{"id":"https://openalex.org/W7118121461","doi":"https://doi.org/10.1186/s12859-025-06305-y","title":"Frag\u2019n\u2019Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments","display_name":"Frag\u2019n\u2019Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments","publication_year":2026,"publication_date":"2026-01-04","ids":{"openalex":"https://openalex.org/W7118121461","doi":"https://doi.org/10.1186/s12859-025-06305-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/41486154"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06305-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06305-y","pdf_url":null,"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://doi.org/10.1186/s12859-025-06305-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093265715","display_name":"Istv\u00e1n Szepesi-Nagy","orcid":"https://orcid.org/0009-0005-8849-9006"},"institutions":[{"id":"https://openalex.org/I101202996","display_name":"Semmelweis University","ror":"https://ror.org/01g9ty582","country_code":"HU","type":"education","lineage":["https://openalex.org/I101202996"]},{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Istvan Szepesi-Nagy","raw_affiliation_strings":["MTA-HUN-REN RCNS Lendulet \"Momentum\" DNA Repair Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudosok Korutja 2, Budapest, 1117, Hungary","Semmelweis University Doctoral School, Budapest, 1085, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MTA-HUN-REN RCNS Lendulet \"Momentum\" DNA Repair Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudosok Korutja 2, Budapest, 1117, Hungary","institution_ids":["https://openalex.org/I80251312"]},{"raw_affiliation_string":"Semmelweis University Doctoral School, Budapest, 1085, Hungary","institution_ids":["https://openalex.org/I101202996"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119966314","display_name":"Roberta Borosta","orcid":null},"institutions":[{"id":"https://openalex.org/I106118109","display_name":"E\u00f6tv\u00f6s Lor\u00e1nd University","ror":"https://ror.org/01jsq2704","country_code":"HU","type":"education","lineage":["https://openalex.org/I106118109"]},{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Roberta Borosta","raw_affiliation_strings":["Doctoral School of Biology, ELTE E\u00f6tv\u00f6s Lor\u00e1nd University, Budapest, 1117, Hungary","MTA-HUN-REN RCNS Lendulet \"Momentum\" DNA Repair Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudosok Korutja 2, Budapest, 1117, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Doctoral School of Biology, ELTE E\u00f6tv\u00f6s Lor\u00e1nd University, Budapest, 1117, Hungary","institution_ids":["https://openalex.org/I106118109"]},{"raw_affiliation_string":"MTA-HUN-REN RCNS Lendulet \"Momentum\" DNA Repair Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudosok Korutja 2, Budapest, 1117, Hungary","institution_ids":["https://openalex.org/I80251312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121891062","display_name":"Zoltan Szabo","orcid":null},"institutions":[{"id":"https://openalex.org/I227486990","display_name":"University of Szeged","ror":"https://ror.org/01pnej532","country_code":"HU","type":"education","lineage":["https://openalex.org/I227486990"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Zoltan Szabo","raw_affiliation_strings":["Department of Medical Chemistry, Albert Szent-Gy\u00f6rgyi Medical School, University of Szeged, Szeged, 6720, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Chemistry, Albert Szent-Gy\u00f6rgyi Medical School, University of Szeged, Szeged, 6720, Hungary","institution_ids":["https://openalex.org/I227486990"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025649527","display_name":"G\u00e1bor Tusn\u00e1dy","orcid":"https://orcid.org/0000-0001-8105-0285"},"institutions":[{"id":"https://openalex.org/I101202996","display_name":"Semmelweis University","ror":"https://ror.org/01g9ty582","country_code":"HU","type":"education","lineage":["https://openalex.org/I101202996"]},{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Gabor E. Tusnady","raw_affiliation_strings":["Department of Bioinformatics, Semmelweis University, Budapest, 1094, Hungary","Protein Bioinformatics Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, 1117, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Semmelweis University, Budapest, 1094, Hungary","institution_ids":["https://openalex.org/I101202996"]},{"raw_affiliation_string":"Protein Bioinformatics Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, 