://openalex.org/W2057058473","https://openalex.org/W2059327215","https://openalex.org/W2067637119","https://openalex.org/W2073470877","https://openalex.org/W2075356606","https://openalex.org/W2090719977","https://openalex.org/W2092818812","https://openalex.org/W2095967914","https://openalex.org/W2096525541","https://openalex.org/W2101394823","https://openalex.org/W2105365608","https://openalex.org/W2107183338","https://openalex.org/W2108021950","https://openalex.org/W2108731397","https://openalex.org/W2114528451","https://openalex.org/W2115993694","https://openalex.org/W2119200818","https://openalex.org/W2120745758","https://openalex.org/W2127360645","https://openalex.org/W2140929996","https://openalex.org/W2144803530","https://openalex.org/W2146567649","https://openalex.org/W2148797284","https://openalex.org/W2148936717","https://openalex.org/W2150371256","https://openalex.org/W2150827955","https://openalex.org/W2154802890","https://openalex.org/W2165496299","https://openalex.org/W2165674132","https://openalex.org/W2172009698","https://openalex.org/W2173552987","https://openalex.org/W2174425372","https://openalex.org/W2179948434","https://openalex.org/W2209102285","https://openalex.org/W2312480201","https://openalex.org/W2316241459","https://openalex.org/W2320251384","https://openalex.org/W2333394028","https://openalex.org/W2334513187","https://openalex.org/W3105963012"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"BACKGROUND:":[0],"Untargeted":[1],"metabolomics":[2,190],"commonly":[3],"uses":[4],"liquid":[5],"chromatography":[6],"mass":[7,16,58,212],"spectrometry":[8,17,59,213],"to":[9,20,40,194],"measure":[10],"abundances":[11],"of":[12,27,37,56,61,130,143,146,169,187,230],"metabolites;":[13],"subsequent":[14],"tandem":[15,57,211],"is":[18,34],"used":[19],"derive":[21],"information":[22],"about":[23],"individual":[24],"compounds.":[25,45],"One":[26],"the":[28,35,54,69,78,117,128,131,139,166,227,231],"bottlenecks":[29],"in":[30],"this":[31,178],"experimental":[32,79],"setup":[33],"interpretation":[36,55],"fragmentation":[38,82,114,208,222],"spectra":[39],"accurately":[41],"and":[42,74,149],"efficiently":[43],"identify":[44],"Fragmentation":[46,84],"trees":[47,65,209],"have":[48],"become":[49],"a":[50,109,121,152,185,203],"powerful":[51],"tool":[52],"for":[53,112,134,138,150,154,177,206],"data":[60,70,80,214],"small":[62],"molecules.":[63],"These":[64],"are":[66],"determined":[67],"from":[68,210],"using":[71,197],"combinatorial":[72,118],"optimization,":[73],"aim":[75],"at":[76],"explaining":[77],"via":[81],"cascades.":[83],"tree":[85,223],"computation":[86],"does":[87],"not":[88],"require":[89],"spectral":[90],"or":[91],"structural":[92],"databases.":[93],"To":[94],"obtain":[95],"biochemically":[96],"meaningful":[97],"trees,":[98,115],"one":[99],"needs":[100],"an":[101,188],"elaborate":[102],"optimization":[103,119],"function":[104],"(scoring).":[105],"RESULTS:":[106],"We":[107,126],"present":[108,202],"new":[110,132,204],"scoring":[111,133,205,221],"computing":[113,207],"transforming":[116],"into":[120],"Maximum":[122],"A":[123],"Posteriori":[124],"estimator.":[125],"demonstrate":[127],"superiority":[129],"two":[135],"tasks:":[136],"both":[137],"de":[140],"novo":[141],"identification":[142],"molecular":[144,228],"formulas":[145],"unknown":[147],"compounds,":[148,157],"searching":[151],"database":[153],"structurally":[155],"similar":[156],"our":[158,170],"method":[159],"SIRIUS":[160,181],"3,":[161],"performs":[162],"significantly":[163],"better":[164],"than":[165],"previous":[167],"version":[168],"method,":[171],"as":[172,174],"well":[173],"other":[175],"methods":[176],"task.":[179],"CONCLUSION:":[180],"3":[182],"can":[183],"be":[184],"part":[186],"untargeted":[189],"workflow,":[191],"allowing":[192],"researchers":[193],"investigate":[195],"unknowns":[196],"automated":[198],"computational":[199],"methods.Graphical":[200],"abstractWe":[201],"based":[215],"on":[216],"Bayesian":[217],"statistics.":[218],"The":[219],"best":[220],"most":[224],"likely":[225],"explains":[226],"formula":[229],"measured":[232],"parent":[233],"ion.":[234]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":31},{"year":2022,"cited_by_count":23},{"year":2021,"cited_by_count":32},{"year":2020,"cited_by_count":31},{"year":2019,"cited_by_count":17},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}