{"id":"https://openalex.org/W2061936826","doi":"https://doi.org/10.1186/1471-2105-15-s7-s9","title":"Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view","display_name":"Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view","publication_year":2014,"publication_date":"2014-05-01","ids":{"openalex":"https://openalex.org/W2061936826","doi":"https://doi.org/10.1186/1471-2105-15-s7-s9","mag":"2061936826","pmid":"https://pubmed.ncbi.nlm.nih.gov/25078324"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-s7-s9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s7-s9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S7-S9","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/counter/pdf/10.1186/1471-2105-15-S7-S9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046228650","display_name":"Rob Smith","orcid":"https://orcid.org/0000-0002-1864-9110"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rob Smith","raw_affiliation_strings":["Department of Computer Science, Brigham Young University, 84606, Provo, USA","Department of Computer Science, Brigham Young University, Provo, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Brigham Young University, 84606, Provo, USA","institution_ids":["https://openalex.org/I100005738"]},{"raw_affiliation_string":"Department of Computer Science, Brigham Young University, Provo, USA#TAB#","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043846151","display_name":"Andrew D. Mathis","orcid":"https://orcid.org/0000-0002-9927-4022"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew D Mathis","raw_affiliation_strings":["Department of Chemistry, Brigham Young University, 84606, Provo, USA","Department of Chemistry, Brigham Young University, Provo, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Brigham Young University, 84606, Provo, USA","institution_ids":["https://openalex.org/I100005738"]},{"raw_affiliation_string":"Department of Chemistry, Brigham Young University, Provo, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064318273","display_name":"Dan Ventura","orcid":"https://orcid.org/0000-0002-3111-2238"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dan Ventura","raw_affiliation_strings":["Department of Computer Science, Brigham Young University, 84606, Provo, USA","Department of Computer Science, Brigham Young University, Provo, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Brigham Young University, 84606, Provo, USA","institution_ids":["https://openalex.org/I100005738"]},{"raw_affiliation_string":"Department of Computer Science, Brigham Young University, Provo, USA#TAB#","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041650906","display_name":"John T. Prince","orcid":"https://orcid.org/0000-0001-9820-4252"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John T Prince","raw_affiliation_strings":["Department of Chemistry, Brigham Young University, 84606, Provo, USA","Department of Chemistry, Brigham Young University, Provo, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Brigham Young University, 84606, Provo, USA","institution_ids":["https://openalex.org/I100005738"]},{"raw_affiliation_string":"Department of Chemistry, Brigham Young University, Provo, USA","institution_ids":["https://openalex.org/I100005738"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5046228650"],"corresponding_institution_ids":["https://openalex.org/I100005738"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.4189,"has_fulltext":true,"cited_by_count":79,"citation_normalized_percentile":{"value":0.89128396,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"15","issue":"S7","first_page":"S9","last_page":"S9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.6269999742507935,"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":0.6269999742507935,"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":0.21799999475479126,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.10559999942779541,"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/data-science","display_name":"Data science","score":0.7219195365905762},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6596747636795044},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4921719431877136},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.48953065276145935},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.41519543528556824},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.17969495058059692},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11098164319992065}],"concepts":[{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.7219195365905762},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6596747636795044},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4921719431877136},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.48953065276145935},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.41519543528556824},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.17969495058059692},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11098164319992065},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008433","descriptor_name":"Mathematics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008433","descriptor_name":"Mathematics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008433","descriptor_name":"Mathematics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","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":