1117, Hungary","institution_ids":["https://openalex.org/I80251312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046205786","display_name":"L\u0151rinc S\u00e1ndor Pongor","orcid":"https://orcid.org/0000-0001-5917-4628"},"institutions":[{"id":"https://openalex.org/I87890613","display_name":"Epigenomics (Germany)","ror":"https://ror.org/0490dah44","country_code":"DE","type":"company","lineage":["https://openalex.org/I87890613"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lorinc S. Pongor","raw_affiliation_strings":["Cancer Genomics and Epigenetics Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), Szeged, 6728, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Genomics and Epigenetics Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), Szeged, 6728, Hungary","institution_ids":["https://openalex.org/I87890613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001538572","display_name":"Gergely R\u00f3na","orcid":"https://orcid.org/0000-0003-3222-7261"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]},{"id":"https://openalex.org/I80251312","display_name":"HUN-REN Research Centre for Natural Sciences","ror":"https://ror.org/03zwxja46","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4387152226","https://openalex.org/I80251312"]}],"countries":["HU","US"],"is_corresponding":true,"raw_author_name":"Gergely Rona","raw_affiliation_strings":["Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA. rona.gergely@ttk.hu","MTA-HUN-REN RCNS Lendulet \"Momentum\" DNA Repair Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudosok Korutja 2, Budapest, 1117, Hungary. rona.gergely@ttk.hu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, 10016, USA. rona.gergely@ttk.hu","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"MTA-HUN-REN RCNS Lendulet \"Momentum\" DNA Repair Research Group, Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Magyar Tudosok Korutja 2, Budapest, 1117, Hungary. rona.gergely@ttk.hu","institution_ids":["https://openalex.org/I80251312"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5001538572"],"corresponding_institution_ids":["https://openalex.org/I57206974","https://openalex.org/I80251312"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.01698088,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":"18","last_page":"18"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9811999797821045,"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":0.9811999797821045,"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":0.0034000000450760126,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.002300000051036477,"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/workflow","display_name":"Workflow","score":0.8492000102996826},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.8130000233650208},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.738099992275238},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5776000022888184},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.5376999974250793},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.44760000705718994},{"id":"https://openalex.org/keywords/quantitative-proteomics","display_name":"Quantitative proteomics","score":0.42719998955726624},{"id":"https://openalex.org/keywords/computer-cluster","display_name":"Computer cluster","score":0.4068000018596649},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.3540000021457672}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8492000102996826},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8130000233650208},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7962999939918518},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.738099992275238},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5776000022888184},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.5376999974250793},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44830000400543213},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.44760000705718994},{"id":"https://openalex.org/C80311884","wikidata":"https://www.wikidata.org/wiki/Q7268939","display_name":"Quantitative proteomics","level":4,"score":0.42719998955726624},{"id":"https://openalex.org/C29140674","wikidata":"https://www.wikidata.org/wiki/Q206637","display_name":"Computer