{"id":"https://openalex.org/W4382047943","doi":"https://doi.org/10.1093/bioinformatics/btad406","title":"TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments","display_name":"TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments","publication_year":2023,"publication_date":"2023-06-24","ids":{"openalex":"https://openalex.org/W4382047943","doi":"https://doi.org/10.1093/bioinformatics/btad406","pmid":"https://pubmed.ncbi.nlm.nih.gov/37364005"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad406","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad406","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad406/50710164/btad406.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad406/50710164/btad406.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052495116","display_name":"Ross McBride","orcid":"https://orcid.org/0000-0002-0032-9506"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Ross McBride","raw_affiliation_strings":["School of Computing Science, University of Glasgow , Glasgow G12 8RZ, United Kingdom","School of Computing Science, University of Glasgow, Glasgow, G12 8QQ, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Computing Science, University of Glasgow , Glasgow G12 8RZ, United Kingdom","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"School of Computing Science, University of Glasgow, Glasgow, G12 8QQ, United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034049617","display_name":"Joe Wandy","orcid":"https://orcid.org/0000-0002-3068-4664"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Joe Wandy","raw_affiliation_strings":["Glasgow Polyomics, University of Glasgow , Glasgow G61 1BD, United Kingdom","Glasgow Polyomics, University of Glasgow, Glasgow, G12 8QQ, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Glasgow Polyomics, University of Glasgow , Glasgow G61 1BD, United Kingdom","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"Glasgow Polyomics, University of Glasgow, Glasgow, G12 8QQ, United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040694942","display_name":"Stefan Weidt","orcid":"https://orcid.org/0000-0003-1127-9214"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stefan Weidt","raw_affiliation_strings":["Glasgow Polyomics, University of Glasgow , Glasgow G61 1BD, United Kingdom","Glasgow Polyomics, University of Glasgow, Glasgow, G12 8QQ, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Glasgow Polyomics, University of Glasgow , Glasgow G61 1BD, United Kingdom","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"Glasgow Polyomics, University of Glasgow, Glasgow, G12 8QQ, United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060432668","display_name":"Simon Rogers","orcid":"https://orcid.org/0000-0003-3578-4477"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Simon Rogers","raw_affiliation_strings":["School of Computing Science, University of Glasgow , Glasgow G12 8RZ, United Kingdom","School of Computing Science, University of Glasgow, Glasgow, G12 8QQ, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Computing Science, University of Glasgow , Glasgow G12 8RZ, United Kingdom","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"School of Computing Science, University of Glasgow, Glasgow, G12 8QQ, United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041834493","display_name":"Vinny Davies","orcid":"https://orcid.org/0000-0003-1896-8936"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Vinny Davies","raw_affiliation_strings":["School of Mathematics and Statistics, University of Glasgow , Glasgow G12 8QQ, United Kingdom","School of Mathematics and Statistics, University of Glasgow, Glasgow, G12 8QQ, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Glasgow , Glasgow G12 8QQ, United Kingdom","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"School of Mathematics and Statistics, University of Glasgow, Glasgow, G12 8QQ, United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043557336","display_name":"R\u00f3n\u00e1n Daly","orcid":"https://orcid.org/0000-0002-1275-6820"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"R\u00f3n\u00e1n Daly","raw_affiliation_strings":["Glasgow Polyomics, University of Glasgow , Glasgow G61 1BD, United Kingdom","Glasgow Polyomics, University of Glasgow, Glasgow, G12 8QQ, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Glasgow Polyomics, University of Glasgow , Glasgow G61 1BD, United Kingdom","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"Glasgow Polyomics, University of Glasgow, Glasgow, G12 8QQ, United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063296381","display_name":"Kevin Bryson","orcid":"https://orcid.org/0000-0002-1163-6368"},"institutions":[{"id":"https://openalex.org/I7882870","display_name":"University of Glasgow","ror":"https://ror.org/00vtgdb53","country_code":"GB","type":"education","lineage":["https://openalex.org/I7882870"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kevin Bryson","raw_affiliation_strings":["School of Computing Science, University of Glasgow , Glasgow G12 8RZ, United Kingdom","School of Computing Science, University of Glasgow, Glasgow, G12 8QQ, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Computing Science, University of Glasgow , Glasgow G12 8RZ, United Kingdom","institution_ids":["https://openalex.org/I7882870"]},{"raw_affiliation_string":"School of Computing Science, University of Glasgow, Glasgow, G12 8QQ, United