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","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":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-15-s7-s9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s7-s9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S7-S9","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:25078324","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25078324","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:europepmc.org:3091673","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4110734","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-s7-s9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s7-s9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S7-S9","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":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2061936826.pdf","grobid_xml":"https://content.openalex.org/works/W2061936826.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W112108890","https://openalex.org/W1091421124","https://openalex.org/W1483118642","https://openalex.org/W1538574688","https://openalex.org/W1575497636","https://openalex.org/W1595251199","https://openalex.org/W1975783279","https://openalex.org/W1980297970","https://openalex.org/W1980793852","https://openalex.org/W1984926446","https://openalex.org/W1988667155","https://openalex.org/W1997504014","https://openalex.org/W2005071799","https://openalex.org/W2017064873","https://openalex.org/W2025804769","https://openalex.org/W2026465178","https://openalex.org/W2035989889","https://openalex.org/W2036740013","https://openalex.org/W2037837681","https://openalex.org/W2038249420","https://openalex.org/W2038615001","https://openalex.org/W2041856956","https://openalex.org/W2044033722","https://openalex.org/W2049221161","https://openalex.org/W2050758433","https://openalex.org/W2058661481","https://openalex.org/W2067440941","https://openalex.org/W2068703118","https://openalex.org/W2068737317","https://openalex.org/W2073371472","https://openalex.org/W2074619822","https://openalex.org/W2084375915","https://openalex.org/W2086216615","https://openalex.org/W2098382263","https://openalex.org/W2105084411","https://openalex.org/W2106017862","https://openalex.org/W2113519164","https://openalex.org/W2115166033","https://openalex.org/W2116687544","https://openalex.org/W2116887561","https://openalex.org/W2118868857","https://openalex.org/W2123790683","https://openalex.org/W2129343699","https://openalex.org/W2131878480","https://openalex.org/W2137274797","https://openalex.org/W2137758708","https://openalex.org/W2137838906","https://openalex.org/W2140695271","https://openalex.org/W2143113016","https://openalex.org/W2144303444","https://openalex.org/W2149329792","https://openalex.org/W2152180036","https://openalex.org/W2154222508","https://openalex.org/W2158447287","https://openalex.org/W2167679437","https://openalex.org/W2169558190","https://openalex.org/W2330976336","https://openalex.org/W2477750087","https://openalex.org/W4206911346","https://openalex.org/W4211085285","https://openalex.org/W4232868252","https://openalex.org/W4244035732","https://openalex.org/W4251398760","https://openalex.org/W4294326454"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W1488408180","https://openalex.org/W2376932109","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2130043461","https://openalex.org/W2357879326"],"abstract_inverted_index":{"BACKGROUND:":[0],"For":[1],"decades,":[2],"mass":[3,57,94],"spectrometry":[4,58],"data":[5,46,53,115],"has":[6],"been":[7],"analyzed":[8],"to":[9,88,135,150],"investigate":[10],"a":[11],"wide":[12],"array":[13],"of":[14,32,42,92],"research":[15],"interests,":[16],"including":[17],"disease":[18],"diagnostics,":[19],"biological":[20],"and":[21,25,101,117,121,133,145],"chemical":[22],"theory,":[23],"genomics,":[24],"drug":[26],"development.":[27],"Progress":[28],"towards":[29],"solving":[30],"any":[31],"these":[33,64],"disparate":[34],"problems":[35,55,103],"depends":[36],"upon":[37],"overcoming":[38],"the":[39,44,71,89],"common":[40],"challenge":[41],"interpreting":[43],"large":[45],"sets":[47,116],"generated.":[48],"Despite":[49],"interim":[50],"successes,":[51],"many":[52],"interpretation":[54],"in":[56,69,104],"are":[59,66],"still":[60],"challenging.":[61],"Further,":[62],"though":[63],"challenges":[65],"inherently":[67],"interdisciplinary":[68,79],"nature,":[70],"significant":[72],"domain-specific":[73],"knowledge":[74],"gap":[75],"between":[76],"disciplines":[77],"makes":[78],"contributions":[80,128],"difficult.":[81],"RESULTS:":[82],"This":[83,124],"paper":[84,125],"provides":[85],"an":[86],"introduction":[87],"burgeoning":[90],"field":[91],"computational":[93],"spectrometry.":[95],"We":[96],"illustrate":[97],"key":[98,118],"concepts,":[99],"vocabulary,":[100],"open":[102,114,151],"MS-omics,":[105],"as":[106,108,113],"well":[107],"provide":[109],"invaluable":[110],"resources":[111],"such":[112],"search":[119],"terms":[120],"references.":[122],"CONCLUSIONS:":[123],"will":[126,138],"facilitate":[127],"from":[129],"mathematicians,":[130],"computer":[131],"scientists,":[132],"statisticians":[134],"MS-omics":[136],"that":[137],"fundamentally":[139],"improve":[140],"results":[141],"over":[142],"existing":[143],"approaches":[144],"inform":[146],"novel":[147],"algorithmic":[148],"solutions":[149],"problems.":[152]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}