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The Sipros algorithm is used in proteomic SIP to identify variably labeled proteins and quantify their isotopic enrichment levels (atom%) by performing enrichment-resolved database searching.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>In this study, Sipros was upgraded to improve the labeled protein identification, isotopic enrichment quantification, and database searching speed. The new Sipros 4 was compared with the existing Sipros 3, Calisp, and MetaProSIP in terms of the number of identifications and the accuracy and precision of atom% quantification on both the peptide and protein levels using standard <jats:italic>E. coli<\/jats:italic> cultures with 1.07 atom%, 2 atom%, 5 atom%, 25 atom%, 50 atom%, and 99 atom% <jats:sup>13<\/jats:sup>C enrichment. Sipros 4 outperformed Calisp and MetaProSIP across all samples, especially in samples with\u2009\u2265\u20095 atom% <jats:sup>13<\/jats:sup>C labeling. The computational speed on Sipros 4 was\u2009&gt;\u200920 times higher than Sipros 3 and was on par with the overall speed of Calisp- and MetaProSIP-based pipelines. Sipros 4 also demonstrated higher sensitivity for the detection of labeled proteins in two <jats:sup>13<\/jats:sup>C-SIP experiments on a real-world soil community. The labeled proteins were used to trace <jats:sup>13<\/jats:sup>C from <jats:sup>13<\/jats:sup>C-methanol and <jats:sup>13<\/jats:sup>C-labeled plant exudates to the consuming soil microorganisms and their newly synthesized proteins.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>Overall, Sipros 4 improved the quality of the proteomic SIP results and reduced the computational cost of SIP database searching, which will make proteomic SIP more useful and accessible to the border community.<\/jats:p>\n                \n              <\/jats:sec>","DOI":"10.1186\/s40168-024-01866-1","type":"journal-article","created":{"date-parts":[[2024,8,8]],"date-time":"2024-08-08T12:02:26Z","timestamp":1723118546000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins"],"prefix":"10.1186","volume":"12","author":[{"given":"Yi","family":"Xiong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan S.","family":"Mueller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shichao","family":"Feng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuan","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chongle","family":"Pan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,8,8]]},"reference":[{"issue":"18","key":"1866_CR1","doi-asserted-by":"publisher","first-page":"3441","DOI":"10.1016\/j.cell.2022.07.020","volume":"185","author":"X Zeng","year":"2022","unstructured":"Zeng X, et al. 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