{"id":"https://openalex.org/W7225145140","doi":"https://doi.org/10.64898/2026.10.29.762921","title":"QC-espresso: Brewing quality in proteomics","display_name":"QC-espresso: Brewing quality in proteomics","publication_year":2026,"publication_date":"2026-11-02","ids":{"openalex":"https://openalex.org/W7225145140","doi":"https://doi.org/10.64898/2026.10.29.762921"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.29.762921","doi":"https://doi.org/10.64898/2026.10.29.762921","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.29.762921","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/02/2026.10.29.762921.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/02/2026.10.29.762921.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033046011","display_name":"Guilherme Pauperio Lanfredi","orcid":"https://orcid.org/0000-0001-8300-7766","observed_orcids":["https://orcid.org/0000-0001-8300-7766"]},"institutions":[{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Guilherme Pauperio Lanfredi","raw_affiliation_strings":["CNPEM - Brazilian Biosciences National Laboratory"],"raw_orcid":"https://orcid.org/0000-0001-8300-7766","affiliations":[{"raw_affiliation_string":"CNPEM - Brazilian Biosciences National Laboratory","institution_ids":["https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023325245","display_name":"Jackson Gabriel Miyamoto","orcid":"https://orcid.org/0000-0002-0768-0390","observed_orcids":["https://orcid.org/0000-0002-0768-0390"]},"institutions":[{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Jackson Gabriel Miyamoto","raw_affiliation_strings":["CNPEM - Brazilian Biosciences National Laboratory"],"raw_orcid":"https://orcid.org/0000-0002-0768-0390","affiliations":[{"raw_affiliation_string":"CNPEM - Brazilian Biosciences National Laboratory","institution_ids":["https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5033046011"],"corresponding_institution_ids":["https://openalex.org/I4210152696","https://openalex.org/I4210158387"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9994999766349792,"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":0.9994999766349792,"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":9.999999747378752e-05,"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":9.999999747378752e-05,"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/data-independent-acquisition","display_name":"data-independent acquisition","score":0.8460000157356262},{"id":"https://openalex.org/keywords/dia-nn","display_name":"DIA-NN","score":0.9259999990463257},{"id":"https://openalex.org/keywords/report-generation","display_name":"report generation","score":0.6370000243186951},{"id":"https://openalex.org/keywords/retention-time","display_name":"retention time","score":0.38499999046325684},{"id":"https://openalex.org/keywords/peak-width","display_name":"peak width","score":0.7820000052452087},{"id":"https://openalex.org/keywords/reproducibility","display_name":"reproducibility","score":0.7149999737739563}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7768999934196472},{"id":"https://openalex.org/C147494362","wikidata":"https://www.wikidata.org/wiki/Q2078905","display_name":"Troubleshooting","level":2,"score":0.7379999756813049},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6241000294685364},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5910000205039978},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.5515000224113464},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.4620000123977661},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4528999924659729},{"id":"https://openalex.org/C188087704","wikidata":"https://www.wikidata.org/wiki/Q369577","display_name":"Standardization","level":2,"score":0.38019999861717224},{"id":"https://openalex.org/C2778160393","wikidata":"https://www.wikidata.org/wiki/Q18670161","display_name":"Mascot","level":2,"score":0.3684000074863434},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.36489999294281006},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3589000105857849},{"id":"https://openalex.org/C39699697","wikidata":"https://www.wikidata.org/wiki/Q869095","display_name":"Brewing","level":3,"score":0.35659998655319214},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.328900009393692},{"id":"https://openalex.org/C163985040","wikidata":"https://www.wikidata.org/wiki/Q1172399","display_name":"Data acquisition","level":2,"score":0.2971000075340271},{"id":"https://openalex.org/C80311884","wikidata":"https://www.wikidata.org/wiki/Q7268939","display_name":"Quantitative proteomics","level":4,"score":0.29089999198913574},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.2897000014781952}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.29.762921","doi":"https://doi.org/10.64898/2026.10.29.762921","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.29.762921","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/02/2026.10.29.762921.