Kingdom","institution_ids":["https://openalex.org/I7882870"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5052495116"],"corresponding_institution_ids":["https://openalex.org/I7882870"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.609,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.69806867,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"39","issue":"7","first_page":null,"last_page":null},"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9944999814033508,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9850000143051147,"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/computer-science","display_name":"Computer science","score":0.6698085069656372},{"id":"https://openalex.org/keywords/fragmentation","display_name":"Fragmentation (computing)","score":0.6523921489715576},{"id":"https://openalex.org/keywords/data-acquisition","display_name":"Data acquisition","score":0.6039391160011292},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.4894479811191559},{"id":"https://openalex.org/keywords/prioritization","display_name":"Prioritization","score":0.4845370650291443},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.4562862813472748},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4453347325325012},{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.4400777220726013},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.42136579751968384},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.27043259143829346},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.25883209705352783}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6698085069656372},{"id":"https://openalex.org/C191015642","wikidata":"https://www.wikidata.org/wiki/Q1132459","display_name":"Fragmentation (computing)","level":2,"score":0.6523921489715576},{"id":"https://openalex.org/C163985040","wikidata":"https://www.wikidata.org/wiki/Q1172399","display_name":"Data acquisition","level":2,"score":0.6039391160011292},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.4894479811191559},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.4845370650291443},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.4562862813472748},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4453347325325012},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.4400777220726013},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.42136579751968384},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.27043259143829346},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.25883209705352783},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002853","descriptor_name":"Chromatography, Liquid","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad406","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad406","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad406/50710164/btad406.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:37364005","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37364005","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:eprints.gla.ac.uk:301638","is_oa":true,"landing_page_url":"http://eprints.gla.ac.uk/view/author/61963.html>,","pdf_url":"https://eprints.gla.ac.uk/301638/2/301638.pdf","source":{"id":"https://openalex.org/S4210235606","display_name":"ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam)","issn_l":"2622-8912","issn":["2622-8912","2622-8920"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:pubmedcentral.nih.gov:10336026","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10336026","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10336026/pdf/btad406.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/btad406","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad406","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad406/50710164/btad406.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[{"id":"https://metadata.un.org/sdg/10","score":0.800000011920929,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G1934935867","display_name":null,"funder_award_id":"Engineering and Physical Sciences R","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G1989121949","display_name":null,"funder_award_id":"EP/R018634/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5187265158","display_name":"Closed-Loop Data Science for Complex, Computationally- and Data-Intensive Analytics","funder_award_id":"EP/R018634/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8352026019","display_name":null,"funder_award_id":"R018634/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4382047943.pdf"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1543068333","https://openalex.org/W1989299822","https://openalex.org/W2071393617","https://openalex.org/W2110017950","https://openalex.org/W2168590651","https://openalex.org/W2504691963","https://openalex.org/W2551876238","https://openalex.org/W2593533643","https://openalex.org/W2805675654","https://openalex.org/W2922522932","https://openalex.org/W2937662637","https://openalex.org/W2979387401","https://openalex.org/W3024889646","https://openalex.org/W3041584148","https://openalex.org/W3146134477","https://openalex.org/W3177921569","https://openalex.org/W4221040855","https://openalex.org/W4323363993"],"related_works":["https://openalex.org/W2506292322","https://openalex.org/W42525420","https://openalex.org/W4283209547","https://openalex.org/W4283390424","https://openalex.org/W2137270828","https://openalex.org/W1976072307","https://openalex.org/W4205440119","https://openalex.org/W4292104203","https://openalex.org/W1561393703","https://openalex.org/W2096576371"],"abstract_inverted_index":{"TopNEXt":[0],"is":[1],"implemented":[2],"as":[3],"part":[4],"of":[5],"the":[6,10],"ViMMS":[7],"framework":[8],"and":[9],"latest":[11],"version":[12,20],"can":[13,26],"be":[14,27],"found":[15,28],"at":[16,29],"https://github.com/glasgowcompbio/vimms.":[17],"A":[18],"stable":[19],"used":[21],"to":[22],"produce":[23],"our":[24],"results":[25],"10.5281/zenodo.7468914.":[30]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}