{"id":"https://openalex.org/W4386156770","doi":"https://doi.org/10.1093/bioinformatics/btad526","title":"DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data","display_name":"DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data","publication_year":2023,"publication_date":"2023-08-01","ids":{"openalex":"https://openalex.org/W4386156770","doi":"https://doi.org/10.1093/bioinformatics/btad526","pmid":"https://pubmed.ncbi.nlm.nih.gov/37624922"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad526","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad526","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad526/51258766/btad526.pdf","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://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad526/51258766/btad526.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014939240","display_name":"Zhenhuan Feng","orcid":"https://orcid.org/0000-0002-0056-8451"},"institutions":[{"id":"https://openalex.org/I2802148028","display_name":"Guangzhou Institutes of Biomedicine and Health","ror":"https://ror.org/02c31t502","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2802148028"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CN","HK"],"is_corresponding":true,"raw_author_name":"Zhenhuan Feng","raw_affiliation_strings":["CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Hong Kong Institute of Science & Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou, Guangdong 510530, China","University of Chinese Academy of Sciences , Beijing 100049, China","University of Chinese Academy of Sciences, Beijing, 100049, China"],"raw_orcid":"https://orcid.org/0000-0002-0056-8451","affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Hong Kong Institute of Science & Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou, Guangdong 510530, China","institution_ids":["https://openalex.org/I2802148028","https://openalex.org/I889458895"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , Beijing 100049, China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111238421","display_name":"Peiyang Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I80626142","display_name":"Xinxiang Medical University","ror":"https://ror.org/038hzq450","country_code":"CN","type":"education","lineage":["https://openalex.org/I80626142"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peiyang Fang","raw_affiliation_strings":["Sanquan College, Xinxiang Medical University , Xinxiang, Henan 453003, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sanquan College, Xinxiang Medical University , Xinxiang, Henan 453003, China","institution_ids":["https://openalex.org/I80626142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060244431","display_name":"Hui Zheng","orcid":"https://orcid.org/0000-0001-6801-0529"},"institutions":[{"id":"https://openalex.org/I2802148028","display_name":"Guangzhou Institutes of Biomedicine and Health","ror":"https://ror.org/02c31t502","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2802148028"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]},{"id":"https://openalex.org/I92039509","display_name":"Guangzhou Medical University","ror":"https://ror.org/00zat6v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I92039509"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Hui Zheng","raw_affiliation_strings":["CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Hong Kong Institute of Science & Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou, Guangdong 510530, China","Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University , Guangzhou, 510530, China","University of Chinese Academy of Sciences , Beijing 100049, China","University of Chinese Academy of Sciences, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Hong Kong Institute of Science & Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou, Guangdong 510530, China","institution_ids":["https://openalex.org/I2802148028","https://openalex.org/I889458895"]},{"raw_affiliation_string":"Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University , Guangzhou, 510530, China","institution_ids":["https://openalex.org/I92039509"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , Beijing 100049, China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061287181","display_name":"Xiaofei Zhang","orcid":"https://orcid.org/0000-0002-2564-9258"},"institutions":[{"id":"https://openalex.org/I2802148028","display_name":"Guangzhou Institutes of Biomedicine and Health","ror":"https://ror.org/02c31t502","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2802148028"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]},{"id":"https://openalex.org/I92039509","display_name":"Guangzhou Medical University","ror":"https://ror.org/00zat6v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I92039509"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Xiaofei Zhang","raw_affiliation_strings":["CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Hong Kong Institute of Science & Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou, Guangdong 510530, China","Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University , Guangzhou, 510530, China","University of Chinese Academy of Sciences , Beijing 100049, China","University of Chinese Academy of Sciences, Beijing, 100049, China"],"raw_orcid":"https://orcid.org/0000-0002-2564-9258","affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Hong Kong Institute of Science & Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou, Guangdong 510530, China","institution_ids":["https://openalex.org/I2802148028","https://openalex.org/I889458895"]},{"raw_affiliation_string":"Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University , Guangzhou, 510530, China","institution_ids":["https://openalex.org/I92039509"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , Beijing 100049, China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5014939240"],"corresponding_institution_ids":["https://openalex.org/I2802148028","https://openalex.org/I4210165038","https://openalex.org/I889458895"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":7.8232,"has_fulltext":true,"cited_by_count":55,"citation_normalized_percentile":{"value":0.98380205,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"39","issue":"8","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":0.9878000020980835,"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":0.9878000020980835,"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":0.0017000000225380063,"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":0.00139999995008111,"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":0.7636371850967407},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.7481676340103149},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7417571544647217},{"id":"https://openalex.org/keywords/automatic-summarization","display_name":"Automatic