{"id":"https://openalex.org/W2144990448","doi":"https://doi.org/10.1109/bibmw.2010.5703775","title":"Using a spike-in experiment to evaluate analysis of LC-MS data","display_name":"Using a spike-in experiment to evaluate analysis of LC-MS data","publication_year":2010,"publication_date":"2010-12-01","ids":{"openalex":"https://openalex.org/W2144990448","doi":"https://doi.org/10.1109/bibmw.2010.5703775","mag":"2144990448"},"language":"en","primary_location":{"id":"doi:10.1109/bibmw.2010.5703775","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2010.5703775","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010628078","display_name":"Leepika Tuli","orcid":null},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leepika Tuli","raw_affiliation_strings":["Lombardi Comprehensive Cancer Center, George town University, Washington D.C., WA, USA","Lombardi Comprehensive Cancer Center , Georgetown University , Washington, DC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lombardi Comprehensive Cancer Center, George town University, Washington D.C., WA, USA","institution_ids":["https://openalex.org/I184565670"]},{"raw_affiliation_string":"Lombardi Comprehensive Cancer Center , Georgetown University , Washington, DC, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045054693","display_name":"Tsung\u2010Heng Tsai","orcid":"https://orcid.org/0000-0001-5211-2985"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tsung-Heng Tsai","raw_affiliation_strings":["Lombardi Comprehensive Cancer Center, George town University, Washington D.C., WA, USA","Lombardi Comprehensive Cancer Center , Georgetown University , Washington, DC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lombardi Comprehensive Cancer Center, George town University, Washington D.C., WA, USA","institution_ids":["https://openalex.org/I184565670"]},{"raw_affiliation_string":"Lombardi Comprehensive Cancer Center , Georgetown University , Washington, DC, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027269811","display_name":"Rency S. Varghese","orcid":"https://orcid.org/0000-0002-4236-7316"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rency S. Varghese","raw_affiliation_strings":["Lombardi Comprehensive Cancer Center, George town University, Washington D.C., WA, USA","Lombardi Comprehensive Cancer Center , Georgetown University , Washington, DC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lombardi Comprehensive Cancer Center, George town University, Washington D.C., WA, USA","institution_ids":["https://openalex.org/I184565670"]},{"raw_affiliation_string":"Lombardi Comprehensive Cancer Center , Georgetown University , Washington, DC, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003800447","display_name":"Amrita K. Cheema","orcid":"https://orcid.org/0000-0003-4877-7583"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amrita Cheema","raw_affiliation_strings":["Lombardi Comprehensive Cancer Center, George town University, Washington D.C., WA, USA","Lombardi Comprehensive Cancer Center , Georgetown University , Washington, DC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lombardi Comprehensive Cancer Center, George town University, Washington D.C., WA, USA","institution_ids":["https://openalex.org/I184565670"]},{"raw_affiliation_string":"Lombardi Comprehensive Cancer Center , Georgetown University , Washington, DC, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025125310","display_name":"Habtom W. Ressom","orcid":"https://orcid.org/0000-0001-9296-2132"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Habtom W. Ressom","raw_affiliation_strings":["Lombardi Comprehensive Cancer Center, George town University, Washington D.C., WA, USA","Lombardi Comprehensive Cancer Center , Georgetown University , Washington, DC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lombardi Comprehensive Cancer Center, George town University, Washington D.C., WA, USA","institution_ids":["https://openalex.org/I184565670"]},{"raw_affiliation_string":"Lombardi Comprehensive Cancer Center , Georgetown University , Washington, DC, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.3277,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.61004508,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"67","last_page":"72"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9998000264167786,"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":0.9993000030517578,"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/normalization","display_name":"Normalization (sociology)","score":0.7231489419937134},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.7086532115936279},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.6643080711364746},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6323484182357788},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5366595983505249},{"id":"https://openalex.org/keywords/liquid-chromatography\u2013mass-spectrometry","display_name":"Liquid chromatography\u2013mass spectrometry","score":0.4412725567817688},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.433646023273468},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.4324142336845398},{"id":"https://openalex.org/keywords/data-pre-processing","display_name":"Data