{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T03:03:41Z","timestamp":1771038221540,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,9]],"date-time":"2025-01-09T00:00:00Z","timestamp":1736380800000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["61972329"],"award-info":[{"award-number":["61972329"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Proteoforms are the different forms of a proteins generated from the genome with various sequence variations, splice isoforms, and post-translational modifications. Proteoforms regulate protein structures and functions. A single protein can have multiple proteoforms due to different modification sites. Proteoform identification is to find proteoforms of a given protein that best fits the input spectrum. Proteoform quantification is to find the corresponding abundances of different proteoforms for a specific protein.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We proposed algorithms for proteoform identification and quantification based on the top-down tandem mass spectrum. In the combination alignments of the HomMTM spectrum and the reference protein, we need to give a correction of the mass for each matched peak within the pre-defined error range. After the correction, we impose that the mass between any two (not necessarily consecutive) matched nodes in the protein is identical to that of the corresponding two matched peaks in the HomMTM spectrum. We design a back-tracking graph to store such kind of information and find a combinatorial path (k paths) with the minimum sum of peak intensity error in this back-tracking graph. The obtained alignment can also show the relative abundance of these proteoforms (paths). Our experimental results demonstrate the algorithm\u2019s capability to identify and quantify proteoform combinations encompassing a greater number of peaks. This advancement holds promise for enhancing the accuracy and comprehensiveness of proteoform quantification, addressing a crucial need in the field of top-down MS-based proteomics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software package are available at https:\/\/github.com\/Zeirdo\/TopMGQuant.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf007","type":"journal-article","created":{"date-parts":[[2025,1,9]],"date-time":"2025-01-09T16:48:03Z","timestamp":1736441283000},"source":"Crossref","is-referenced-by-count":1,"title":["Proteoform identification and quantification based on alignment graphs"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3044-0552","authenticated-orcid":false,"given":"Zhaohui","family":"Zhan","sequence":"first","affiliation":[{"name":"Department of Engineering, Shenzhen MSU-BIT University , Shenzhen, 518172,","place":["China"]},{"name":"Department of Computer Science, City University of Hong Kong , Hong Kong, 999077,","place":["China"]}]},{"given":"Lusheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , Hong Kong, 999077,","place":["China"]},{"name":"City University of Hong Kong Shenzhen Research Institution , 518057,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,1,9]]},"reference":[{"key":"2025012702463167400_btaf007-B1","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1021\/acs.jproteome.7b00685","article-title":"Proteoform suite: software for constructing, quantifying, and visualizing proteoform families","volume":"17","author":"Cesnik","year":"2018","journal-title":"J Proteome Res"},{"key":"2025012702463167400_btaf007-B2","doi-asserted-by":"crossref","first-page":"2527","DOI":"10.1074\/mcp.M900144-MCP200","article-title":"A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry","volume":"8","author":"DiMaggio","year":"2009","journal-title":"Mol Cell Proteomics"},{"key":"2025012702463167400_btaf007-B3","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1038\/s41592-020-0764-5","article-title":"Multiplexed mass spectrometry of individual ions improves measurement of proteoforms and their complexes","volume":"17","author":"Kafader","year":"2020","journal-title":"Nat Methods"},{"key":"2025012702463167400_btaf007-B4","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1093\/bioinformatics\/btw806","article-title":"A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra","volume":"33","author":"Kou","year":"2017","journal-title":"Bioinformatics"},{"key":"2025012702463167400_btaf007-B5","doi-asserted-by":"crossref","first-page":"3495","DOI":"10.1093\/bioinformatics\/btw398","article-title":"Toppic: a software tool for top-down mass spectrometry-based proteoform identification and characterization","volume":"32","author":"Kou","year":"2016","journal-title":"Bioinformatics"},{"key":"2025012702463167400_btaf007-B6","doi-asserted-by":"crossref","first-page":"5830","DOI":"10.1021\/pr400849y","article-title":"Identification of ultramodified proteins using top-down tandem mass spectra","volume":"12","author":"Liu","year":"2013","journal-title":"J Proteome Res"},{"key":"2025012702463167400_btaf007-B7","doi-asserted-by":"crossref","first-page":"e1800361","DOI":"10.1002\/pmic.201800361","article-title":"Identification and quantification of proteoforms by mass spectrometry","volume":"19","author":"Schaffer","year":"2019","journal-title":"Proteomics"},{"key":"2025012702463167400_btaf007-B8","doi-asserted-by":"crossref","first-page":"3688","DOI":"10.1074\/mcp.O113.037218","article-title":"Mixgf: spectral probabilities for mixture spectra from more than one peptide","volume":"13","author":"Wang","year":"2014","journal-title":"Mol Cell Proteomics"},{"key":"2025012702463167400_btaf007-B9","doi-asserted-by":"crossref","first-page":"1476","DOI":"10.1074\/mcp.M000136-MCP201","article-title":"Peptide identification from mixture tandem mass spectra","volume":"9","author":"Wang","year":"2010","journal-title":"Mol Cell Proteomics"},{"key":"2025012702463167400_btaf007-B10","doi-asserted-by":"crossref","first-page":"bbab599","DOI":"10.1093\/bib\/bbab599","article-title":"Proteoform identification based on top-down tandem mass spectra with peak error corrections","volume":"23","author":"Zhan","year":"2022","journal-title":"Brief Bioinform"},{"key":"2025012702463167400_btaf007-B11","doi-asserted-by":"crossref","first-page":"btae149","DOI":"10.1093\/bioinformatics\/btae149","article-title":"Fast peak error correction algorithms for proteoform identification using top-down tandem mass spectra","volume":"40","author":"Zhan","year":"2024","journal-title":"Bioinformatics"},{"key":"2025012702463167400_btaf007-B12","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1186\/s12859-018-2273-4","article-title":"A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra","volume":"19","author":"Zhu","year":"2018","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf007\/61396797\/btaf007.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/1\/btaf007\/61396797\/btaf007.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/1\/btaf007\/61396797\/btaf007.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T02:46:50Z","timestamp":1737946010000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf007\/7950664"}},"subtitle":[],"editor":[{"given":"Xin","family":"Gao","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,12,26]]},"references-count":12,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,12,26]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf007","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,1]]},"published":{"date-parts":[[2024,12,26]]},"article-number":"btaf007"}}