{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T04:22:35Z","timestamp":1684210955071},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2020,12,26]],"date-time":"2020-12-26T00:00:00Z","timestamp":1608940800000},"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\/501100012190","name":"Ministry of Science and Higher Education of the Russian Federation","doi-asserted-by":"publisher","award":["# 075-00337-20-02","# 0714-2020-0006"],"id":[{"id":"10.13039\/501100012190","id-type":"DOI","asserted-by":"publisher"}]},{"name":"N.N. Semenov Federal Research Center"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,9]]},"abstract":"Abstract<\/jats:title>\n \n Summary<\/jats:title>\n Mass spectrometry (MS) methods are widely used for the analysis of biological and medical samples. Recently developed methods, such as DESI, REIMS and NESI allow fast analyses without sample preparation at the cost of higher variability of spectra. In biology and medicine, MS profiles are often used with machine learning (classification, regression, etc.) algorithms and statistical analysis, which are sensitive to outliers and intraclass variability. Here, we present spectra similarity matrix (SSM) Display software, a tool for fast visual outlier detection and variance estimation in mass spectrometric profiles. The tool speeds up the process of manual spectra inspection, improves accuracy and explainability of outlier detection, and decreases the requirements to the operator experience. It was shown that the batch effect could be revealed through SSM analysis and that the SSM calculation can also be used for tuning novel ion sources concerning the quality of obtained mass spectra.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n Source code, example datasets, binaries and other information are available at https:\/\/github.com\/EvgenyZhvansky\/R_matrix.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa1072","type":"journal-article","created":{"date-parts":[[2020,12,15]],"date-time":"2020-12-15T17:54:46Z","timestamp":1608054886000},"page":"140-142","source":"Crossref","is-referenced-by-count":0,"title":["The software for interactive evaluation of mass spectra stability and reproducibility"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-6427-2553","authenticated-orcid":false,"given":"E S","family":"Zhvansky","sequence":"first","affiliation":[{"name":"Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology , Moscow, Russia"}]},{"given":"A A","family":"Sorokin","sequence":"additional","affiliation":[{"name":"Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology , Moscow, Russia"}]},{"given":"D S","family":"Bormotov","sequence":"additional","affiliation":[{"name":"Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology , Moscow, Russia"}]},{"given":"K V","family":"Bocharov","sequence":"additional","affiliation":[{"name":"Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology , Moscow, Russia"}]},{"given":"D S","family":"Zavorotnyuk","sequence":"additional","affiliation":[{"name":"Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology , Moscow, Russia"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-2987-1048","authenticated-orcid":false,"given":"D G","family":"Ivanov","sequence":"additional","affiliation":[{"name":"Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology , Moscow, Russia"},{"name":"Laboratory of Biomolecular Mass Spectrometry, Emanuel Institute for Biochemical Physics of the Russian Academy of Sciences , Moscow, Russia"}]},{"given":"E N","family":"Nikolaev","sequence":"additional","affiliation":[{"name":"Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology , Moscow, Russia"}]},{"given":"I A","family":"Popov","sequence":"additional","affiliation":[{"name":"Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology , Moscow, Russia"}]}],"member":"286","published-online":{"date-parts":[[2020,12,26]]},"reference":[{"key":"2023051510472659300_btaa1072-B1","doi-asserted-by":"crossref","first-page":"6915","DOI":"10.1021\/ac050989d","article-title":"Desorption electrospray ionization mass spectrometry for high-throughput analysis of pharmaceutical samples in the ambient environment","volume":"77","author":"Chen","year":"2005","journal-title":"Anal. 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Rep"},{"key":"2023051510472659300_btaa1072-B5","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1038\/s41416-018-0048-3","article-title":"The surgical intelligent knife distinguishes normal, borderline and malignant gynaecological tissues using rapid evaporative ionisation mass spectrometry (REIMS)","volume":"118","author":"Phelps","year":"2018","journal-title":"Br. J. Cancer"},{"key":"2023051510472659300_btaa1072-B6","doi-asserted-by":"crossref","first-page":"4058","DOI":"10.1039\/C7AN01334E","article-title":"Analysis of human gliomas by swab touch spray-mass spectrometry: applications to intraoperative assessment of surgical margins and presence of oncometabolites","volume":"142","author":"Pirro","year":"2017","journal-title":"Analyst"},{"key":"2023051510472659300_btaa1072-B7","doi-asserted-by":"crossref","first-page":"8240","DOI":"10.1002\/anie.200902546","article-title":"In vivo, in situ tissue analysis using rapid evaporative ionization mass spectrometry","volume":"48","author":"Sch\u00e4fer","year":"2009","journal-title":"Angew. Chem. Int. Ed. Engl"},{"key":"2023051510472659300_btaa1072-B8","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.2174\/1568026619666190729154543","article-title":"Untangling the metabolic reprogramming in brain cancer: discovering key molecular players using mass spectrometry","volume":"19","author":"Sorokin","year":"2019","journal-title":"Curr. Top. Med. Chem"},{"key":"2023051510472659300_btaa1072-B9","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1038\/s41598-018-37560-0","article-title":"Metrics for evaluating the stability and reproducibility of mass spectra","volume":"9","author":"Zhvansky","year":"2019","journal-title":"Sci. Rep"},{"key":"2023051510472659300_btaa1072-B10","first-page":"e4640","article-title":"Assessment of variation of inline cartridge extraction mass spectra","author":"Zhvansky","year":"2020","journal-title":"J. Mass Spectrom"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa1072\/35379453\/btaa1072.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/1\/140\/50321510\/btaa1072.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/1\/140\/50321510\/btaa1072.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T10:49:20Z","timestamp":1684147760000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/1\/140\/6050705"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,12,26]]},"references-count":10,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,4,9]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa1072","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,1,1]]},"published":{"date-parts":[[2020,12,26]]}}}