{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:21Z","timestamp":1740185121985,"version":"3.37.3"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2021,7,28]],"date-time":"2021-07-28T00:00:00Z","timestamp":1627430400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31600751"],"award-info":[{"award-number":["31600751"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"W. Yin and the Ministry of Science and Technology of China","award":["2017ZX10203205"],"award-info":[{"award-number":["2017ZX10203205"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Mass cytometry (Cytometry by Time-Of-Flight, CyTOF) is a single-cell technology that is able to quantify multiplex biomarker expressions and is commonly used in basic life science and translational research. However, the widely used Gadolinium (Gd)-based contrast agents (GBCAs) in magnetic resonance imaging (MRI) scanning in clinical practice can lead to signal contamination on the Gd channels in the CyTOF analysis. This Gd contamination greatly affects the characterization of the real signal from Gd-isotope-conjugated antibodies, severely impairing the CyTOF data quality and ruining downstream single-cell data interpretation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We first in-depth characterized the signals of Gd isotopes from a control sample that was not stained with Gd-labeled antibodies but was contaminated by Gd isotopes from GBCAs, and revealed the collinear intensity relationship across Gd contamination signals. We also found that the intensity ratios of detected Gd contamination signals to the reference Gd signal were highly correlated with the natural abundance ratios of corresponding Gd isotopes. We then developed a computational method named by GdClean to remove the Gd contamination signal at the single-cell level in the CyTOF data. We further demonstrated that the GdClean effectively cleaned up the Gd contamination signal while preserving the real Gd-labeled antibodies signal in Gd channels. All of these shed lights on the promising applications of the GdClean method in preprocessing CyTOF datasets for revealing the true single-cell information.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The R package GdClean is available on GitHub at https:\/\/github.com\/JunweiLiu0208\/GdClean.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab537","type":"journal-article","created":{"date-parts":[[2021,7,27]],"date-time":"2021-07-27T11:11:01Z","timestamp":1627384261000},"page":"4787-4792","source":"Crossref","is-referenced-by-count":2,"title":["GdClean: removal of Gadolinium contamination in mass cytometry data"],"prefix":"10.1093","volume":"37","author":[{"given":"Junwei","family":"Liu","sequence":"first","affiliation":[{"name":"Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, School of Basic Medical Science and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou 310058, China"}]},{"given":"Lulu","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310000, China"}]},{"given":"Saisi","family":"Qu","sequence":"additional","affiliation":[{"name":"Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, School of Basic Medical Science and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou 310058, China"}]},{"given":"Tongtong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Hepatobiliary and Pancreatic Surgery, The Center for Integrated Oncology and Precision Medicine, Affiliated Hangzhou First People\u2019s Hospital, Zhejiang University , Hangzhou 310006, China"}]},{"given":"Danyang","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310058, China"}]},{"given":"Qinghua","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Biological Testing, Zhejiang Puluoting Health Technology Co., Ltd , Hangzhou 311121, China"}]},{"given":"Tian","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biological Testing, Zhejiang Puluoting Health Technology Co., Ltd , Hangzhou 311121, China"}]},{"given":"Hongyu","family":"Shi","sequence":"additional","affiliation":[{"name":"Department of Biological Testing, Zhejiang Puluoting Health Technology Co., Ltd , Hangzhou 311121, China"}]},{"given":"Kaichen","family":"Song","sequence":"additional","affiliation":[{"name":"Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, School of Basic Medical Science and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou 310058, China"}]},{"given":"Weijia","family":"Fang","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310000, China"}]},{"given":"Wei","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, School of Basic Medical Science and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou 310058, China"}]},{"given":"Weiwei","family":"Yin","sequence":"additional","affiliation":[{"name":"Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, School of Basic Medical Science and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University , Hangzhou 310058, China"},{"name":"Department of Thoracic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou 310058, China"}]}],"member":"286","published-online":{"date-parts":[[2021,7,28]]},"reference":[{"key":"2023051607124544600_btab537-B1","doi-asserted-by":"crossref","first-page":"6813","DOI":"10.1021\/ac901049w","article-title":"Mass cytometry: technique for real time single cell 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