summarization","score":0.5644947290420532},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.4408632218837738},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3591167628765106},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2586733102798462},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.23108407855033875},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.2095530927181244},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10227280855178833}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7636371850967407},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.7481676340103149},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7417571544647217},{"id":"https://openalex.org/C170858558","wikidata":"https://www.wikidata.org/wiki/Q1394144","display_name":"Automatic summarization","level":2,"score":0.5644947290420532},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.4408632218837738},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3591167628765106},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2586733102798462},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.23108407855033875},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2095530927181244},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10227280855178833},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad526","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad526","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad526/51258766/btad526.pdf","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:37624922","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37624922","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:10466079","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10466079","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10466079/pdf/btad526.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad526","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad526","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad526/51258766/btad526.pdf","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":[{"display_name":"Industry, innovation and infrastructure","score":0.49000000953674316,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G5723663663","display_name":null,"funder_award_id":"2020B1212060052","funder_id":"https://openalex.org/F4320335795","funder_display_name":"Science and Technology Planning Project of Guangdong Province"},{"id":"https://openalex.org/G6710182877","display_name":null,"funder_award_id":"2021YFA1101304","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7645750448","display_name":null,"funder_award_id":"2021YFA1100401","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7756524304","display_name":null,"funder_award_id":"2019QN01Y051","funder_id":"https://openalex.org/F4320334009","funder_display_name":"Guangdong Provincial Pearl River Talents Program"}],"funders":[{"id":"https://openalex.org/F4320334009","display_name":"Guangdong Provincial Pearl River Talents Program","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335795","display_name":"Science and Technology Planning Project of Guangdong Province","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4386156770.pdf"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1989277387","https://openalex.org/W2146512944","https://openalex.org/W2179438025","https://openalex.org/W2214074259","https://openalex.org/W2261507005","https://openalex.org/W2278988761","https://openalex.org/W2340761255","https://openalex.org/W2463195069","https://openalex.org/W2524808906","https://openalex.org/W2787897791","https://openalex.org/W2799323124","https://openalex.org/W2900569176","https://openalex.org/W2950595506","https://openalex.org/W3013726226","https://openalex.org/W3020339446","https://openalex.org/W3040704860","https://openalex.org/W3161162069","https://openalex.org/W3175752499","https://openalex.org/W3204545069","https://openalex.org/W4233110100","https://openalex.org/W4233698560","https://openalex.org/W4280504434","https://openalex.org/W6727679459","https://openalex.org/W6797786779"],"related_works":["https://openalex.org/W1982829397","https://openalex.org/W2347437365","https://openalex.org/W2106414650","https://openalex.org/W1999412725","https://openalex.org/W4390205769","https://openalex.org/W2124137418","https://openalex.org/W2391458050","https://openalex.org/W3022402204","https://openalex.org/W2086860678","https://openalex.org/W2114732768"],"abstract_inverted_index":{"SUMMARY:":[0],"Mass":[1],"spectrometry":[2],"(MS)-based":[3],"proteomics":[4,33,44,81,100,115,138],"has":[5],"become":[6],"the":[7,13,30,105,168,180],"most":[8],"powerful":[9],"approach":[10],"to":[11,73,112,154,179],"study":[12],"proteome":[14],"of":[15,32,79,94],"given":[16],"biological":[17,122],"and":[18,25,56,68,120,135,148,174],"clinical":[19],"samples.":[20],"Advancements":[21],"in":[22],"sample":[23],"preparation":[24],"MS":[26],"detection":[27],"have":[28,35],"extended":[29],"application":[31,153],"but":[34],"also":[36],"brought":[37],"new":[38],"demands":[39],"on":[40],"data":[41,45,82,101,156],"analysis.":[42,102,157],"Appropriate":[43],"analysis":[46,71,106,146],"workflow":[47,107,147],"mainly":[48],"requires":[49],"quality":[50],"control,":[51],"hypothesis":[52],"testing,":[53],"functional":[54],"mining,":[55],"visualization.":[57],"Although":[58],"there":[59],"are":[60],"numerous":[61],"tools":[62],"for":[63,99,133],"each":[64],"process,":[65],"an":[66,91],"efficient":[67],"universal":[69],"tandem":[70],"toolkit":[72,131],"obtain":[74],"a":[75,129,142,150],"quick":[76],"overall":[77],"view":[78],"various":[80],"is":[83,128,162],"still":[84],"urgently":[85],"needed.":[86],"Here,":[87],"we":[88,96],"present":[89],"DEP2,":[90],"updated":[92],"version":[93],"DEP":[95],"previously":[97],"established,":[98],"We":[103],"amended":[104],"by":[108],"incorporating":[109],"alternative":[110],"approaches":[111],"accommodate":[113],"diverse":[114],"data,":[116],"introducing":[117],"peptide-protein":[118],"summarization":[119],"coupling":[121],"function":[123],"exploration.":[124],"In":[125],"summary,":[126],"DEP2":[127,161],"well-rounded":[130],"designed":[132],"protein-":[134],"peptide-level":[136],"quantitative":[137],"data.":[139],"It":[140],"features":[141],"more":[143],"flexible":[144],"differential":[145],"includes":[149],"user-friendly":[151],"Shiny":[152],"facilitate":[155],"AVAILABILITY":[158],"AND":[159],"IMPLEMENTATION:":[160],"available":[163],"at":[164,183],"https://github.com/mildpiggy/DEP2,":[165],"released":[166],"under":[167],"MIT":[169],"license.":[170],"For":[171],"further":[172],"information":[173],"usage":[175],"details,":[176],"please":[177],"refer":[178],"package":[181],"website":[182],"https://mildpiggy.github.io/DEP2/.":[184]},"counts_by_year":[{"year":2026,"cited_by_count":15},{"year":2025,"cited_by_count":30},{"year":2024,"cited_by_count":10}],"updated_date":"2026-05-09T13:55:54.758798","created_date":"2025-10-10T00:00:00"}
