{"id":"https://openalex.org/W2155843164","doi":"https://doi.org/10.1093/bioinformatics/bts244","title":"Speeding up tandem mass spectral identification using indexes","display_name":"Speeding up tandem mass spectral identification using indexes","publication_year":2012,"publication_date":"2012-04-27","ids":{"openalex":"https://openalex.org/W2155843164","doi":"https://doi.org/10.1093/bioinformatics/bts244","mag":"2155843164","pmid":"https://pubmed.ncbi.nlm.nih.gov/22543365"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts244","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/13/1692/23687207/bts244.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/13/1692/23687207/bts244.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100437902","display_name":"Xiaowen Liu","orcid":"https://orcid.org/0000-0003-4139-1127"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]},{"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"]}],"countries":["IT","US"],"is_corresponding":true,"raw_author_name":"Xiaowen Liu","raw_affiliation_strings":["1 Department of Computer Science and Engineering, University of California, San Diego, California, 92093, USA and 2Department of Information Engineering, University of Padova, Padova 35131, Italy"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and Engineering, University of California, San Diego, California, 92093, USA and 2Department of Information Engineering, University of Padova, Padova 35131, Italy","institution_ids":["https://openalex.org/I138689650","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022410513","display_name":"Alessandro Mammana","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/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Alessandro Mammana","raw_affiliation_strings":["1 Department of Computer Science and Engineering, University of California, San Diego, California, 92093, USA and 2Department of Information Engineering, University of Padova, Padova 35131, Italy"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and Engineering, University of California, San Diego, California, 92093, USA and 2Department of Information Engineering, University of Padova, Padova 35131, Italy","institution_ids":["https://openalex.org/I138689650","https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028801735","display_name":"Vineet Bafna","orcid":"https://orcid.org/0000-0002-5810-6241"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]},{"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"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Vineet Bafna","raw_affiliation_strings":["1 Department of Computer Science and Engineering, University of California, San Diego, California, 92093, USA and 2Department of Information Engineering, University of Padova, Padova 35131, Italy"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and Engineering, University of California, San Diego, California, 92093, USA and 2Department of Information Engineering, University of Padova, Padova 35131, Italy","institution_ids":["https://openalex.org/I138689650","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100437902"],"corresponding_institution_ids":["https://openalex.org/I138689650","https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6308,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.66392647,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"28","issue":"13","first_page":"1692","last_page":"1697"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9997000098228455,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9997000098228455,"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":0.9976000189781189,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9962999820709229,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.7121909260749817},{"id":"https://openalex.org/keywords/tandem-mass-spectrometry","display_name":"Tandem mass spectrometry","score":0.673029899597168},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6247714161872864},{"id":"https://openalex.org/keywords/tandem","display_name":"Tandem","score":0.6096726059913635},{"id":"https://openalex.org/keywords/diagonal","display_name":"Diagonal","score":0.511725902557373},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.3788887858390808},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3469245433807373},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3400523066520691},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33420079946517944},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19322124123573303},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.14517709612846375},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.11913427710533142},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.05305871367454529}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.7121909260749817},{"id":"https://openalex.org/C31827203","wikidata":"https://www.wikidata.org/wiki/Q874296","display_name":"Tandem mass spectrometry","level":3,"score":0.673029899597168},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6247714161872864},{"id":"https://openalex.org/C2777814067","wikidata":"https://www.wikidata.org/wiki/Q1752317","display_name":"Tandem","level":2,"score":0.6096726059913635},{"id":"https://openalex.org/C130367717","wikidata":"https://www.wikidata.org/wiki/Q189791","display_name":"Diagonal","level":2,"score":0.511725902557373},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.3788887858390808},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3469245433807373},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3400523066520691},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33420079946517944},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19322124123573303},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.14517709612846375},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.11913427710533142},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.05305871367454529},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053719","descriptor_name":"Tandem Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts244","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/13/1692/23687207/bts244.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22543365","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22543365","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:europepmc.org:2690376","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3381964","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3381964","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3381964","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts244","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/13/1692/23687207/bts244.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2155843164.pdf","grobid_xml":"https://content.openalex.org/works/W2155843164.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1964443249","https://openalex.org/W1967467171","https://openalex.org/W1981593008","https://openalex.org/W1996113955","https://openalex.org/W2011503307","https://openalex.org/W2025955263","https://openalex.org/W2026465178","https://openalex.org/W2043828494","https://openalex.org/W2045985536","https://openalex.org/W2047275456","https://openalex.org/W2058135122","https://openalex.org/W2060373419","https://openalex.org/W2075036506","https://openalex.org/W2106309221","https://openalex.org/W2122785579","https://openalex.org/W2146482199","https://openalex.org/W2150746288","https://openalex.org/W4238269894","https://openalex.org/W6649303037","https://openalex.org/W6681444707"],"related_works":["https://openalex.org/W4323262585","https://openalex.org/W2023186083","https://openalex.org/W4211086969","https://openalex.org/W2890607860","https://openalex.org/W2025127327","https://openalex.org/W4380869615","https://openalex.org/W2798825245","https://openalex.org/W2519652201","https://openalex.org/W2103021125","https://openalex.org/W2051901836"],"abstract_inverted_index":{"In":[0],"this":[1],"article,":[2],"we":[3],"define":[4],"two":[5,24,31,40],"scoring":[6],"functions":[7],"for":[8,38],"identifying":[9],"peptides/proteins":[10],"with":[11,58],"PTMs":[12],"from":[13],"MS/MS":[14],"spectra:":[15],"match":[16],"scores":[17],"and":[18,44],"diagonal":[19],"scores,":[20],"as":[21,23],"well":[22],"spectral":[25],"identification":[26],"problems":[27],"based":[28],"on":[29,54],"the":[30,39,49],"scores.":[32],"We":[33],"propose":[34],"several":[35],"index-based":[36,50],"algorithms":[37,51],"problems.":[41],"Both":[42],"theoretical":[43],"experimental":[45],"analyses":[46],"show":[47],"that":[48],"significantly":[52],"improve":[53],"speed":[55],"when":[56],"compared":[57],"existing":[59],"algorithms.":[60]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