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.29.762921","doi":"https://doi.org/10.64898/2026.10.29.762921","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.29.762921","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/02/2026.10.29.762921.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"},{"id":"https://openalex.org/F4320321992","display_name":"Minist\u00e9rio da Ci\u00eancia, Tecnologia e Inova\u00e7\u00e3o","ror":"https://ror.org/050zdnc69"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320327334","display_name":"Centro Nacional de Pesquisa em Energia e Materiais","ror":"https://ror.org/05m235j20"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225145140.pdf","grobid_xml":"https://content.openalex.org/works/W7225145140.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W2012913476","https://openalex.org/W2105889769","https://openalex.org/W2199791113","https://openalex.org/W2290131530","https://openalex.org/W2529750106","https://openalex.org/W2991106430","https://openalex.org/W3138737153","https://openalex.org/W4284882692","https://openalex.org/W4323365131","https://openalex.org/W4391538499","https://openalex.org/W4412116389","https://openalex.org/W4413305479","https://openalex.org/W7129334830","https://openalex.org/W7162542665"],"related_works":["https://openalex.org/W7223204009","https://openalex.org/W3093284294","https://openalex.org/W7165638431","https://openalex.org/W4406668343","https://openalex.org/W7223154857","https://openalex.org/W4412116389","https://openalex.org/W7224528944","https://openalex.org/W7131355035","https://openalex.org/W3175073006","https://openalex.org/W7129334830"],"abstract_inverted_index":{"Data-independent":[0],"acquisition":[1,45],"(DIA)":[2],"proteomics":[3,34,184],"has":[4],"become":[5],"a":[6,38,72,84,113,147,152,170],"standard":[7],"approach":[8,42],"for":[9,43,173],"high-throughput":[10],"proteomics,":[11],"with":[12,77,130,151,155],"DIA-NN":[13,31,73],"emerging":[14],"as":[15],"one":[16],"of":[17,104,126,178],"the":[18,26,78,102,124,159],"most":[19],"widely":[20],"adopted":[21],"data-analysis":[22],"platforms.":[23],"However,":[24],"despite":[25],"detailed":[27],"information":[28],"available":[29,189],"in":[30,65,132,143],"output":[32],"reports,":[33],"researchers":[35],"may":[36],"lack":[37],"streamlined":[39],"and":[40,49,67,82,92,120,123,134,163,176],"reproducible":[41],"assessing":[44],"quality,":[46],"identification":[47,106],"consistency,":[48],"quantitative":[50],"reliability":[51],"across":[52],"experiments.":[53,185],"QC-espresso":[54,138,186],"addresses":[55],"this":[56],"need":[57],"through":[58,146],"an":[59],"automated,":[60],"report-centered":[61],"quality-control":[62,179],"workflow":[63],"implemented":[64],"R":[66,144],"Quarto.":[68],"The":[69,166],"tool":[70],"processes":[71],"report.parquet":[74],"file":[75],"together":[76],"corresponding":[79],"FASTA":[80],"database":[81],"generates":[83],"structured":[85],"HTML":[86],"report":[87,168],"containing":[88],"plots,":[89],"run-level":[90],"statistics,":[91],"exportable":[93],"summary":[94],"tables.":[95],"Application":[96],"to":[97,109],"three":[98],"experimental":[99],"datasets":[100],"allowed":[101],"visualization":[103],"lower":[105],"depth":[107],"related":[108],"high":[110],"contaminant":[111],"content;":[112],"chromatographic":[114],"transition":[115],"accompanied":[116],"by":[117],"altered":[118],"retention-time":[119],"peak-width":[121],"behavior;":[122],"co-occurrence":[125],"systematic":[127],"mass-error":[128],"bias":[129],"changes":[131],"precursor-":[133],"protein-level":[135],"quantitative-quality":[136],"metrics.":[137],"can":[139],"be":[140],"executed":[141],"directly":[142],"or":[145],"portable":[148],"Windows":[149],"distribution":[150],"graphical":[153],"launcher,":[154],"both":[156],"modes":[157],"using":[158],"same":[160],"analytical":[161],"modules":[162],"report-generation":[164],"workflow.":[165],"resulting":[167],"provides":[169],"consistent":[171],"record":[172],"local":[174],"inspection":[175],"troubleshooting":[177],"metrics":[180],"within":[181],"individual":[182],"DIA":[183],"is":[187],"freely":[188],"at":[190],"https://github.com/lanfredig/QC-espresso_DIA.":[191]},"counts_by_year":[],"updated_date":"2026-11-05T12:25:35.769452","created_date":"2026-11-04T00:00:00"}