cluster","level":2,"score":0.4068000018596649},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.3540000021457672},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.34139999747276306},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.3386000096797943},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.33469998836517334},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.33340001106262207},{"id":"https://openalex.org/C2776207758","wikidata":"https://www.wikidata.org/wiki/Q5303302","display_name":"Downstream (manufacturing)","level":2,"score":0.33169999718666077},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3068999946117401},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.3050000071525574},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.2987000048160553},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.29679998755455017},{"id":"https://openalex.org/C184185385","wikidata":"https://www.wikidata.org/wiki/Q6085263","display_name":"Isobaric labeling","level":5,"score":0.29679998755455017},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.29499998688697815},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.2937999963760376},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.2906000018119812},{"id":"https://openalex.org/C163985040","wikidata":"https://www.wikidata.org/wiki/Q1172399","display_name":"Data acquisition","level":2,"score":0.2791999876499176},{"id":"https://openalex.org/C34905852","wikidata":"https://www.wikidata.org/wiki/Q3943646","display_name":"Stable isotope labeling by amino acids in cell culture","level":4,"score":0.2655999958515167},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.25130000710487366},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.25110000371932983}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-025-06305-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06305-y","pdf_url":null,"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:41486154","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41486154","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":"Journal Article"},{"id":"pmh:oai:publicatio.bibl.u-szeged.hu:40458","is_oa":true,"landing_page_url":"http://publicatio.bibl.u-szeged.hu/40458/1/s12859-025-06305-y.pdf","pdf_url":"http://publicatio.bibl.u-szeged.hu/40458/1/s12859-025-06305-y.pdf","source":{"id":"https://openalex.org/S4306400675","display_name":"SZTE Publicatio Repozit\u00f3rium (University of Szeged)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I227486990","host_organization_name":"University of Szeged","host_organization_lineage":["https://openalex.org/I227486990"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Foly\u00f3iratcikk"},{"id":"pmh:oai:doaj.org/article:6718841c8e0d4128b2fa841f58d0482b","is_oa":true,"landing_page_url":"https://doaj.org/article/6718841c8e0d4128b2fa841f58d0482b","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 27, Iss 1, Pp 1-20 (2026)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12828970","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12828970/","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/s12859-025-06305-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06305-y","pdf_url":null,"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":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.42045122385025024}],"awards":[{"id":"https://openalex.org/G1604127254","display_name":null,"funder_award_id":"BO/00697/23","funder_id":"https://openalex.org/F4320322192","funder_display_name":"Magyar Tudom\u00e1nyos Akad\u00e9mia"},{"id":"https://openalex.org/G3013902902","display_name":null,"funder_award_id":"K-146314","funder_id":"https://openalex.org/F4320326762","funder_display_name":"Nemzeti Kutat\u00e1si Fejleszt\u00e9si \u00e9s Innov\u00e1ci\u00f3s Hivatal"},{"id":"https://openalex.org/G3678385133","display_name":null,"funder_award_id":"KSZF-143/2023","funder_id":"https://openalex.org/F2608926379","funder_display_name":"Hungarian Research Network"},{"id":"https://openalex.org/G6087596596","display_name":null,"funder_award_id":"LP2023-15/2023","funder_id":"https://openalex.org/F4320322192","funder_display_name":"Magyar Tudom\u00e1nyos Akad\u00e9mia"},{"id":"https://openalex.org/G712847520","display_name":null,"funder_award_id":"EK\u00d6P-2024-124","funder_id":"https://openalex.org/F4320335908","funder_display_name":"Nemzeti Kutat\u00e1si, Fejleszt\u00e9si \u00e9s Innovaci\u00f3s Alap"},{"id":"https://openalex.org/G829028414","display_name":null,"funder_award_id":"IG5670-2024","funder_id":"https://openalex.org/F4320321673","funder_display_name":"EMBO"}],"funders":[{"id":"https://openalex.org/F2608926379","display_name":"Hungarian