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Current studies of AA substitutions rely mainly on genomic and transcriptomic evidence, while proteome-level characterization remains underexplored, even though such substitutions can arise beyond DNA and RNA mutations. Here we address this gap with PIPI-C, an open-search mass spectrometry tool, and establish an integrated AA substitutomics pipeline to profile AA substitutions across five cancer cohorts and dissect the regulatory roles of substitution-bearing proteins. By cross-referencing 13,399 identified AA substitutions with matched whole-exome sequencing data, we observed no overlap with patient somatic mutations. Specifically, 61% of these substitutions required two or more base alterations and could not be derived from single-nucleotide variants, rendering them exclusively detectable at the proteomic level. The remaining 39% of substitutions were compatible with single-base variations. PIPI-C captured these candidate substitutions at the proteome scale, consistent with a translational-stage origin as reported for alternate RNA decoding in mammals. We further identified notable substitutions, including F43S and E91D in hemoglobin subunit beta, P584T in filamin A, and A175N in fructose-bisphosphate aldolase B, and our pipeline provides a framework for generating hypotheses about AA substitutions in cancer escape.<\/jats:p>","DOI":"10.1021\/acs.jproteome.6c00455","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T18:01:16Z","timestamp":1788285676000},"page":"5452-5468","source":"Crossref","is-referenced-by-count":1,"title":["Amino Acid Substitutomics:\nProfiling Amino Acid Substitutions\nat the Proteomic Scale Unveils Biological Implications and Escape\nHypotheses in Cancer"],"prefix":"10.1021","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5051-9658","authenticated-orcid":true,"given":"Peize","family":"Zhao","sequence":"first","affiliation":[{"name":"The Hong Kong University of Science and Technology , , ,","place":["Hong Kong, China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8402-1156","authenticated-orcid":true,"given":"Shengzhi","family":"Lai","sequence":"additional","affiliation":[{"name":"The Hong Kong University of Science and Technology , , ,","place":["Hong Kong, China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4747-9090","authenticated-orcid":true,"given":"Shuaijian","family":"Dai","sequence":"additional","affiliation":[{"name":"Central South University , , , ,","place":["Changsha, Hunan Province, China, 410013"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2322-7748","authenticated-orcid":true,"given":"Chen","family":"Zhou","sequence":"additional","affiliation":[{"name":"The Hong Kong University of Science and Technology , , ,","place":["Hong Kong, China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ning","family":"Li","sequence":"additional","affiliation":[{"name":"The Hong Kong University of Science and Technology , , ,","place":["Hong Kong, China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5510-6916","authenticated-orcid":true,"given":"Weichuan","family":"Yu","sequence":"additional","affiliation":[{"name":"The Hong Kong University of Science and Technology , , ,","place":["Hong Kong, China, 999077"]},{"name":"The Hong Kong University of Science and Technology , , ,","place":["Hong Kong, China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,27]]},"reference":[{"issue":"3","key":"2026100208422059000_cit1","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1001\/jamaoncol.2021.6987","article-title":"Cancer incidence, mortality, years of life lost, years\nlived with disability, and disability-adjusted life years for 29 cancer\ngroups from 2010 to 2019: A systematic analysis for the global burden\nof disease study 2019","volume":"8","author":"Kocarnik","year":"2022","journal-title":"JAMA Oncol"},{"issue":"3","key":"2026100208422059000_cit2","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/S1535-6108(03)00216-2","article-title":"Cell signaling\nand cancer","volume":"4","author":"Martin","year":"2003","journal-title":"Cancer Cell"},{"issue":"50","key":"2026100208422059000_cit3","doi-asserted-by":"publisher","first-page":"7455","DOI":"10.1038\/sj.onc.1209085","article-title":"Perturbations of\nthe AKT signaling pathway in human\ncancer","volume":"24","author":"Altomare","year":"2005","journal-title":"Oncogene"},{"issue":"5","key":"2026100208422059000_cit4","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of cancer: The next generation","volume":"144","author":"Hanahan","year":"2011","journal-title":"Cell"},{"issue":"1","key":"2026100208422059000_cit5","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1038\/s12276-020-0375-3","article-title":"Amino acids in cancer","volume":"52","author":"Lieu","year":"2020","journal-title":"Exp. Mol. Med."},{"issue":"1","key":"2026100208422059000_cit6","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1038\/s41419-024-06435-w","article-title":"Amino acid metabolism in tumor biology\nand therapy","volume":"15","author":"Chen","year":"2024","journal-title":"Cell Death Dis."},{"key":"2026100208422059000_cit7","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1038\/s41586-026-10678-2","article-title":"Alternate RNA decoding\nresults in stable and abundant proteins in mammals","volume":"656","author":"Tsour","year":"2026","journal-title":"Nat."},{"issue":"6","key":"2026100208422059000_cit8","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1200\/JCO.2011.39.2316","article-title":"Cancer\ngenomics: Technology,\ndiscovery, and translation","volume":"30","author":"Tran","year":"2012","journal-title":"J. Clin. Oncol."},{"issue":"3","key":"2026100208422059000_cit9","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1038\/ng1107","article-title":"The genetics\nand genomics of cancer","volume":"33","author":"Balmain","year":"2003","journal-title":"Nat. Genet."},{"issue":"9","key":"2026100208422059000_cit10","doi-asserted-by":"publisher","first-page":"1452","DOI":"10.1038\/s12276-020-0422-0","article-title":"Single-cell transcriptomics in cancer:\nComputational challenges and opportunities","volume":"52","author":"Fan","year":"2020","journal-title":"Exp. Mol. Med."},{"issue":"3","key":"2026100208422059000_cit11","doi-asserted-by":"publisher","first-page":"42","DOI":"10.5306\/wjco.v9.i3.42","article-title":"Epitranscriptomics\nof Cancer","volume":"9","author":"Tusup","year":"2018","journal-title":"World J. Clin. 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