pre-processing","score":0.422634482383728},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3908824324607849},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.3756744861602783},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3413751423358917},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.28893887996673584}],"concepts":[{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.7231489419937134},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.7086532115936279},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.6643080711364746},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6323484182357788},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5366595983505249},{"id":"https://openalex.org/C64489805","wikidata":"https://www.wikidata.org/wiki/Q873864","display_name":"Liquid chromatography\u2013mass spectrometry","level":3,"score":0.4412725567817688},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.433646023273468},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.4324142336845398},{"id":"https://openalex.org/C10551718","wikidata":"https://www.wikidata.org/wiki/Q5227332","display_name":"Data pre-processing","level":2,"score":0.422634482383728},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3908824324607849},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.3756744861602783},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3413751423358917},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.28893887996673584},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibmw.2010.5703775","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2010.5703775","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W19615206","https://openalex.org/W1597678601","https://openalex.org/W1797925867","https://openalex.org/W1826423984","https://openalex.org/W1964010911","https://openalex.org/W1965942536","https://openalex.org/W1974746262","https://openalex.org/W1989299822","https://openalex.org/W1996644428","https://openalex.org/W2002928661","https://openalex.org/W2020087074","https://openalex.org/W2023096047","https://openalex.org/W2027974246","https://openalex.org/W2038249420","https://openalex.org/W2051978415","https://openalex.org/W2058472554","https://openalex.org/W2059315009","https://openalex.org/W2061567983","https://openalex.org/W2071777796","https://openalex.org/W2105381419","https://openalex.org/W2107231094","https://openalex.org/W2111208057","https://openalex.org/W2121916988","https://openalex.org/W2129450490","https://openalex.org/W2139564441","https://openalex.org/W2152180036","https://openalex.org/W2154012818","https://openalex.org/W2156022009","https://openalex.org/W2158447287","https://openalex.org/W2160110467","https://openalex.org/W2167443016","https://openalex.org/W2167813588","https://openalex.org/W2169558190"],"related_works":["https://openalex.org/W2989490741","https://openalex.org/W3092506759","https://openalex.org/W2367545121","https://openalex.org/W4248881655","https://openalex.org/W2482165163","https://openalex.org/W3010890513","https://openalex.org/W120741642","https://openalex.org/W138569904","https://openalex.org/W2390914021","https://openalex.org/W2389417819"],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2,16,107,111],"liquid":[3],"chromatography-mass":[4],"spectrometry":[5],"(LC-MS)":[6],"technology":[7],"have":[8,22,68],"led":[9],"to":[10,71,85,99,137],"newer":[11],"approaches":[12],"for":[13,25,31],"measuring":[14],"changes":[15,110],"peptide/protein":[17],"abundances.":[18],"Label-free":[19],"LC-MS":[20,47,73,115,121],"methods":[21,48],"been":[23,69],"used":[24],"extraction":[26],"of":[27,33,42,87,103],"quantitative":[28],"information":[29,135],"and":[30,60,62,132],"detection":[32,39,141],"differentially":[34],"abundant":[35],"peptides/proteins.":[36],"However,":[37],"difference":[38,140],"by":[40,118],"analysis":[41],"data":[43,116],"derived":[44],"from":[45,114],"label-free":[46,120],"requires":[49],"various":[50],"preprocessing":[51],"steps":[52],"including":[53],"filtering,":[54],"baseline":[55],"correction,":[56],"peak":[57],"detection,":[58],"alignment,":[59],"normalization,":[61],"transformation.":[63],"Although":[64],"several":[65],"specialized":[66],"tools":[67,106,126],"developed":[70],"analyze":[72],"data,":[74],"determining":[75],"the":[76,101],"most":[77],"appropriate":[78],"computational":[79],"pipeline":[80],"remains":[81],"challenging":[82],"partly":[83],"due":[84],"lack":[86],"established":[88],"gold":[89],"standards.":[90],"In":[91],"this":[92],"paper,":[93],"we":[94],"use":[95],"a":[96,119],"spike-in":[97],"experiment":[98],"evaluate":[100],"performance":[102],"three":[104],"software":[105],"accurately":[108],"detecting":[109],"peptide":[112,129],"abundances":[113],"obtained":[117],"method.":[122],"We":[123],"observe":[124],"that":[125,127],"incorporate":[128],"isotope":[130],"cluster":[131],"multiple":[133],"charge":[134],"lead":[136],"more":[138],"accurate":[139],"with":[142],"fewer":[143],"false":[144],"positives.":[145]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
