{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:20:36Z","timestamp":1790036436325,"version":"4.0.1"},"reference-count":59,"publisher":"Wiley","issue":"3-4","license":[{"start":{"date-parts":[[2023,11,23]],"date-time":"2023-11-23T00:00:00Z","timestamp":1700697600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100017790","name":"European Proteomics Infrastructure Consortium providing access","doi-asserted-by":"publisher","award":["823839"],"award-info":[{"award-number":["823839"]}],"id":[{"id":"10.13039\/100017790","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["analyticalsciencejournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteomics"],"published-print":{"date-parts":[[2024,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Top\u2010down proteomics (TDP) directly analyzes intact proteins and thus provides more comprehensive qualitative and quantitative proteoform\u2010level information than conventional bottom\u2010up proteomics (BUP) that relies on digested peptides and protein inference. While significant advancements have been made in TDP in sample preparation, separation, instrumentation, and data analysis, reliable and reproducible data analysis still remains one of the major bottlenecks in TDP. A key step for robust data analysis is the establishment of an objective estimation of proteoform\u2010level false discovery rate (FDR) in proteoform identification. The most widely used FDR estimation scheme is based on the target\u2010decoy approach (TDA), which has primarily been established for BUP. We present evidence that the TDA\u2010based FDR estimation may not work at the proteoform\u2010level due to an overlooked factor, namely the erroneous deconvolution of precursor masses, which leads to incorrect FDR estimation. We argue that the conventional TDA\u2010based FDR in proteoform identification is in fact protein\u2010level FDR rather than proteoform\u2010level FDR unless precursor deconvolution error rate is taken into account. To address this issue, we propose a formula to correct for proteoform\u2010level FDR bias by combining TDA\u2010based FDR and precursor deconvolution error rate.<\/jats:p>","DOI":"10.1002\/pmic.202300068","type":"journal-article","created":{"date-parts":[[2023,11,24]],"date-time":"2023-11-24T20:01:29Z","timestamp":1700856089000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top\u2010down proteomics"],"prefix":"10.1002","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3776-3098","authenticated-orcid":false,"given":"Kyowon","family":"Jeong","sequence":"first","affiliation":[{"name":"Applied Bioinformatics Computer Science Department University of T\u00fcbingen  T\u00fcbingen Germany"},{"name":"Institute for Bioinformatics and Medical Informatics University of T\u00fcbingen  T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp T.","family":"Kaulich","sequence":"additional","affiliation":[{"name":"Systematic Proteome Research &amp; 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