{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T19:32:52Z","timestamp":1784835172654,"version":"3.55.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2023,8,25]],"date-time":"2023-08-25T00:00:00Z","timestamp":1692921600000},"content-version":"vor","delay-in-days":24,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100016691","name":"Guangdong Pearl River Talents Program","doi-asserted-by":"publisher","award":["2019QN01Y051"],"award-info":[{"award-number":["2019QN01Y051"]}],"id":[{"id":"10.13039\/100016691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"crossref","award":["2021YFA1100401"],"award-info":[{"award-number":["2021YFA1100401"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"crossref","award":["2021YFA1101304"],"award-info":[{"award-number":["2021YFA1101304"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Mass spectrometry (MS)-based proteomics has become the most powerful approach to study the proteome of given biological and clinical samples. Advancements in sample preparation and MS detection have extended the application of proteomics but have also brought new demands on data analysis. Appropriate proteomics data analysis workflow mainly requires quality control, hypothesis testing, functional mining, and visualization. Although there are numerous tools for each process, an efficient and universal tandem analysis toolkit to obtain a quick overall view of various proteomics data is still urgently needed. Here, we present DEP2, an updated version of DEP we previously established, for proteomics data analysis. We amended the analysis workflow by incorporating alternative approaches to accommodate diverse proteomics data, introducing peptide-protein summarization and coupling biological function exploration. In summary, DEP2 is a well-rounded toolkit designed for protein- and peptide-level quantitative proteomics data. It features a more flexible differential analysis workflow and includes a user-friendly Shiny application to facilitate data analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>DEP2 is available at https:\/\/github.com\/mildpiggy\/DEP2, released under the MIT license. For further information and usage details, please refer to the package website at https:\/\/mildpiggy.github.io\/DEP2\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad526","type":"journal-article","created":{"date-parts":[[2023,8,25]],"date-time":"2023-08-25T18:05:46Z","timestamp":1692986746000},"source":"Crossref","is-referenced-by-count":71,"title":["DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0056-8451","authenticated-orcid":false,"given":"Zhenhuan","family":"Feng","sequence":"first","affiliation":[{"name":"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"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peiyang","family":"Fang","sequence":"additional","affiliation":[{"name":"Sanquan College, Xinxiang Medical University , Xinxiang, Henan 453003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Zheng","sequence":"additional","affiliation":[{"name":"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"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"},{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2564-9258","authenticated-orcid":false,"given":"Xiaofei","family":"Zhang","sequence":"additional","affiliation":[{"name":"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"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"},{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,8,25]]},"reference":[{"key":"2023083011541070600_btad526-B1","doi-asserted-by":"crossref","first-page":"D649","DOI":"10.1093\/nar\/gkx1132","article-title":"The reactome pathway knowledgebase","volume":"46","author":"Fabregat","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023083011541070600_btad526-B2","doi-asserted-by":"crossref","first-page":"4965","DOI":"10.1093\/bioinformatics\/btaa620","article-title":"ProVision: a web-based platform for rapid analysis of proteomics data processed by MaxQuant","volume":"36","author":"Gallant","year":"2020","journal-title":"Bioinformatics"},{"key":"2023083011541070600_btad526-B3","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1021\/acs.jproteome.5b00981","article-title":"Accounting for the multiple natures of missing values in Label-Free quantitative proteomics data sets to compare imputation 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