{"id":"https://openalex.org/W3177921569","doi":"https://doi.org/10.1093/bioinformatics/btab279","title":"MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition","display_name":"MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition","publication_year":2021,"publication_date":"2021-04-26","ids":{"openalex":"https://openalex.org/W3177921569","doi":"https://doi.org/10.1093/bioinformatics/btab279","mag":"3177921569","pmid":"https://pubmed.ncbi.nlm.nih.gov/34252948"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab279","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab279","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i231/39620413/btab279.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i231/39620413/btab279.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018943031","display_name":"Zeyuan Zuo","orcid":null},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zeyuan Zuo","raw_affiliation_strings":["Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009618961","display_name":"Liu Cao","orcid":"https://orcid.org/0000-0002-6326-712X"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liu Cao","raw_affiliation_strings":["Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112660533","display_name":"Louis-F\u00e9lix Nothia","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I6750721","display_name":"University of Montana","ror":"https://ror.org/0078xmk34","country_code":"US","type":"education","lineage":["https://openalex.org/I6750721"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Louis-F\u00e9lix Nothia","raw_affiliation_strings":["Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , La Jolla, CA 92093, USA"],"affiliations":[{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I6750721","https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033781263","display_name":"Hosein Mohimani","orcid":"https://orcid.org/0000-0003-3980-2505"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hosein Mohimani","raw_affiliation_strings":["Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5033781263","https://openalex.org/A5112660533"],"corresponding_institution_ids":["https://openalex.org/I36258959","https://openalex.org/I6750721","https://openalex.org/I74973139"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9761,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.74512189,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"37","issue":"Supplement_1","first_page":"i231","last_page":"i236"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":1.0,"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":1.0,"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":0.9995999932289124,"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.998199999332428,"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/fragmentation","display_name":"Fragmentation (computing)","score":0.7071878910064697},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6100846529006958},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.5817270874977112},{"id":"https://openalex.org/keywords/mass-spectrum","display_name":"Mass spectrum","score":0.5747302174568176},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5310920476913452},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5061978697776794},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.41906577348709106},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38781827688217163},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3781493306159973},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3599439859390259},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.338736891746521},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.16115477681159973},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14085835218429565},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.13247686624526978}],"concepts":[{"id":"https://openalex.org/C191015642","wikidata":"https://www.wikidata.org/wiki/Q1132459","display_name":"Fragmentation (computing)","level":2,"score":0.7071878910064697},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6100846529006958},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.5817270874977112},{"id":"https://openalex.org/C40325409","wikidata":"https://www.wikidata.org/wiki/Q2360668","display_name":"Mass spectrum","level":3,"score":0.5747302174568176},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5310920476913452},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5061978697776794},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.41906577348709106},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38781827688217163},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3781493306159973},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3599439859390259},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.338736891746521},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.16115477681159973},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14085835218429565},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.13247686624526978}],"mesh":[{"descriptor_ui":"D007477","descriptor_name":"Ions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btab279","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab279","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i231/39620413/btab279.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34252948","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34252948","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:osti.gov:1816667","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1816667","pdf_url":"https://www.osti.gov/servlets/purl/1816667","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:2524100","is_oa":true,"landing_page_url":"www.osti.gov/servlets/purl/2524100","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:osti.gov:2524104","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2524104","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8336448","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8336448","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab279","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab279","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i231/39620413/btab279.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3482999810","display_name":null,"funder_award_id":"DE-SC0021340","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5727082869","display_name":null,"funder_award_id":"DP2GM137413","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320306151","display_name":"Alfred P. Sloan Foundation","ror":"https://ror.org/052csg198"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332603","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3177921569.pdf","grobid_xml":"https://content.openalex.org/works/W3177921569.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1543068333","https://openalex.org/W1969860457","https://openalex.org/W1981098361","https://openalex.org/W1985258161","https://openalex.org/W1989299822","https://openalex.org/W1997363341","https://openalex.org/W2018690353","https://openalex.org/W2020103130","https://openalex.org/W2035809951","https://openalex.org/W2060494738","https://openalex.org/W2063123613","https://openalex.org/W2079843936","https://openalex.org/W2086689797","https://openalex.org/W2099036524","https://openalex.org/W2136626461","https://openalex.org/W2313734891","https://openalex.org/W2514341189","https://openalex.org/W2520784563","https://openalex.org/W2546443756","https://openalex.org/W2584220830","https://openalex.org/W2593533643","https://openalex.org/W2618709112","https://openalex.org/W2788856035","https://openalex.org/W2799347062","https://openalex.org/W2805675654","https://openalex.org/W2893437991","https://openalex.org/W2919275760","https://openalex.org/W2921795729","https://openalex.org/W2981262779","https://openalex.org/W3174482775"],"related_works":["https://openalex.org/W2333051822","https://openalex.org/W2335176593","https://openalex.org/W2018265659","https://openalex.org/W1991329955","https://openalex.org/W2034476164","https://openalex.org/W2317609945","https://openalex.org/W1997777946","https://openalex.org/W1965372791","https://openalex.org/W2155742966","https://openalex.org/W2012682718"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":5}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
