{"id":"https://openalex.org/W3088700323","doi":"https://doi.org/10.1186/s12859-020-03752-7","title":"A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data","display_name":"A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data","publication_year":2020,"publication_date":"2020-09-23","ids":{"openalex":"https://openalex.org/W3088700323","doi":"https://doi.org/10.1186/s12859-020-03752-7","mag":"3088700323","pmid":"https://pubmed.ncbi.nlm.nih.gov/32972355"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03752-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03752-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03752-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03752-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059263304","display_name":"Jessica Henning","orcid":"https://orcid.org/0000-0001-8941-3490"},"institutions":[{"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":false,"raw_author_name":"Jessica Henning","raw_affiliation_strings":["Department of Computer Science, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA","institution_ids":["https://openalex.org/I6750721"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046228650","display_name":"Rob Smith","orcid":"https://orcid.org/0000-0002-1864-9110"},"institutions":[{"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":"Rob Smith","raw_affiliation_strings":["Department of Computer Science, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA. robert.smith@mso.umt.edu","Department of Computer Science, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA"],"raw_orcid":"https://orcid.org/0000-0002-1864-9110","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA. robert.smith@mso.umt.edu","institution_ids":["https://openalex.org/I6750721"]},{"raw_affiliation_string":"Department of Computer Science, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA","institution_ids":["https://openalex.org/I6750721"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5046228650"],"corresponding_institution_ids":["https://openalex.org/I6750721"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.2412,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.76943749,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"21","issue":"1","first_page":"418","last_page":"418"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.3946000039577484,"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":0.3946000039577484,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.17810000479221344,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.06129999831318855,"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":0.7659076452255249},{"id":"https://openalex.org/keywords/ground-truth","display_name":"Ground truth","score":0.7045279145240784},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6966726183891296},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.584206759929657},{"id":"https://openalex.org/keywords/mascot","display_name":"Mascot","score":0.49580177664756775},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.4896869957447052},{"id":"https://openalex.org/keywords/software-suite","display_name":"Software suite","score":0.4509330987930298},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4460330605506897},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37211230397224426},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2895890474319458},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09730470180511475}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7659076452255249},{"id":"https://openalex.org/C146849305","wikidata":"https://www.wikidata.org/wiki/Q370766","display_name":"Ground truth","level":2,"score":0.7045279145240784},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6966726183891296},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.584206759929657},{"id":"https://openalex.org/C2778160393","wikidata":"https://www.wikidata.org/wiki/Q18670161","display_name":"Mascot","level":2,"score":0.49580177664756775},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.4896869957447052},{"id":"https://openalex.org/C2778736646","wikidata":"https://www.wikidata.org/wiki/Q1143070","display_name":"Software suite","level":3,"score":0.4509330987930298},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4460330605506897},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37211230397224426},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2895890474319458},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09730470180511475},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-020-03752-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03752-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03752-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32972355","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32972355","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:296e16ebdd1d429594f4b6062738d9f7","is_oa":true,"landing_page_url":"https://doaj.org/article/296e16ebdd1d429594f4b6062738d9f7","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss 1, Pp 1-10 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7517820","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7517820","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03752-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03752-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03752-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions"}],"awards":[{"id":"https://openalex.org/G1242579996","display_name":"Collaborative Research: The Willow AGEP Alliance: A Model to Advance Native American STEM Faculty","funder_award_id":"1723006","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2613026419","display_name":null,"funder_award_id":"1552240","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7220261401","display_name":"Collaborative Research: The Willow AGEP Alliance: A Model to Advance Native American STEM Faculty","funder_award_id":"1723196","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7781845692","display_name":"Collaborative Research: The Willow AGEP Alliance: A Model to Advance Native American STEM Faculty","funder_award_id":"1723248","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3088700323.pdf","grobid_xml":"https://content.openalex.org/works/W3088700323.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W75747240","https://openalex.org/W112108890","https://openalex.org/W1989299822","https://openalex.org/W2045160307","https://openalex.org/W2080752012","https://openalex.org/W2115166033","https://openalex.org/W2131878480","https://openalex.org/W2144594011","https://openalex.org/W2168590651","https://openalex.org/W2323071858","https://openalex.org/W2767592750","https://openalex.org/W2770942940","https://openalex.org/W2893817846","https://openalex.org/W2900258560"],"related_works":["https://openalex.org/W2385312588","https://openalex.org/W2169674474","https://openalex.org/W4382677331","https://openalex.org/W2392571238","https://openalex.org/W2355263872","https://openalex.org/W1996701734","https://openalex.org/W2140556529","https://openalex.org/W2361926007","https://openalex.org/W3183652449","https://openalex.org/W2370057615"],"abstract_inverted_index":{"BACKGROUND:":[0],"Mass":[1],"spectrometry":[2],"(MS)":[3],"uses":[4],"mass-to-charge":[5],"ratios":[6],"of":[7,16,22,51,64,68,97,170,182],"measured":[8],"particles":[9],"to":[10,45,164],"decode":[11],"the":[12,47,65,69,127,168],"identities":[13],"and":[14,41,49,61,80,83,95,134,140,142,149,153,166,180],"quantities":[15],"molecules":[17],"in":[18,138],"a":[19,107,112],"sample.":[20],"Interpretation":[21],"raw":[23],"MS":[24,35,98],"depends":[25],"upon":[26],"data":[27,53,99,137],"processing":[28,54,100],"algorithms":[29,77],"that":[30,110],"render":[31],"it":[32,42],"human-interpretable.":[33],"Quantitative":[34],"workflows":[36],"are":[37],"complex":[38],"experimental":[39],"chains":[40],"is":[43,78,188],"crucial":[44],"know":[46],"performance":[48],"bias":[50],"each":[52],"method":[55],"as":[56],"they":[57],"impact":[58],"accuracy,":[59],"coverage,":[60],"statistical":[62],"significance":[63],"result.":[66],"Creation":[67],"ground":[70,122,184],"truth":[71,185],"necessary":[72],"for":[73,86,119,131,145],"quantitatively":[74],"evaluating":[75],"MS1-aware":[76],"difficult":[79],"tedious":[81],"task,":[82],"better":[84],"software":[85,108,125,159],"creating":[87,120],"such":[88],"datasets":[89],"would":[90],"facilitate":[91],"more":[92],"extensive":[93],"evaluation":[94],"improvement":[96],"algorithms.":[101,173],"RESULTS:":[102],"We":[103],"present":[104],"JS-MS":[105,175],"2.0,":[106],"suite":[109],"provides":[111],"dependency-free,":[113],"browser-based,":[114],"one":[115],"click,":[116],"cross-platform":[117],"solution":[118],"MS1":[121,136,183],"truth.":[123],"The":[124,158],"retains":[126],"first":[128],"version's":[129],"capacity":[130],"loading,":[132],"viewing,":[133],"navigating":[135],"2-":[139],"3-D,":[141],"adds":[143],"tools":[144],"capturing,":[146],"editing,":[147],"saving,":[148],"viewing":[150],"isotopic":[151,155],"envelope":[152],"extracted":[154],"chromatogram":[156],"features.":[157],"can":[160],"also":[161],"be":[162],"used":[163],"view":[165],"explore":[167],"results":[169],"feature":[171],"finding":[172],"CONCLUSIONS:":[174],"2.0":[176],"enables":[177],"faster":[178],"creation":[179],"inspection":[181],"data.":[186],"It":[187],"publicly":[189],"available":[190],"with":[191],"an":[192],"MIT":[193],"license":[194],"at":[195],"github.com/optimusmoose/jsms.":[196]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