Research Network","ror":"https://ror.org/04w6pnc49"},{"id":"https://openalex.org/F4320321673","display_name":"EMBO","ror":"https://ror.org/04wfr2810"},{"id":"https://openalex.org/F4320322192","display_name":"Magyar Tudom\u00e1nyos Akad\u00e9mia","ror":"https://ror.org/02ks8qq67"},{"id":"https://openalex.org/F4320326762","display_name":"Nemzeti Kutat\u00e1si Fejleszt\u00e9si \u00e9s Innov\u00e1ci\u00f3s Hivatal","ror":null},{"id":"https://openalex.org/F4320335908","display_name":"Nemzeti Kutat\u00e1si, Fejleszt\u00e9si \u00e9s Innovaci\u00f3s Alap","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1991694145","https://openalex.org/W2045117578","https://openalex.org/W2053943711","https://openalex.org/W2141091417","https://openalex.org/W2146512944","https://openalex.org/W2302501749","https://openalex.org/W2463195069","https://openalex.org/W2544360569","https://openalex.org/W2605897695","https://openalex.org/W2607310450","https://openalex.org/W2977773286","https://openalex.org/W2982402173","https://openalex.org/W2982668485","https://openalex.org/W2991106430","https://openalex.org/W3024746958","https://openalex.org/W3043316508","https://openalex.org/W3111413289","https://openalex.org/W3156436721","https://openalex.org/W3204730247","https://openalex.org/W3208165604","https://openalex.org/W4210469056","https://openalex.org/W4289711170","https://openalex.org/W4302758067","https://openalex.org/W4318981577","https://openalex.org/W4363675162","https://openalex.org/W4372332501","https://openalex.org/W4384024546","https://openalex.org/W4384028715","https://openalex.org/W4385298067","https://openalex.org/W4398140722","https://openalex.org/W4400324900","https://openalex.org/W4402414406","https://openalex.org/W4404046121","https://openalex.org/W4409246191","https://openalex.org/W6911818963"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"Analysing":[1],"large-scale":[2],"mass":[3],"spectrometry-based":[4],"complex":[5],"proteomics":[6,151],"datasets":[7],"often":[8],"overwhelm":[9],"desktop":[10],"computational":[11],"resources":[12],"and":[13,29,55,61,75,90,108,122,138],"require":[14],"manual":[15],"configuration":[16],"for":[17],"analysis.":[18],"While":[19],"FragPipe":[20,141],"delivers":[21],"rapid":[22],"peptide":[23],"identification":[24],"across":[25,115],"diverse":[26],"sample":[27],"preparation":[28],"acquisition":[30],"modes":[31],"(DDA,":[32],"DIA,":[33,121],"TMT),":[34],"it":[35],"remains":[36],"challenging":[37],"to":[38,67,161],"deploy":[39],"at":[40],"scale.":[41],"RESULTS:":[42],"We":[43,111],"introduce":[44],"Frag\u2019n\u2019Flow,":[45],"a":[46,97],"Nextflow\u2010based":[47],"pipeline":[48,86],"that":[49,84],"encapsulates":[50],"FragPipe,":[51],"automates":[52],"input":[53],"manifest":[54],"workflow":[56],"generation,":[57],"manages":[58],"tool":[59],"dependencies":[60],"includes":[62],"downstream":[63],"data":[64],"analysis":[65,148],"options":[66],"enable":[68],"reproducible,":[69],"high\u2010performance":[70],"analyses":[71],"on":[72,96],"HPC,":[73],"cloud,":[74],"cluster":[76],"environments.":[77],"Benchmarking":[78],"against":[79],"other":[80],"workflow-based":[81],"solutions":[82],"shows":[83],"our":[85],"maintains":[87],"quantitative":[88],"accuracy":[89],"cuts":[91],"runtime":[92],"nearly":[93],"in":[94],"half":[95],"typical":[98],"DIA":[99],"dataset":[100],"of":[101,140,149],"~":[102],"58":[103],"GB,":[104],"while":[105],"alleviating":[106],"memory":[107],"I/O":[109],"bottlenecks.":[110],"validate":[112],"Frag\u2019n\u2019Flow":[113,145,169],"results":[114],"three":[116],"representative":[117],"datasets,":[118],"label-free":[119],"DDA,":[120],"TMT,":[123],"successfully":[124],"recapitulating":[125],"published":[126],"biological":[127],"signatures":[128],"with":[129,142],"minimal":[130],"user":[131],"intervention.":[132],"CONCLUSIONS:":[133],"By":[134],"combining":[135],"the":[136,147,154],"sensitivity":[137],"speed":[139],"Nextflow\u2019s":[143],"orchestration,":[144],"enables":[146],"large\u2010scale":[150],"data,":[152],"empowering":[153],"scientific":[155],"community,":[156],"without":[157],"extensive":[158],"computation":[159],"expertise,":[160],"extract":[162],"new":[163],"insights":[164],"from":[165],"existing":[166],"MS":[167],"datasets.":[168],"is":[170],"available":[171],"at:":[172],"https://github.com/ronalabrcns/FragNFlow":[173],".":[174]},"counts_by_year":[],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2026-01-04T00:00:00"}