{"id":"https://openalex.org/W4400378009","doi":"https://doi.org/10.1093/bioinformatics/btae417","title":"Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data","display_name":"Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data","publication_year":2024,"publication_date":"2024-07-01","ids":{"openalex":"https://openalex.org/W4400378009","doi":"https://doi.org/10.1093/bioinformatics/btae417","pmid":"https://pubmed.ncbi.nlm.nih.gov/38960865"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae417","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae417","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btae417","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100444181","display_name":"Yichi Zhang","orcid":"https://orcid.org/0000-0001-9944-1997"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yichi Zhang","raw_affiliation_strings":["Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China"],"affiliations":[{"raw_affiliation_string":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019328678","display_name":"Chenghui Hu","orcid":null},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenghui Hu","raw_affiliation_strings":["Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China"],"affiliations":[{"raw_affiliation_string":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091165765","display_name":"Xiaohui Wu","orcid":"https://orcid.org/0000-0003-0356-7785"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohui Wu","raw_affiliation_strings":["Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China"],"affiliations":[{"raw_affiliation_string":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062009063","display_name":"Jian Song","orcid":"https://orcid.org/0000-0001-5841-6365"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Song","raw_affiliation_strings":["Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China"],"affiliations":[{"raw_affiliation_string":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China","institution_ids":["https://openalex.org/I3923682"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100444181"],"corresponding_institution_ids":["https://openalex.org/I3923682"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6994,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.64530041,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"40","issue":"7","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":1.0,"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":1.0,"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":0.9998999834060669,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9994000196456909,"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/python","display_name":"Python (programming language)","score":0.8591813445091248},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.679778516292572},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.5782434940338135},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.565441906452179},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5154984593391418},{"id":"https://openalex.org/keywords/calibration","display_name":"Calibration","score":0.4544007480144501},{"id":"https://openalex.org/keywords/open-source-software","display_name":"Open source software","score":0.4366811513900757},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.3816070556640625},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3350682258605957},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3104497492313385},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.18045124411582947},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16029760241508484},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13484352827072144},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.10593464970588684}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8591813445091248},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.679778516292572},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.5782434940338135},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.565441906452179},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5154984593391418},{"id":"https://openalex.org/C165838908","wikidata":"https://www.wikidata.org/wiki/Q736777","display_name":"Calibration","level":2,"score":0.4544007480144501},{"id":"https://openalex.org/C2988343187","wikidata":"https://www.wikidata.org/wiki/Q1130645","display_name":"Open source software","level":3,"score":0.4366811513900757},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.3816070556640625},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3350682258605957},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3104497492313385},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.18045124411582947},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16029760241508484},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13484352827072144},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.10593464970588684}],"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":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"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":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","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":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae417","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae417","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38960865","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38960865","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:pubmedcentral.nih.gov:11223842","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11223842","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11223842/pdf/btae417.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae417","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae417","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.5099999904632568,"display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2082826544","display_name":null,"funder_award_id":"Postdoctoral","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4156249640","display_name":null,"funder_award_id":"T2222007","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321605","display_name":"Government of Jiangsu Province","ror":"https://ror.org/004svx814"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W2018126724","https://openalex.org/W2039058260","https://openalex.org/W2079843936","https://openalex.org/W2407264476","https://openalex.org/W2745376284","https://openalex.org/W2887294942","https://openalex.org/W2903074009","https://openalex.org/W2905174207","https://openalex.org/W2947763854","https://openalex.org/W2991106430","https://openalex.org/W3179726909","https://openalex.org/W4384028715"],"related_works":["https://openalex.org/W3080200277","https://openalex.org/W4376877853","https://openalex.org/W2557718140","https://openalex.org/W4399490472","https://openalex.org/W67092138","https://openalex.org/W1493891899","https://openalex.org/W4250928611","https://openalex.org/W166480398","https://openalex.org/W1612808768","https://openalex.org/W167327709"],"abstract_inverted_index":{"Calib-RT":[0],"is":[1,25],"released":[2],"as":[3,18],"an":[4],"open":[5],"source":[6,23],"software":[7],"under":[8],"the":[9],"MIT":[10],"license":[11],"and":[12],"can":[13],"be":[14],"installed":[15],"from":[16],"PyPi":[17],"a":[19],"python":[20],"module.":[21],"The":[22],"code":[24],"available":[26],"on":[27],"GitHub":[28],"at":[29],"https://github.com/chenghui03/Calib_RT.":[30]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
